|
Status |
Public on Jun 12, 2023 |
Title |
OCT4-GFP negative somatic cells, dexamethasone treated, biological rep 3, male |
Sample type |
SRA |
|
|
Source name |
OCT4-GFP negative somatic cells sorted from PN1 testis
|
Organism |
Mus musculus |
Characteristics |
tissue: testis cell type: OCT4-GFP negative somatic cells developmental stage: PN1 treatment: dexamethasone Sex: male mouse strain: Tg(Pou5f1-EGFP)2Mnn
|
Treatment protocol |
Pregnant dams were dosed by IP injection at E17.5 and E18.5 with either 10 μg dex (Sigma) per gram of body weight, or with an equal volume of saline control. After birth at PN0, pups were injected via subcutnaeous injection with the same dose of dex (or saline), scaled by body weight. Testes were collected at PN1, 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 |
SOMAdex3 gene_count_male.csv gene_fpkm_male.csv DGE_SOMA_DEXvsSAL_male_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) |
GSE234672 |
Differential susceptibility of male and female germ cells to glucocorticoid-mediated signaling [RNAseq_DEX_Male] |
GSE234681 |
Differential susceptibility of male and female germ cells to glucocorticoid-mediated signaling |
|
Relations |
BioSample |
SAMN35714084 |
SRA |
SRX20657938 |