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Series GSE109049 Query DataSets for GSE109049
Status Public on Nov 06, 2018
Title 10x Genonics single-cell RNA-seq of immature (P6) ID4-EGFP mouse spermatogonia & testis cells
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary To reveal distinct transcriptomes associated with spermatogonial stem cell renewal vs. initiation of differentiation, single-cell transcriptomes from P6 ID4-EGFP+ spermatogonia (sorted for brightest or dimmest) or unselected testis cells were used for Drop-Seq analysis. The GFP-bright and dim phenotypes exhibit distinct fates when assayed by transplantation, with ID4-EGFPbright cells highly enriched for SSCs, and ID4-EGFPdim cells enriched for progenitors. We used the 10x Genomics Chromium (a commercial Drop-Seq variant) to perform single-cell RNA-seq
Overall design Unselected or sorted P6 ID4-EGFP+ spermatogonia (sorted separately as EGFP-bright or EGFP-dim) were used for this study. Data are from a total of 13,094 cells.
Contributor(s) Hermann BP, Cheng K, Singh A, Roa-de-la-Cruz L, Mutoji KN, Gildersleeve H, Chen I, Mayo M, Westernströer B, Law NC, Oatley MJ, Velte EK, Niedenberger BA, Fritze D, Silber S, Geyer CB, Oatley JM, McCarrey JR
Citation(s) 30404016
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 HD090007 Origin and functional significance of the spermatogonial stem cell transcriptome barcode THE UNIVERSITY OF TEXAS AT SAN ANTONIO Brian Peter Hermann
R01 HD078679 Epimutations in Offspring Produced by Assisted Reproductive Technologies (ART) THE UNIVERSITY OF TEXAS AT SAN ANTONIO John R MCCARREY
Submission date Jan 10, 2018
Last update date Feb 11, 2019
Contact name Brian P. Hermann
Phone 210-458-8047
Organization name University of Texas at San Antonio
Department Department of Biology
Street address 1 UTSA Circle
City San Antonio
State/province TX
ZIP/Postal code 78249
Country USA
Platforms (1)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
Samples (3)
GSM2928504 P6-Id4-EGFP-bright
GSM2928505 P6-Id4-EGFP-dim
GSM2928506 P6-Id4-EGFP-unselected
BioProject PRJNA429481
SRA SRP128740

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
GSE109049_P6-Id4GFP-10X_filteredmatrix.mtx.gz 139.1 Mb (ftp)(http) MTX
GSE109049_P6-Id4GFP-10X_filteredmatrixbarcodes.tsv.gz 53.2 Kb (ftp)(http) TSV
GSE109049_P6-Id4GFP-10X_filteredmatrixgenes.tsv.gz 212.8 Kb (ftp)(http) TSV
GSE109049_RAW.tar 145.0 Mb (http)(custom) TAR (of MTX, TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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