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Sample GSM4589768 Query DataSets for GSM4589768
Status Public on Sep 26, 2022
Title High fat diet fasted (16h) liver_sample3
Sample type SRA
 
Source name Liver
Organism Mus musculus
Characteristics tissue: Liver
weeks on diet: 16
strain: C56B6/J
treatment: High fat diet fasted (16h)
Extracted molecule total RNA
Extraction protocol Livers were removed and flash frozen in liquid nitrogen RNA was harvested using TRIzol and the Qiagen RNAeasy kit with Dnase treatment. RNA was quanified by Agilent 2100 bioanalsyer.
PolyA enrichment was performed using NEBNext Poly(A) mRNA magnetic Isolation and libraries prepared using NEBNext Ultra II RNA Library Prep kit for Illumina
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description HFD_Fast_Liver_3
Data processing Illumina CASAVA 1.8.4 software used for basecalling.
Reads were mapped to mm10 whole genome using tophat2 (2.0.11) with argument “--library-type fr-firststrand"
Gene annotations were obtained from iGenome GRCm38. Gene-based read count were obtained using featureCounts function from Rsubread Bioconductor package 
Genome_build: mm10
Supplementary_files_format_and_content: csv file includes Gene counts for each Sample
 
Submission date Jun 03, 2020
Last update date Sep 26, 2022
Contact name LMS Bioinformatics Core
E-mail(s) bioinformatics@lms.mrc.ac.uk
Organization name MRC London Institute of Medical Sciences
Department Bioinformatics Core
Street address Hammersmith Hospital Campus, Du Cane Road
City London
ZIP/Postal code W12 0NN
Country United Kingdom
 
Platform ID GPL17021
Series (2)
GSE151750 RNAseq of liver of CD and HFD fed mice in fed or fasted conditions
GSE151753 Characterization of the role of RBFOX2 in the liver
Relations
BioSample SAMN15096529
SRA SRX8466185

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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