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Dataset View [GSE36552]

SeriesGSE36552
TitleTracing pluripotency of human early embryos and embryonic stem cells by single cell RNA-seq
Year2013
CountryChina
ArticleTang 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
PMID23934149
Bio ProjectSRA: http://www.ncbi.nlm.nih.gov/sra?term=SRP011546
SraBioProject: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA153427
Overall DesginWe 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.
SummaryFind 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 ProtocolAmplied 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 processingReads 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
PlatformGPL11154
Public OnPublic on Aug 10 2013

Cell Groups

Differential Expression Gene List

KEGG GO Others   

Gene SymbolEnsembl IDFDR
CELF1ENSG000001491871.84973446503102e-27
FAM115A2.5737238871262e-26
TNRC6AENSG000000909051.85861386258322e-25
MAP9ENSG000001641146.17650742003852e-23
EPC1ENSG000001206166.52377832694825e-21
TNRC6BENSG000001003547.70817966285855e-19
COL12A1ENSG000001117992.34682918499457e-17
KIAA07762.39543052819086e-17
DAPP1ENSG000000701901.0307049804223e-16
MED10ENSG000001333981.0307049804223e-16
Displaying 1-10 of 1756 results.