| Series | GSE36552 |
| Title | Tracing pluripotency of human early embryos and embryonic stem cells by single cell RNA-seq |
|---|---|
| Year | 2013 |
| Country | China |
| Article | Tang F,Qiao J,Li R,Lao K,Wen L,Wu X,Li M,Huang J,Yan J,Zheng X,Lian Y,Liu P,Li R,Wu J,Yang L,Guo H,Yang M,Yan L.Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells.Nature structural & molecular biology.2013 Sep |
| PMID | 23934149 |
| Bio Project | SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRP011546 |
| Sra | BioProject: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA153427 |
| Overall Desgin | We get transcriptome of 124 individual cells from human pre-implantation embryos and human embryonic stem cells by applying single cell RNA-seq technique we recently developed[1][2][3][4]. We did in-depth bioinformatic analysis to these data and found very dynamic expression of protein-coding genes. |
| Summary | Find the casual relationship between gene expression network and cellular phenotype at single cell resolution. We collected donated human pre-implatation embryos, and the embryonic stem cells derived from them, isolate individual cells, prepared single cell cDNAs, and sequenced them by HiSeq2000. Then we analyzed the expression of known RefSeq genes. |
| Experimental Protocol | Amplied single cell cDNAs were further amplied for another ten cycles of PCR. Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manufacturer suggestion protocol Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol |
| Data processing | Reads mapping:We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8. [Ref: Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis.; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_M21.expression.txt: hg19 Reads mapping:We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) [1] to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8. [1]. Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60.; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis.; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_M22.expression.txt: hg19 Reads mapping:We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) [1] to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8. [1]. Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60.; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis.; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_M23.expression.txt: hg19 Reads mapping:We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) [1] to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8. [1]. Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60.; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis.; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_C1.expression.txt: hg19 Reads mapping:We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) [1] to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8. [1]. Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60.; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis.; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_C2.expression.txt: hg19 Reads mapping:We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) [1] to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8. [1]. Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60.; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis.; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_C3.expression.txt: hg19 Reads mapping:We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) [1] to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8. [1]. Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60.; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis.; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_B1.expression.txt: hg19 Reads mapping:We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) [1] to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8. [1]. Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60.; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis.; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_B2.expression.txt: hg19 Reads mapping:We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) [1] to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8. [1]. Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60.; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis.; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_B3.expression.txt: hg19 Reads mapping:We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) [1] to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8. [1]. Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60.; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis.; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_B4.expression.txt: hg19 Reads mapping:We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) [1] to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8. [1]. Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60.; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis.; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_B5.expression.txt: hg19 Reads mapping:We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) [1] to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8. [1]. Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60.; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis.; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_B6.expression.txt: hg19 Reads mapping:We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) [1] to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8. [1]. Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60.; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis.; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_M1.expression.txt: hg19 Reads mapping:We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) [1] to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8. [1]. Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60.; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis.; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_M2.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_C4.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_C5.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_C6.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_C7.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_L1.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_L2.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_L3.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_L4.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_L5.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_L6.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_L7.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_L8.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_A1.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_A2.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_A3.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_A4.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_A5.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_A6.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_A7.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_A8.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_E1.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_E2.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_E3.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_E4.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_K1.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_K2.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_K3.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_K4.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_K5.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_K6.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_K7.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_K8.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_D1.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_D2.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_D3.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_D4.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_D5.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_D6.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_D7.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_D8.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_F1.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_F2.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_F3.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_F4.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_F5.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_F6.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_F7.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_F8.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_G2.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_G3.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_G4.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_G5.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_G6.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_G7.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_G8.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_G9.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_G10.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_G11.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_G12.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_G13.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_H1.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_H2.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_H3.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_H4.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_H5.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_H6.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_H7.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_H8.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_H9.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_H10.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_R1.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_R2.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_R3.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_R4.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_R5.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_R6.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_R7.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_R8.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_M4.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_M5.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_M6.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_M7.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_M8.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_M10.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_P1.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_P2.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_P5.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_P7.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_P9.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_P11.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_P12.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_P13.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_P14.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_P15.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_P17.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_S1.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_S2.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_S3.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_S4.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_S5.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_S6.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_S7.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_S8.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_S9.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_S10.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_S11.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_S12.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_S13.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_S14.expression.txt: hg19 Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options aln -o 1 -e 60 -i 15 -q 10 -t 8 [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]; Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis; Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]; Merge the *.bed files from samples in the same stage [available on Series records]; Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]; Genome_build: hg19; Sample_S15.expression.txt: hg19 |
| Platform | GPL11154 |
| Public On | Public on Aug 10 2013 |
| Gene Symbol | Ensembl ID | FDR |
|---|---|---|
| DEPDC7 | ENSG00000121690 | 8.41644143094134e-19 |
| TNRC6A | ENSG00000090905 | 8.41644143094134e-19 |
| PGAM4 | ENSG00000226784 | 1.40661475044845e-18 |
| CIR1 | ENSG00000138433 | 5.76031738069462e-17 |
| FOXQ1 | ENSG00000164379 | 8.29383882789837e-17 |
| SEC62 | ENSG00000008952 | 2.59203465150874e-16 |
| IGSF11 | ENSG00000144847 | 1.61176212355244e-13 |
| MEX3D | ENSG00000181588 | 2.38360584903069e-13 |
| TUBB | ENSG00000183311 | 2.79216361235963e-13 |
| BRI3 | ENSG00000164713 | 4.97795641604312e-13 |