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Sample GSM8005763 Query DataSets for GSM8005763
Status Public on Jan 31, 2024
Title RNA-seq: Prelim iPSC con rep 2
Sample type SRA
 
Source name iPSC
Organism Mus musculus
Characteristics cell type: iPSC
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 PRE_iPSC_EtOH_2_S2_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 SAMN38050620
SRA SRX22318405

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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