|
| Status |
Public on Dec 31, 2024 |
| Title |
iwat, wt_sfa, 3 |
| Sample type |
SRA |
| |
|
| Source name |
iWAT
|
| Organism |
Mus musculus |
| Characteristics |
tissue: iWAT
genotype: WT
diet: SFA
Sex: Male
age: 18-22 weeks
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol and RNeasy Mini Kit with on-column DNase I digestion (Qiagen)
Library preparation and sequencing was performed at the UCLA Technology Center for Genomics & Bioinformatics. Illumina sequencing-compatible cDNA libraries were synthesized from mRNA enriched by Poly-A capture. 200bp paired-end sequencing cDNA libraries were analyzed with an Agilent TapeStation and sequenced on an Illumina NovaSeq S1 at 200 cycles. Read depth per sample averaged around 130M reads. Raw sequencing reads were demultiplexed using bcl2fastq (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
A3_S15
|
| Data processing |
Fastq files were checked for quality, filtered, trimmed, and corrected for base pair mismatches using fastp (Version 0.23.2)
Salmon was used with full selective alignment to map reads to the mouse transcriptome and quantify transcript counts [mm10 - Ensembl – Release 97]
Transcript counts were summarized to the gene level using tximport package for R.
Assembly: mm10
Supplementary files format and content: .csv files contain Salmon-derived transcript abundances and raw counts from tximport summarized to the gene level
|
| |
|
| Submission date |
Nov 28, 2022 |
| Last update date |
Dec 31, 2024 |
| Contact name |
Peter Tontonoz |
| E-mail(s) |
ptontonoz@mednet.ucla.edu
|
| Organization name |
University of California, Los Angeles
|
| Department |
Pathology & Laboratory Medicine
|
| Lab |
Tontonoz Lab
|
| Street address |
675 Charles E Young Dr.
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE218938 |
Transcriptional profiling of mature murine adipocytes of the inguinal white adipose tissue depot following LPCAT3 deletion and dietary PUFA manipulation [bulk RNA-seq] |
| GSE218943 |
Transcriptional profiling of mature murine adipocytes of the inguinal white adipose tissue depot following LPCAT3 deletion and dietary PUFA manipulation |
|
| Relations |
| BioSample |
SAMN31898147 |
| SRA |
SRX18404660 |
