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Sample GSM4425523 Query DataSets for GSM4425523
Status Public on Mar 20, 2023
Title Normal 4
Sample type SRA
 
Source name liver tissue
Organism Homo sapiens
Characteristics tissue: liver tissue
with nash: No
Extracted molecule total RNA
Extraction protocol RNAiso Plus Total RNA extraction reagent (Cat#9109, TAKARA)
VAHTS Stranded mRNA-seq Library Prep Kit for Illumina®(Cat#NR602-02,Vazyme)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Description X2
Data processing Sequenced raw reads were preprocessed by removing rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads with Seqtk (https:// github.com/lh3/seqtk).
Obtained clean reads were mapped to the mouse mm10 reference genome with two mismatches by Hisat2 (version 2.0.4). After genome mapping, Cufflinks v2.1.1 was run with a reference annotation to generate FPKM (fragments per kilobase of exon model per million mapped reads)values for known gene models.
The p-value significance threshold was set by the false discovery rate (FDR) strictly controlled using the Benjamini and Hochberg algorithm. The fold-changes were estimated according to the FPKM in each sample. Differentially expressed genes were identified using Cuffdiff with the following filter criteria: FDR≤0.05 and fold-change≥2.
Genome_build: hg38
Supplementary_files_format_and_content: raw count and FPKM
 
Submission date Mar 20, 2020
Last update date Mar 20, 2023
Contact name Kangpeng Jin
E-mail(s) jinkangpeng@njmu.edu.cn
Phone 18502511055
Organization name The Affiliated Drum Tower Hospital of Nanjing 9 University Medical School
Department Department of Hepatobiliary Surgery
Lab the Lab of Department of Hepatobiliary Surgery
Street address 321 Zhongshan Road
City Nanjing
State/province Jiangsu Province
ZIP/Postal code 210008
Country China
 
Platform ID GPL20795
Series (1)
GSE147304 RNA-Seq analylsis of human NASH and Normal liver tissues
Relations
BioSample SAMN14418366
SRA SRX7963120

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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