|
| Status |
Public on May 12, 2020 |
| Title |
HSD male rat liver tissue S1P1_D12 |
| Sample type |
SRA |
| |
|
| Source name |
311L
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
gender: male
age: 8-10 weeks
animal id: 311
tissue: liver
chemical: TCAB
dose(mg/kg): 0.3
|
| Treatment protocol |
Eight to ten concentrations plus vehicle control were tested for each of the eighteen selected chemicals with n = 4 rats per exposure concentration. Exposure concentrations for each chemical were selected based on those used in the chronic or sub-chronic toxicity study and included concentrations that were both higher and lower than those previously tested. Whenever possible, the gavage vehicle was matched to that used in the chronic or sub-chronic study; however, multiple chemicals were orally administered in feed (MTE, DEHP, PFOA, EE2, and TCPP) or drinking water (BDCA and ACR) in the chronic or sub-chronic study. On day 5, the rats were weighed and euthanized via exsanguination.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The liver and left and right kidneys were collected, weighed, and the left liver lobe and right kidney were preserved in RNAlater (Qiagen, Valencia, CA) and stored at 4°C for RNA extraction. Total RNA was extracted from liver and kidney within 1 week of harvest using the RNeasy Mini Kit (Qiagen) with a DNA digestion step. RNA was sent frozen to BioSpyder (Carlsbad, CA) for HTT analysis using the rat S1500+ TempO-Seq platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
HSD male rat liver tissue
|
| Data processing |
TempO-Seq data are analyzed using the Tempo-SeqR software package using the statistical computing language R. The input for TempO-Seq data analysis is a folder of zipped FASTQ files. Each FASTQ file contains the reads and quality scores for one sample. Each FASTQ file is aligned using the Bowtie algorithm to a pseudotranscriptome input by the user. The output for TempO-Seq data analysis is a table of counts with each column representing a sample and each row representing a gene.
Data normalization was not done
Supplementary_files_format_and_content: Raw data matrix all smaples
|
| |
|
| Submission date |
Mar 16, 2020 |
| Last update date |
May 12, 2020 |
| Contact name |
Will Gwinn |
| Organization name |
National Institute of Health Sciences
|
| Department |
National Toxicology Program
|
| Lab |
Marcus Jackson
|
| Street address |
111 Alexander Dr.
|
| City |
Research Triangle Park |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE147072 |
Evaluation of 5-Day In Vivo Rat Liver and Kidney with High-Throughput Transcriptomics for Estimating Benchmark Doses of Apical Outcomes |
|
| Relations |
| BioSample |
SAMN14386063 |
| SRA |
SRX7921268 |
