|
| Status |
Public on Mar 04, 2024 |
| Title |
VAT_9 |
| Sample type |
SRA |
| |
|
| Source name |
VAT
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: VAT
Sex: Male
strain: Sprague-Dawley
treatment: Sham
|
| Treatment protocol |
Animals were exposed for 4 hours daily for 28 days to PCB 52 using a nose-only inhalation system by passing dried, high-efficiency particulate air (HEPA)-filtered air through the PCB 52-coated glass beads at a flow rate of 12 L/min.
|
| Growth protocol |
28-day-old male and female Sprague-Dawley rats (Charles River, Wilmington, MA) were allowed to acclimate for 8 days, followed by a 30 min. and a 2 hour training day in the nose-only apparatus. All rats were provided food (sterile Teklad 5% stock diet, Harlan, Madison, WI) and water ad libitum. 24 rats were weighed and assigned to the sham or PCB 52 exposure groups using a random number generator at 39 days of age for males 42 days of age for females to begin PCB 52 exposure.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Portions of the tissue (~100 mg) were rinsed with PBS and placed in a lysing matrix tube containing 1 mL of TRIzol. Sample solutions were then aliquoted to RNeasy spin columns, followed by the QIAGEN RNeasy Kits protocol to clean and isolate RNA from the tissue samples. Samples with RINs below 8 were excluded from further analysis.
mRNA enrichment: poly (A) capture or rRNA removal
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
cDNA library was constructed using the ribosomal depletion methods, and reads were sequenced in 120 bp paired-end sequences per the Illumina 1.9 encoding Novogene protocols
Sample data integrity was examined using FASTQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, version 0.11.9) for quality control of fastq files.
Sequence reads were then mapped to the UCSC rn6 rat reference genome using HISAT2
Gene counts were generated from the BAM files using SummarizedExperiments (version 1.28.0) with the UCSC Rattus Norvegicus (rn6) reference genome
Assembly: Rn6
Supplementary files format and content: CSV file includes raw counts for each sample
|
| |
|
| Submission date |
Feb 27, 2024 |
| Last update date |
Mar 04, 2024 |
| Contact name |
Aloysius John Klingelhutz |
| E-mail(s) |
al-klingelhutz@uiowa.edu
|
| Organization name |
University of Iowa
|
| Department |
Microbiology and Immunology
|
| Lab |
Klingelhutz Lab
|
| Street address |
3-612 BSB, 51 Newton Road
|
| City |
Iowa City |
| State/province |
IA |
| ZIP/Postal code |
52242 |
| Country |
USA |
| |
|
| Platform ID |
GPL25947 |
| Series (1) |
| GSE259369 |
Effects of PCB 52 Exposure Via Sub-Acute Nose-Only Inhalation on Gene Expression in Fat Depots of Adolescent Rats |
|
| Relations |
| BioSample |
SAMN40161277 |
| SRA |
SRX23764279 |
