|
| Status |
Public on Jun 10, 2017 |
| Title |
B_WT_P05_4 |
| Sample type |
SRA |
| |
|
| Source name |
Brown adipose tissue, WT, P0.5
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
genotype/variation: Wild type
tissue: Brown adipose tissue
age: postnatal day 0.5
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues were homogenized in TRIsure reagent (Bioline), and total RNA was extracted using isolate II RNA mini kit (Bioline).
Libraries were prepared according to Illumina TruSeq Stranded mRNA Library Prep Kit. RNA sequencing was performed by the Functional Genomics Core of UCSF.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Processed data file: ac_fat_raw_counts.txt
|
| Data processing |
Base calling was performed using RTA2 (real time analysis), which is included in the Illumina software.
Reads were mapped to mm9 using Tophat version 2.1.0 (default parameters).
Gene levels counts were obtained using featureCounts (Subread package, parameters -t exon -g gene_id).
Data were normalized (TMM option) and differential expression evaluated at the gene level with the edgeR package.
P-values were adjusted for multiple hypothesis testing using the Benjamini-Hochberg false discovery control procedure.
Gene ontology term enrichment was performed with Funcassociate 2.0.
Alternative splicing patterns were visualized using the Integrated Genome Viewer.
Junction reads corresponding to alternative splice isoforms were tallied from SAM format files using in-house Python scripts.
Plots were generating using ggplot2.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Tab-delimited text file includes raw count for all samples.
|
| |
|
| Submission date |
Jun 10, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
minwoo Lee |
| E-mail(s) |
[email protected]
|
| Organization name |
University of California, San Francisco
|
| Department |
CVRI
|
| Lab |
Chawla lab
|
| Street address |
555 Mission bay blvd south
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE83229 |
IL-33 and ST2 license beige and brown adipocytes for uncoupled respiration |
|
| Relations |
| BioSample |
SAMN05226573 |
| SRA |
SRX1837187 |
