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Sample GSM2267848 Query DataSets for GSM2267848
Status Public on Aug 15, 2016
Title Sample 13
Sample type SRA
 
Source name High fat Diet+Vehicle
Organism Mus musculus
Characteristics strain: C57BL/6
gender: male
tissue: white adipose
diet: high fat
treatment: vehicle
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from adipose tissue using the qiagen RNA isolation kit and its quality was verified using the Agilent 2100 Bioanalyzer (Agilent Technologies).
1µg of total RNA was enriched for Poly A RNA using the Dynabeads® mRNA DIRECT™ Micro Purification Kit according to manufacturer’s standard protocol. The resulting enriched RNA samples were then used to prepare barcoded libraries for sequencing using the Ion Total RNAseq V2 kit and the Ion Xpress 1-48 Barcode kit. Libraries were amplified 16 cycles and the quality of the libraries was confirmed on an Agilent Bioanalyzer using a DNA High Sensitivity chip. The libraries were pooled based on concentrations from the High Sensitivity chip, purified on a Pippin Prep gel, quantified by the Agilent Bioanalyzer and sequenced on an Ion Torrent Proton sequencer.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
 
Data processing The sequencing run here had a mean read length of 168 bp and consisted of 79.3 million reads total for the two samples (34.5 million for sample 9 and 44.8 million for sample 10).
These were aligned to the mouse mm9 trancsriptome using RNA-STAR 2.5.2
Reads counts were gather and normalized using trimmed mean of M-values (TMM) method
Differential genes were identified using 2 fold change and p <= 0.05 for student'sttest
Adjusted p values were calculated using Benjamini and Hochberg method. Only genes with an adjusted p value <= 0.05 were considered differentially expressed.
Genome_build: mouse mm9 transcriptome
 
Submission date Aug 11, 2016
Last update date May 15, 2019
Contact name Daniel Lee Johnson
E-mail(s) djohn166@uthsc.edu
Phone 9014483743
Organization name UTHSC
Department Molecular Informatics Core
Street address 71 S Manassas
City Memphis
State/province Tennessee
ZIP/Postal code 38163
Country USA
 
Platform ID GPL18635
Series (1)
GSE85498 Effect of Estrogen Receptor Beta Ligand on Gene Expression in White Adipose Tissue
Relations
BioSample SAMN05560437
SRA SRX2013340

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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