|
Status |
Public on May 28, 2020 |
Title |
CCL4-07-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: CCl4 - 2ul/g body weight CCl4:olive oil [1:1 (v/v)] mix time point: 3 days after IP
|
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 |
D708_D503
|
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 |
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 |
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 |
|
Relations |
BioSample |
SAMN13292056 |
SRA |
SRX7156527 |