|
| Status |
Public on Jan 31, 2024 |
| Title |
RNA-seq: Sertoli con rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Sertoli Cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Sertoli Cells
treatment: Control
|
| Treatment protocol |
For all cell types except PGCLCs, 1 μM BPS was added to media gassed with 5% CO2, 5% O2, and balanced N2 and then injected into sealed T-25 cell culture flasks and left to incubate for 24 hours. The media was gassed to ensure enrichment to 5% CO2, which is normally regulated by the cell incubator, limiting the potential for the pH to change in the media during this exposure period due to the absorption of CO2 by incubating cells. Following 24 hours of exposure, media containing BPS was removed and cells were washed and allowed to recover in fresh untreated media (without BPS or EtOH) for 24 hours prior to harvesting. PGCLCs were not suitable for this exposure paradigm as EpiLCs undergo differentiation to PGCLCs in cell aggregates formed in low-adherence round-bottom 96 well plates and cannot be maintained in T-25 sealed flasks. Therefore, diluted BPS was added to PGCLC media and added to cells in round-bottom 96 well plates to incubate for 24 hours prior to a shortened wash and “chase” period of 8 hours prior to cell sorting.
|
| Growth protocol |
See the publication for a full description of specific growth protocols for each cell types included in the study.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from cells using Trizol and contaminating genomic DNA was removed by RQ1 DNase (M6101) treatment according to the manufacturer’s instructions (Promega Corporation, WI USA).
Strand-specific RNA-seq libraries were prepared with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® sequencing (E7760S) according to the manufacturer’s protocol (New England Biolabs, MA USA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
SER_E_2_S58_R1_001
|
| Data processing |
The quality of the fastq reads was checked using FastQC. Reads were aligned to the mm10 mouse reference genome using the Rsubreads package to produce read counts. These were then used for differential gene expression analysis using the edgeR package. Briefly, gene counts were normalized using the trimmed mean of M-value normalization (TMM) method before determining counts per million (CPM) values. For a gene to be classified as showing differential gene expression between BPS-treated and EtOH vehicle-only control samples, a threshold of both a Benjamini-Hochberg adjusted p-value ≤ 0.05 and a false discovery rate (FDR) ≤ 0.05 had to be met.
Assembly: mm10
Supplementary files format and content: CPM
|
| |
|
| Submission date |
Jan 08, 2024 |
| Last update date |
Jan 31, 2024 |
| Contact name |
Jake Dean Lehle |
| E-mail(s) |
jakelehle@gmail.com
|
| Phone |
5129928144
|
| Organization name |
The University of Texas at San Antonio
|
| Department |
NDRB
|
| Lab |
McCarrey
|
| Street address |
16631 Vance Jackson Rd APT#1220
|
| City |
San Antonio |
| State/province |
TX |
| ZIP/Postal code |
78249 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE252720 |
Endocrine disruptor-induced epimutagenesis in vitro: Insight into molecular mechanisms [RNA-Seq] |
| GSE252723 |
Endocrine disruptor-induced epimutagenesis in vitro: Insight into molecular mechanisms |
|
| Relations |
| BioSample |
SAMN38050632 |
| SRA |
SRX22318409 |
