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Sample GSM3518514 Query DataSets for GSM3518514
Status Public on Dec 31, 2019
Title W4_Lep1
Sample type SRA
 
Source name liver
Organism Rattus norvegicus
Characteristics tissue: liver
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from snap-frozen liver samples using TRIzol (Life Technologies) according to the manufacturer’s instructions. RNA purity was checked using the Nano Photometer spectrophotometer (IMPLEN). RNA concentration was measured using Qubit RNA Assay Kit in Qubit 2.0 Flurometer (Life Technologies). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies).
the libraries were sequenced on an Illumina Hiseq X platform and 150 bp paired-end reads were generated sequencing libraries were generated using the rRNA- depleted RNA by NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, USA)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Data processing Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to rn6 or Macaca5 reference genome using hisat2 v2.1.0 with default parameters.
Gene expression for each sample was quantified using featureCounts(v 1.6.1) and DEseq2(v 1.2.0).
Genome_build: rn6;Macaca_fascicularis_5.0
Supplementary_files_format_and_content: rat_all_normat.csv: abundance measurements(DESeq2, log2-transformed)
Supplementary_files_format_and_content: geneCounts_featureCounts_macaca.tab: abundance measurements(raw counts)
 
Submission date Dec 18, 2018
Last update date Dec 31, 2019
Contact name Gran Young
Organization name Tongji University
Street address 1239th, Siping Road, Yangpu district
City Shanghai
State/province --- Select a state ---
ZIP/Postal code 200082
Country China
 
Platform ID GPL24688
Series (1)
GSE124002 Leptin deficiency leads to a unique natural history of NASH in rats
Relations
BioSample SAMN10606739
SRA SRX5146492

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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