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Sample GSM8131996 Query DataSets for GSM8131996
Status Public on Apr 22, 2024
Title mutant-1 - 9 months, Tumor-2
Sample type SRA
 
Source name liver
Organism Mus musculus
Characteristics tissue: liver
cell line: not applicable :primary material
cell type: mostly transformed hepatocyte
genotype: mutant
Sex: Male
strain: C57BL/6
treatment: Dox OFF at 3 weeks during 9 months
Extracted molecule total RNA
Extraction protocol RNA was extracted using Trizol -Sample RNA Integrity Numbers were in the range 7.5-8.2 (average 7.9) for the 2 months samples and in the range 7.2 to 9.1 (median 8.5) for the 9 months samples, when assayed on an Agilent 2100 Bioanalyzer.
PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" kit (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by PCR with Illumina PE primers (8 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description LB03017
Data processing Image analysis, per-cycle basecalling and quality score assignment was performed with Illumina Real Time Analysis software. Conversion of Illumina BCL files to bam format was performed with the Illumina2bam tool (Wellcome Trust Sanger Institute - NPG).
Reads were converted from .bam to .fastq format using bedtools v2.27.1 (1) and compressed using gzip
Reads in fastq format were aligned to the mouse reference genome version GRCm38 with Gencode mV23 annotations using STAR aligner version 2.6.1a in 2-pass mode. Raw reads per gene were counted by STAR. Differential gene expression was calculated using DESeq2 version 1.22.2. TPM were generated by RSEM
Assembly: mm10 murine reference genome downloaded from Ensembl (2018-09-28, link last accessed 2023-02-10):
Supplementary files format and content: includes raw counts for each sample
 
Submission date Mar 06, 2024
Last update date Apr 22, 2024
Contact name Latifa Bakiri
Organization name Medical University of Vienna
Department Laboratory Medicine
Street address Lazarettgasse 14, BT25/2, 6th floor Lab 2
City Vienna
ZIP/Postal code 1090
Country Austria
 
Platform ID GPL13112
Series (1)
GSE261005 Liver cancer development driven by the AP-1/c-Jun~Fra2 dimer through c-Myc
Relations
BioSample SAMN40283137
SRA SRX23855582

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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