|
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.
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|
|
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
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|
|
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 |