2021-04-15
ENA first public
2020-11-25
ENA last update
ERC000011
ENA-CHECKLIST
SAMEA7625696
External Id
Co-author
INSDC center alias
Co-author
INSDC center name
2021-04-15T00:32:16Z
INSDC first public
2020-11-25T18:28:59Z
INSDC last update
public
INSDC status
ERS5383983
SRA accession
E-MTAB-9815:Sample 26
Submitter Id
54
year
age
ArrayExpress
http://www.ebi.ac.uk/efo/EFO_0009737
broker name
human
http://purl.obolibrary.org/obo/NCBITaxon_9606
common name
Protocols: Our “BioNASH” Cohort consisted of 58 consecutive patients recruited by the NAFLD Service at Cambridge University Hospitals NHS Foundation Trust. This study was approved by the local Ethics Committee (Reference number: 06/Q0106/70). All patients gave their informed consent for the use of data (biochemistry and clinical history) and samples for research purposes; the principles of the Declaration of Helsinki were followed. All the patients had a clinical diagnosis of NAFLD (patients with alternate diagnoses and etiologies were excluded), histology scored by an expert pathologist, and snap-frozen tissue for research purposes. Human biopsies’ RNA was isolated using STAT-60 (AMS biotechnology, CS-502) according to the following procedure: 1) biopsies were homogenised in STAT-60 (1 ml) using a tissue homogeniser, mixed (vortexing) and centrifuged at 13,000 g for 5 minutes at RT; 2) the supernatant was mixed (vortexing) with 200 ml chloroform (Sigma, Cat 650471) and centrifuged (12,000g) for 15 minutes at 4°C; 3) the supernatant was then mixed with 500 ml isopropanol (Sigma, cat 33539) and centrifuged at 10,000g for 10 minutes at 4°C to pellet the RNA; 4) the pellet was washed with 75% ethanol (1 ml) and allowed to dry until evaporation; 5) RNA was re-suspended in RNAse free water (Thermo Fisher Scientific, Delaware USA). All reagents, plastic ware, and supplies used were nuclease-free, sterile, and of molecular biology grade. RNA purity (A260/A280>1.80) and concentration were determined using the Nanodrop spectrophotometer (Thermo Fisher Scientific, Delaware USA). RNA integrity was studied using the 2100 Bioanalyzer (Agilent) and RNA 6000 Nano Kits (Agilent, Santa Clara, California, USA). RNA Integrity Number (RIN) of 7 was considered the lowest cut-off for RNA sequencing. RNA from tissues (600 ng RNA) were used to generate barcoded sequencing libraries using Illumina TruSeq® Stranded mRNA Library Preparation Kit (Illumina) following manufacturer’s instructions. Library preparation was performed by the Genomics and Transcriptomic Core at the Institute of Metabolic Science
description
adult
http://www.ebi.ac.uk/efo/EFO_0001272
developmental stage
non-alcoholic steatohepatitis
http://www.ebi.ac.uk/efo/EFO_1001249
disease
NASH Fibrosis Stage 3-4
disease staging
D709_D504
individual
Homo sapiens
http://purl.obolibrary.org/obo/NCBITaxon_9606
organism
Homo sapiens
http://purl.obolibrary.org/obo/NCBITaxon_9606
organism
liver
http://purl.obolibrary.org/obo/UBERON_0002107
organism part
female
http://purl.obolibrary.org/obo/PATO_0000383
sex
Sample 26
title