|
| Status |
Public on May 01, 2024 |
| Title |
[Liver] [Pair-fed + Vehicle] [Replicate 4] |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
strain: C57BL/6J
Sex: male
diet: pair-fed
agent: Vehicle
|
| Treatment protocol |
Male C57BL/6J mice were exposed to 0.2 mg/kg PCB126 or corn oil vehicle prior to ethanol feeding in the chronic-binge model.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the standard RNA-STAT60 and chloroform method. Samples were then treated with DNase, Amplification Grade I to digest single- and double-stranded DNA species. Finally, RNA samples were treated with RNAClean XP beads at a 1:1 volume ratio to further purify our samples to remove salts, dNTPs, and miscellaneous enzymes
The TruSeq Stranded mRNA Library Prep Kit (Illumina) was used for library construction
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
IL0052_204_10_S4
|
| Data processing |
Sequencing was performed on an Illumina NextSeq 2000
Raw sequences were checked for quality values using fastQC v0.10.1. Quality trimming was not deemed necessary.
The sequences were directly aligned to the GRCm39 reference assembly using Star version 2.6.
Read counts for gene regions were obtained with HTSeq v.0.10.0 using GRCm39.106.gtf.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited file of HTSeq raw counts
|
| |
|
| Submission date |
Sep 29, 2023 |
| Last update date |
May 01, 2024 |
| Contact name |
Eric Christian Rouchka |
| E-mail(s) |
eric.rouchka@louisville.edu
|
| Organization name |
University of Louisville
|
| Department |
Biochemistry and Molecular Genetics
|
| Lab |
KY INBRE Bioinformatics Core
|
| Street address |
522 East Gray Street
|
| City |
Louisville |
| State/province |
Kentucky |
| ZIP/Postal code |
40292 |
| Country |
USA |
| |
|
| Platform ID |
GPL30172 |
| Series (1) |
| GSE244388 |
PCB126 Modifies the Murine Hepatic Transcriptome and Metallome to Promote Alcohol-associated Liver Disease Pathogenesis |
|
| Relations |
| BioSample |
SAMN37610694 |
| SRA |
SRX21936858 |
