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| 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
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| 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
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| 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.
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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 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 |
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| Submission date |
Jan 10, 2018 |
| Last update date |
Feb 11, 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 (1) |
| GPL21493 |
Illumina HiSeq 3000 (Mus musculus) |
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| Samples (3) |
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| Relations |
| BioProject |
PRJNA429481 |
| SRA |
SRP128740 |
| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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