|
| Status |
Public on Jun 12, 2023 |
| Title |
OCT4-GFP positive germ cells, dexamethasone treated, biological rep 2, female |
| Sample type |
SRA |
| |
|
| Source name |
OCT4-GFP positive germ cells sorted from E15.5 ovary
|
| Organism |
Mus musculus |
| Characteristics |
tissue: ovary
cell type: OCT4-GFP positive germ cells
developmental stage: E15.5
treatment: dexamethasone
Sex: female
mouse strain: Tg(Pou5f1-EGFP)2Mnn
|
| Treatment protocol |
Pregnant dams were dosed by IP injection at E12.5, E13.5, E14.5 and E15.5 with either 10 μg dex (Sigma) per gram of body weight, or with an equal volume of saline vehicle control. Ovaries were collected at E15.5, and germ cells FACS sorted from somatic cells using OCT4-GFP transgene.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was harvested using RNeasy Micro Kit (QIAgen)
mRNA was purified from total RNA using poly-dT beads, fragmented, and then used for first strand cDNA sythesis with random hexamer primers (followed by second strand cDNA synthesis). Fragments were end repaired, A-tailed, ligated to sequencing adapters, size selected, PCR amplified, and libraries purified. Libraries were quantified on Qubit and QC'ed on Agilent Bioanalyzer for quality and size distribution.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
PGCdex2
gene_count_female.csv
gene_fpkm_female.csv
DGE_GERM_DEXvsSAL_female_ALL.csv
|
| Data processing |
Raw fastq reads were processed to remove adapter sequences, reads containing poly-N, and low quality reads
Reads were aligned to mm10 reference genome using Hisat2 v2.0.5.
Counts of reads mapping to each gene were determined using featureCounts v1.5.0-p3, followed by calculation of FPKM values.
Pairwise differential expression analysis was performed using DESeq2 v1.20.0. P-values were adjusted using Benjamini and Hochber FDR.
Assembly: mm10
Supplementary files format and content: CSV file containing raw counts for each sample
Supplementary files format and content: CSV file containing FPKM normalized counts for each sample
Supplementary files format and content: CSV file containing pairwise differential gene expression output from DESeq2
|
| |
|
| Submission date |
Jun 12, 2023 |
| Last update date |
Jun 12, 2023 |
| Contact name |
Steven Anthony Cincotta |
| E-mail(s) |
scincotta13@gmail.com
|
| Phone |
631-384-4489
|
| Organization name |
UCSF
|
| Street address |
35 Medical Center Way
|
| City |
San Francisco |
| State/province |
California |
| ZIP/Postal code |
94122 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE234663 |
Differential susceptibility of male and female germ cells to glucocorticoid-mediated signaling [RNAseq_DEX_Female] |
| GSE234681 |
Differential susceptibility of male and female germ cells to glucocorticoid-mediated signaling |
|
| Relations |
| BioSample |
SAMN35714002 |
| SRA |
SRX20657907 |
