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Series GSE44346 Query DataSets for GSE44346
Status Public on Jan 22, 2014
Title RNA-Seq and RNA Polymerase II ChIP-Seq of mouse spermatogenesis
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary To characterize gene expression in spermatogenesis we sequenced eight mRNA samples from testes of juvenile mice aged between 6 and 38 days post partum. We then classified gene expression profiles and found over 1,000 meiotically-expressed protein-coding genes that have not been previously reported in relation to spermatogenesis. Furthermore, we developed an in silico de-convolution approach to estimate cell type-specific gene expression from temporal gene expression profiles and applied it to our dataset. To further characterize transcription during spermatogenesis, we determined RNA polymerase II (RNAPII) distribution along the genome using ChIP-Seq.
Overall design mRNA sequencing at 8 time points during spermatogenesis was used to characterize differential gene expression; RNA Pol II ChIP-Seq at two time points was used to estimate RNA Pol II accumulation at promoters.
Contributor(s) Margolin G, Khil PP, Kim J, Bellani MA, Camerini-Otero RD
Citation(s) 24438502
Submission date Feb 15, 2013
Last update date May 15, 2019
Contact name Gennady Margolin
Organization name National Institutes of Health
Street address 5 Memorial Drive
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platforms (2)
GPL9185 Illumina Genome Analyzer (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (12)
GSM1083627 mouse testis 6dpp mRNA
GSM1083628 mouse testis 10dpp mRNA
GSM1083629 mouse testis 12dpp mRNA
BioProject PRJNA189510
SRA SRP018695

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
GSE44346_INPUT.wig.gz 134.7 Mb (ftp)(http) WIG
GSE44346_RAW.tar 347.7 Mb (http)(custom) TAR (of BED, WIG)
GSE44346_kgCanon_RPKMbyCT_clusters.txt.gz 283.0 Kb (ftp)(http) TXT
GSE44346_kgCanon_RPKMbyDpp_clusters.txt.gz 916.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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