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Sample GSM2196873 Query DataSets for GSM2196873
Status Public on Jun 10, 2017
Title B_WT_P05_2
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) wannasmile12@gmail.com
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 SAMN05226571
SRA SRX1837185

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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