|
Status |
Public on May 28, 2020 |
Title |
HCC-FREE2 |
Sample type |
SRA |
|
|
Source name |
Liver Tissue
|
Organism |
Homo sapiens |
Characteristics |
background disease: Alcoholic liver disease (cirrhotic) tissue: Liver paired tissues: PAIRED TO HCC2
|
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 |
A004
|
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 |
SAMN13292098 |
SRA |
SRX7156541 |