Series | GSE71318 |
Title | Tracing the expression of circular RNAs in human preimplantation embryos |
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Year | 2016 |
Country | China |
Article | Not set |
PMID | NA |
Bio Project | BioProject: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA291062 |
Sra | SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRP061636 |
Overall Desgin | We sequenced individual single cells or embryos at seven consecutive stages (mature oocytes, zygotes, 2-cell, 4-cell, 8-cell embryos, morulae, and blastocysts) and single hESC using single-cell RNA seq. |
Summary | We systematically analyzed transcriptome in individual human oocytes and preimplantation embryos with a new single-cell RNA seq method we recently developed. |
Experimental Protocol | The RNAs in individual oocyte or embryo were reverse transcribed and amplified using the single RNA-seq method we recently developed.; Libraries were constructed with TruSeq DNA library preparation kit (Illumina) The RNAs in individual oocyte or embryo were reverse transcribed and amplified using the single RNA-seq method we recently developed.; Libraries were constructed with TruSeq DNA library preparation kit (Illumina); RNA-seq (single-cell) |
Data processing | Illumina CASAVA version 1.8 were used to the basecalling.; Reads were trimmed to remove the adapter sequences and low quality bases.; RNA-seq reads were aligned to the human refference genome (hg19) using Tophat software; Raw read counts and RPKM calculated by HTSeq; Genome_build: hg19; Supplementary_files_format_and_content: txt files reflect RPKM of each gene with Refseq ID. Illumina CASAVA version 1.8 were used to the basecalling.; Reads were trimmed to remove the adapter sequences and low quality bases.; RNA-seq reads were aligned to the human refference genome (hg19) using Tophat software; Raw read counts and RPKM calculated by HTSeq; Genome_build: hg19; Supplementary_files_format_and_content: txt files reflect RPKM of each gene in Refseq. |
Platform | GPL16791 |
Public On | Public on May 13 2016 |
Gene Symbol | Ensembl ID | FDR |
---|---|---|
H2AFZ | ENSG00000164032 | 0.00217962551783518 |
HNRNPD | ENSG00000138668 | 0.00217962551783518 |
PEBP1 | ENSG00000089220 | 0.00217962551783518 |
PTP4A1 | ENSG00000112245 | 0.00224786197074896 |
ATG12 | ENSG00000145782 | 0.00241623343559094 |
DDX39A | ENSG00000123136 | 0.00251565617020116 |
IP6K1 | ENSG00000176095 | 0.00251565617020116 |
MAD2L1BP | ENSG00000124688 | 0.00251565617020116 |
NSG1 | ENSG00000168824 | 0.00251565617020116 |
DDIT3 | ENSG00000175197 | 0.00259117164244474 |