|
| Status |
Public on Jun 01, 2022 |
| Title |
TCE_Female_Rat16_AS |
| Sample type |
SRA |
| |
|
| Source name |
placental tissue
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain:
tissue: placenta
dam: dam 16
Sex: female
treatment: 480 mg/kg/day trichloroethylene
treatment duration: gestation days 6-16
|
| Treatment protocol |
Timed-pregnant Wistar rats were exposed to 480 mg TCE mg/kg/day, 200 mg/kg/day NAC or co-exposure with both chemicals via ingestion (treated mini vanilla wafer) on gestation days 6-16 (tissue collection day).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from placental tissue using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s recommended protocol with a modification. A FastPrep-24 tissue lyser (MP Biomedicals; Solon, OH, USA) was utilized prior to the gDNA elimination step to achieve maximum quality tissue homogenization. DNA was extracted from placental using the NucleoSpin Tissue kit (Machery-Nagel; Düren, Germany) according to the manufacture’s recommended protocol. RNA and DNA concentrations were determined using a NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific; Waltham, MA, USA). Isolated nucleic acids were subsequently stored at -80°C until further processing.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were aligned to the rat genome using STAR, with the options "outFilterMultimapNmax 10" and "sjdbScore 2".
Aligned reads were assigned to Rnor_6.0 genes using featureCounts.
Genes with mean read counts-per-million less than six across all samples were filtered out and excluded from the analysis to reduce dispersion due to low expression levels.
Data were normalized using the median of ratios method .
RUV(Remove Unwanted Variation) normalization factors were generated for each sample using the RUVSeq package RUVr function
Differential gene expression testing was performed using the DESeq2 package (version 1.28.1) for R statistical computing. Negative binomial general linear modeling was used for differential gene expression testing.
Genome_build: rn6
|
| |
|
| Submission date |
Mar 04, 2021 |
| Last update date |
Jun 01, 2022 |
| Contact name |
Elana Elkin |
| Organization name |
University of Michigan
|
| Department |
Department of Environmental Health Sciences
|
| Lab |
Bakulski
|
| Street address |
1415 Washington Heights
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL25947 |
| Series (1) |
| GSE168232 |
Transcriptional responses to maternal trichloroethylene and/or N-acetyl cysteine exposure in Wistar rat placental tissue |
|
| Relations |
| BioSample |
SAMN18138801 |
| SRA |
SRX10237693 |
