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Series GSE131656 Query DataSets for GSE131656
Status Public on May 23, 2019
Title Unique Epigenetic Programming Distinguishes Regenerative Spermatogonial Stem Cells in the Developing Mouse Testis (ChIP-seq)
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Background: Spermatogonial stem cells (SSCs) sustain the process of steady-state spermatogenesis in the mammalian testis, which is critical to the ongoing production of sperm and male fertility. SSCs can both self-renew to perpetuate the SSC population, and give rise to progenitors to propel the spermatogenic differentiation pathway. SSCs are detectable as a small subpopulation of undifferentiated spermatogonia that demonstrate regenerative capacity in a transplantation assay, and can be selectively recovered on the basis of expression of an Id4-eGfp sortable marker transgene. Enriched populations of SSCs and progenitors display consistent differences in gene expression patterns suggesting they represent discrete spermatogonial subtypes.
Results: Here we describe distinct spermatogonial subtype-specific epigenetic programming profiles associated with subtype-specific differential gene expression on the basis of genome-wide patterns of six different histone modifications, chromatin accessibility, and DNA methylation. We find that similarly expressed genes show no differences in epigenetic programming, whereas differentially expressed genes show distinct histone modification patterns as well as subtype-specific differences in patterns of distal intergenic low-methylated regions. Motif-enrichment analysis of differentially programmed elements predicts a set of transcription factors that may regulate this spermatogonial subtype-specific epigenetic programming, and gene-specific chromatin immunoprecipitation analyses confirm subtype-specific differences in binding of a subset of these factors to target genes.
Conclusions: Taken together, these results indicate that SSCs and progenitors are discrete spermatogonial subtypes that appear to be differentially programmed to carry out mutually exclusive functions including self-renewal and maintenance of regenerative capacity in SSCs and lineage commitment and loss of regenerative capacity in progenitors.
 
Overall design ChIP-seq of P6 ID4-eGFP Bright and Dim mice spermatogonia were generated by deep sequencing, in triplicate.
 
Contributor(s) Cheng K, McCarrey JR
Citation(s) 33083754
Submission date May 22, 2019
Last update date Oct 27, 2020
Contact name keren cheng
E-mail(s) keren.cheng@outlook.com
Organization name University of Pennsylvania
Department Biomedical Sciences
Street address 3800 Spruce Street
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platforms (1)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
Samples (42)
GSM3791861 ChIPseq.ID4eGFP_Bright_H3K4me1_Replicate1
GSM3791862 ChIPseq.ID4eGFP_Bright_H3K4me1_Replicate2
GSM3791863 ChIPseq.ID4eGFP_Bright_H3K4me1_Replicate3
This SubSeries is part of SuperSeries:
GSE131657 Unique Epigenetic Programming Distinguishes Regenerative Spermatogonial Stem Cells in the Developing Mouse Testis
Relations
BioProject PRJNA544307
SRA SRP199233

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
GSE131656_B.H3K27ac_BigWig.bw 702.2 Mb (ftp)(http) BW
GSE131656_B.H3K27me3_BigWig.bw 846.2 Mb (ftp)(http) BW
GSE131656_B.H3K4me1_BigWig.bw 598.3 Mb (ftp)(http) BW
GSE131656_B.H3K4me2_BigWig.bw 868.5 Mb (ftp)(http) BW
GSE131656_B.H3K4me3_BigWig.bw 549.9 Mb (ftp)(http) BW
GSE131656_B.H3K9me3_BigWig.bw 497.2 Mb (ftp)(http) BW
GSE131656_Bright_H3K27ac_peaks.bed.gz 778.7 Kb (ftp)(http) BED
GSE131656_Bright_H3K27me3_peaks.bed.gz 1000.2 Kb (ftp)(http) BED
GSE131656_Bright_H3K4me1_peaks.bed.gz 3.1 Mb (ftp)(http) BED
GSE131656_Bright_H3K4me2_peaks.bed.gz 1.6 Mb (ftp)(http) BED
GSE131656_Bright_H3K4me3_peaks.bed.gz 1.5 Mb (ftp)(http) BED
GSE131656_Bright_H3K9me3_peaks.bed.gz 1.9 Mb (ftp)(http) BED
GSE131656_D.H3K27ac_BigWig.bw 1.1 Gb (ftp)(http) BW
GSE131656_D.H3K27me3_BigWig.bw 1.3 Gb (ftp)(http) BW
GSE131656_D.H3K4me1_BigWig.bw 1.0 Gb (ftp)(http) BW
GSE131656_D.H3K4me2_BigWig.bw 957.8 Mb (ftp)(http) BW
GSE131656_D.H3K4me3_BigWig.bw 592.4 Mb (ftp)(http) BW
GSE131656_D.H3K9me3_BigWig.bw 420.4 Mb (ftp)(http) BW
GSE131656_Dim_H3K27ac_peaks.bed.gz 3.2 Mb (ftp)(http) BED
GSE131656_Dim_H3K27me3_peaks.bed.gz 2.7 Mb (ftp)(http) BED
GSE131656_Dim_H3K4me1_peaks.bed.gz 5.1 Mb (ftp)(http) BED
GSE131656_Dim_H3K4me2_peaks.bed.gz 1.8 Mb (ftp)(http) BED
GSE131656_Dim_H3K4me3_peaks.bed.gz 1.5 Mb (ftp)(http) BED
GSE131656_Dim_H3K9me3_peaks.bed.gz 2.2 Mb (ftp)(http) BED
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