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Sample GSM4162235 Query DataSets for GSM4162235
Status Public on May 28, 2020
Title HCC4
Sample type SRA
 
Source name Liver Tissue
Organism Homo sapiens
Characteristics background disease: Hepatocellular carcinoma
tissue: Liver
paired tissues: PAIRED TO HCC-FREE4
Treatment protocol Liver tissues were snap-frozen and stored at -80*C until RNA extraction.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using miRNeasy kits (Qiagen) according to manufacturer instructions. Samples were stored in aliquot at – 80 °C prior to use. All reagents, plastic ware, and supplies used were sterile, nuclease free, and of molecular biology grade. RNA purity (A260/A280>1.80) and concentration were determined using nanodrop spectrophotometer (Thermo Fisher scientific, Delaware USA). RNA integrity was studied using the 2100 Bioanalyzer System (Agilent) and RNA 6000 Nano Kit. A RNA Integrity Number (RIN) of >7 was considered the lowest cut-off for RNA Sequencing.
Sequencing library were constructed using Illumina’s TruSeq Stranded total RNA Library Preparation Kit.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description A019
Data processing Reads are mapped using STAR V2.5.1 to the human GRCh38 genome.
Gene-level counts were generated using subread (feature counts) V 1.6.1 with Ensembl Transcript GTF V74.
Genome_build: GRCh38
Supplementary_files_format_and_content: *tab: Tab-delimited text files
 
Submission date Nov 15, 2019
Last update date Sep 23, 2020
Contact name Davide Chiarugi
E-mail(s) ims-bioinformatics@medschl.cam.ac.uk
Organization name WT-MRC Institute of Metabolic Science
Department Metabolic Research Laboratories
Street address Box 289, Addenbrooke’s Hospital
City Cambridge
ZIP/Postal code CB2 0QQ
Country United Kingdom
 
Platform ID GPL20301
Series (2)
GSE140462 Multifaceted rewiring of the hepatic lipidome during proliferation and carcinogenesis - PART 2 (Human HCC - "Fatty Liver" background)
GSE140463 Multifaceted rewiring of the hepatic lipidome during proliferation and carcinogenesis
Relations
BioSample SAMN13292101
SRA SRX7156550

Supplementary file Size Download File type/resource
GSM4162235_SLX-14779.A019.tab.gz 4.2 Mb (ftp)(http) TAB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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