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Sample GSM3310559 Query DataSets for GSM3310559
Status Public on Nov 01, 2018
Title Ctrl-3-pgVAT
Sample type SRA
 
Source name pgVAT
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: pgVAT
group: Ctrl
Extracted molecule total RNA
Extraction protocol Total RNA from fat tissue were extract by RNeasy Mini Kit (Qiagen) according to manufacturer’s recommendations and validated by the Agilent 2100 Bioanalyzer.
Sequencing libraries were generated using NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB, USA).
150 bp paired-end reads were sequenced on Illumina Hiseq Xten platform in CapitalBio technology corporation (Beijng).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Data processing The paired-end clean reads were aligned to the reference genome using STAR and each gene reads numbers were count by HTseq.
Differential expression gene (DEG) analysis was performed by DEseq2 package in which gene length and dispersion bias was corrected.
The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate (FDR).
Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: SUB_readcount.csv: raw_counts_scWAT
Supplementary_files_format_and_content: EP_readcount.csv: raw_counts_pgVAT
 
Submission date Jul 30, 2018
Last update date Nov 01, 2018
Contact name Li Li
Organization name UT Southwestern Medical Center
Street address 5323 Harry Hines Boulevard
City Dallas
State/province TX
ZIP/Postal code 75390
Country USA
 
Platform ID GPL21273
Series (1)
GSE117843 Microbiota Depletion Impairs Adaptive Thermogenesis of Both Brown and Beige Adipose Tissue
Relations
BioSample SAMN09737988
SRA SRX4483231

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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