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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
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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
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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.
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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 |
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Submission date |
Jan 10, 2018 |
Last update date |
Mar 25, 2019 |
Contact name |
Brian P. Hermann |
E-mail(s) |
Brian.Hermann@utsa.edu
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Phone |
210-458-8047
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Organization name |
University of Texas at San Antonio
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Department |
Department of Biology
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Street address |
1 UTSA Circle
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City |
San Antonio |
State/province |
TX |
ZIP/Postal code |
78249 |
Country |
USA |
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Platforms (2) |
GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
GPL21493 |
Illumina HiSeq 3000 (Mus musculus) |
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Samples (8)
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Relations |
BioProject |
PRJNA429468 |
SRA |
SRP128722 |
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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
Processed data are available on Series record |
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