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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 12, 2023 |
| Title |
E15.5 ovary, GR homozygous deletion |
| Sample type |
SRA |
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| Source name |
E15.5 ovary, enriched for OCT4-GFP germ cells
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| Organism |
Mus musculus |
| Characteristics |
tissue: ovary
cell type: OCT4-GFP germ cells
developmental stage: E15.5
genotype: GR deletion
Sex: female
mouse strain: Tg(Pou5f1-EGFP)2Mnn Nr3c1tm1.1Jda
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| Extracted molecule |
total RNA |
| Extraction protocol |
Fetal ovaries were dissected into ice cold 0.4% BSA in PBS, washed once, transferred to 0.25% Trypsin-EDTA and incubated in a 37°C water bath for 30 minutes, with gentle pipetting every 10-15 minutes to facilitate the dissociation. After 30 minutes, DNase I (1 mg / mL) was added at a 1:10 dilution, and samples were incubated another 10 minutes at 37°C. Samples were pipetted to ensure complete digestion, and then an equal volume of ice-cold FBS was added to inactivate trypsin. To prepare for FACS sorting, Sytox Blue viability dye was added to samples at 1:1000 dilution, and then samples were filtered through a 35 μm filter into FACS tubes. Samples were sorted to a BD FACSAria II, mixed at a 60:40 ratio of germ cells to somatic cells, and then submitted for single cell capture using the 10X Chromium platform.
Libraries were prepared using the Illumina 10X Single Cell 3' v3 kit, as per the manufacturer's instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Illumina 10X Single Cell 3' v3
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| Data processing |
All demultiplexing, barcode processing, feature counting, and aggregation were performed using Cell Ranger.
All downstream data processing was performed using Seurat v 3.2.3
Assembly: mm10
Supplementary files format and content: Tab-separated barcode files and feature files, as well as matrix files.
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| Submission date |
Jun 12, 2023 |
| Last update date |
Jun 13, 2023 |
| Contact name |
Steven Anthony Cincotta |
| E-mail(s) |
scincotta13@gmail.com
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| Phone |
631-384-4489
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| Organization name |
UCSF
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| Street address |
35 Medical Center Way
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| City |
San Francisco |
| State/province |
California |
| ZIP/Postal code |
94122 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE234679 |
Differential susceptibility of male and female germ cells to glucocorticoid-mediated signaling [scRNAseq_Female] |
| GSE234681 |
Differential susceptibility of male and female germ cells to glucocorticoid-mediated signaling |
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| Relations |
| BioSample |
SAMN35712898 |
| SRA |
SRX20657684 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7473202_DEL_barcodes.tsv.gz |
85.0 Kb |
(ftp)(http) |
TSV |
| GSM7473202_DEL_features.tsv.gz |
245.2 Kb |
(ftp)(http) |
TSV |
| GSM7473202_DEL_matrix.mtx.gz |
182.7 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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