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Series GSE109033 Query DataSets for GSE109033
Status Public on Nov 06, 2018
Title 10x Genonics Drop-seq single-cell RNA-seq of isolated Adult ID4-EGFP mouse spermatogonia, spermatocytes, spermatids & steady-state spermatogenic cells
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary To reveal distinct transcriptomes associated with various spermatogenic cells, including spermatogonial stem cells and all of their subsequent progeny, single-cell transcriptomes from Adult ID4-EGFP+ spermatogonia (sorted for brightest or dimmest), StaPut-enriched spermatocytes and spermatids, or unselected steady-state spermatogenic cells were used for 10x Genomics 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 (Drop-Seq) to perform single-cell RNA-seq
 
Overall design Unselected or sorted Adult ID4-EGFP+ spermatogonia (sorted separately as EGFP-bright or EGFP-dim), three replicate preparations of steady-state unselected spermatogenic cells, and isolated adult spermatocytes and spermatids were used for this study. Data are from a total of 17,491 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 HD078679 Epimutations in Offspring Produced by Assisted Reproductive Technologies (ART) THE UNIVERSITY OF TEXAS AT SAN ANTONIO John R MCCARREY
R01 HD090007 Origin and functional significance of the spermatogonial stem cell transcriptome barcode THE UNIVERSITY OF TEXAS AT SAN ANTONIO Brian Peter Hermann
Submission date Jan 10, 2018
Last update date Mar 25, 2019
Contact name Brian P. Hermann
E-mail(s) Brian.Hermann@utsa.edu
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 (2)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
Samples (8)
GSM2928336 Ad-Id4-EGFP-bright
GSM2928337 Ad-Id4-EGFP-dim
GSM2928338 Ad-Id4-EGFP-unselected
Relations
BioProject PRJNA429468
SRA SRP128722

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
GSE109033_Ad-Id4GFP-bright-dim-CD9bright_filteredmatrix.mtx.gz 75.7 Mb (ftp)(http) MTX
GSE109033_Ad-Id4GFP-bright-dim-CD9bright_filteredmatrixbarcodes.tsv.gz 30.0 Kb (ftp)(http) TSV
GSE109033_Ad-Id4GFP-bright-dim-CD9bright_filteredmatrixgenes.tsv.gz 212.8 Kb (ftp)(http) TSV
GSE109033_AdultMouseBarcode_filteredbarcodes.tsv.gz 57.2 Kb (ftp)(http) TSV
GSE109033_AdultMouseBarcode_filteredgenes.tsv.gz 212.8 Kb (ftp)(http) TSV
GSE109033_AdultMouseBarcode_filteredmatrix.mtx.gz 166.2 Mb (ftp)(http) MTX
GSE109033_AdultMouseSpermatogenesis-reps1-3_barcodes.tsv.gz 21.0 Kb (ftp)(http) TSV
GSE109033_AdultMouseSpermatogenesis-reps1-3_genes.tsv.gz 212.8 Kb (ftp)(http) TSV
GSE109033_AdultMouseSpermatogenesis-reps1-3_matrix.mtx.gz 57.0 Mb (ftp)(http) MTX
GSE109033_RAW.tar 218.4 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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