|
| Status |
Public on Oct 26, 2020 |
| Title |
Control |
| Sample type |
SRA |
| |
|
| Source name |
Cultured germ cells p9-12
|
| Organism |
Mus musculus |
| Characteristics |
replicate: 1
treatment: 0ng FGF
cell type: cultured germ cells
passages: 9-12
|
| Treatment protocol |
Germ cell culture with mouse serum-free media + treatment (see characteristics)
|
| Growth protocol |
Germ cell culture with mouse serum-free media + 20ng/ml GDNF + 150ng/ml GFRA1 + 1ng/ml FGF2 between passages 9 and 12.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were treated with BioLegend anti-KIT antibody and encapsulated with 10X Chromium Next GEM Single Cells 3' Kit v3.1 with Feature Barcoding according to respective manufacturers' protocols.
Library generated per 10X Next GEM 3.1 protocol. Sequenced on NextSeq500 (Illumina) 75 cycle-cycle high output to depth of 30k reads per cell
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Control (no FGF)
|
| Data processing |
Fastq files generated with CellRanger
Count matricies generated with CellRanger and loom files created using velocyto
QC, filtering and UMAP generated with Seurat v.3.1
Pseudotime generated with Monocle v3
Genome_build: Mouse reference mm10 (GENCODE vM23/Ensembl 98)
Supplementary_files_format_and_content: csv file containing contrasts between each treatment and the 0ng FGF control
|
| |
|
| Submission date |
Oct 25, 2020 |
| Last update date |
Jul 10, 2024 |
| Contact name |
Eoin Christopher Whelan |
| E-mail(s) |
ewhelan@vet.upenn.edu
|
| Phone |
2158988805
|
| Organization name |
University of Pennsylvania School of Veterinary Medicine
|
| Department |
Biomedical Sciences
|
| Lab |
Sasaki
|
| Street address |
3800 Spruce St
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE160061 |
FGF9 Promotes Mouse Spermatogonial Stem Cell Proliferation Mediated by p38 MAPK Signaling [single-cell RNA-seq] |
| GSE160063 |
FGF9 Promotes Mouse Spermatogonial Stem Cell Proliferation Mediated by p38 MAPK Signaling |
|
| Relations |
| BioSample |
SAMN16547518 |
| SRA |
SRX9358303 |
