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Sample GSM4162220 Query DataSets for GSM4162220
Status Public on May 28, 2020
Title PH-T0-15-WT
Sample type SRA
Source name Whole Liver Tissue
Organism Mus musculus
Characteristics strain: C57BL/6J
genotype/variation: Wild Type
Sex: Male
tissue: Whole Liver
treatment: Resected Liver - Baseline control
time point: Day 0 (resected liver)
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 STAT-60 (AMS biotechnology, CS-111)/chloroform (200 uL; Sigma, Cat 650471)/isopropanol (500 uL; Sigma, cat 33539)/75% ethanol (1ml) according to previously published protocol (PMID: 26679101). 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 8 was considered the lowest cut-off for RNA Sequencing.
Sequencing library were constructed using Illumina mRNA library prep kit.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
Description D712_D505
Data processing Reads are aligned using STAR V2.5.1 to the mouse GRCm38 genome.
Gene-level counts were generated using subread (feature counts) V 1.6.2 with Ensembl Transcript GTF V74.
Genome_build: GRCm38
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
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 GPL21103
Series (2)
GSE140461 Multifaceted rewiring of the hepatic lipidome during proliferation and carcinogenesis - PART 1 (Liver Regeneration)
GSE140463 Multifaceted rewiring of the hepatic lipidome during proliferation and carcinogenesis
BioSample SAMN13292048
SRA SRX7156535

Supplementary file Size Download File type/resource 3.6 Mb (ftp)(http) TAB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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