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Series GSE41908 Query DataSets for GSE41908
Status Public on Oct 31, 2012
Title Transcriptome profiling of wild type primordial germ cells (PGC) by RNAseq
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: To identify molecular pathways underlying epigenetic reprogramming in early germ cell precursors, we examined global gene expression of wild type primordial germ cells using mRNA sequencing.
Methods: Given the limited number of PGCs collected from E9.5 to E13.5 (ranging from 300 to 5000), we used a low-input RNA sequencing method, Smart-Seq. RNA libraries were pooled and sequenced by Illumina Hiseq.
Results: We generated >22 million uniquely mapped reads per sample and identified >10 thousand transcripts per genotype (RPKM>0.1). Hierarchical clustering and correlation analysis on gene expression indicates samples were clearly separated according to their genotypes with Spearman correlation coefficient of 0.98/0.99 within biological replicates. Compared with E9.5 PGCs, 479 genes were significantly up-regulated and 248 genes were down-regulated in E11.5 PGCs. When compared with E11.5 PGCs, male E13.5 PGCs had 362 up-regulated, and 239 down-regulated genes, whereas female E13.5 PGCs had 1163 up-regulated and 333 down-regulated genes. Overall, the number of up-regulated genes was greater than that of the down-regulated genes in every comparison, suggesting that gene expression is generally activated during PGC reprogramming.
 
Overall design mRNA profiles of primordial germ cells derived from developmental embryos stages (E9.5, E11.5 and E13.5) were generated by deep sequencing, in duplicates (E9.5 and E11.5) or triplicates (E13.5f and E13.5m), using Illumina Hiseq.
 
Citation(s) 23151479, 23399596
Submission date Oct 29, 2012
Last update date May 15, 2019
Contact name Kun Zhang
E-mail k4zhang@ucsd.edu
Organization name University of California, San Diego
Department Bioengineering
Lab Integrative Genomics Laboratory
Street address 9500 Gilman Dr Mailcode: 0412
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
 
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (12)
GSM1027242 WT rep1
GSM1027243 WT rep2
GSM1027244 WT rep3
Relations
BioProject PRJNA178509
SRA SRP016882

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE41908_E11.5_E13.5f_cuffdiff1.2.txt.gz 790.8 Kb (ftp)(http) TXT
GSE41908_E11.5_E13.5m_cuffdiff1.2.txt.gz 784.1 Kb (ftp)(http) TXT
GSE41908_E9.5_E11.5_cuffdiff1.2.txt.gz 772.1 Kb (ftp)(http) TXT
GSE41908_RNAseq_cuffdiff.txt.gz 550.9 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data is available on Series record

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