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Sample GSM3840122 Query DataSets for GSM3840122
Status Public on Jan 30, 2020
Title 70-HFD control
Sample type SRA
 
Source name Liver
Organism Mus musculus
Characteristics tissue: liver
sample id: 15089X10
diet: High fat diet
treatment: Control
Extracted molecule total RNA
Extraction protocol 30-50 mg tissue was homogenized using bullet blender and the lysate was used for the RNA extraction using the RNAeasy kit (Qiagen) as per the manufacturer instructions
Illumina TruSeq Stranded RNA Kit with Ribo-Zero Gold
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing The mouse GRCm38 FASTA and GTF files were downloaded from Ensembl release 92.
The reference database was created using STAR version 2.5.4a with splice junctions optimized for 50 base pair reads. 
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates. 
Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.5.1. 
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2.
Genome_build: GRCm38
Supplementary_files_format_and_content: Raw counts (featureCounts output files combined into a single tab-delimited matrix).
 
Submission date May 31, 2019
Last update date Jan 30, 2020
Contact name Chris Stubben
Organization name Huntsman Cancer Institute
Department University of Utah
Street address 2000 Cir of Hope Dr
City Salt Lake City
State/province Utah
ZIP/Postal code 84103
Country USA
 
Platform ID GPL24247
Series (1)
GSE132056 Removing a Double Bond from Ceramides Ameliorates Insulin Resistance and Hepatic Steatosis
Relations
BioSample SAMN11918193
SRA SRX5944719

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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