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| Status |
Public on Apr 22, 2024 |
| Title |
control-6 - 2 months |
| Sample type |
SRA |
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| Source name |
liver
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| Organism |
Mus musculus |
| Characteristics |
tissue: liver
cell line: not applicable :primary material
cell type: mostly hepatocyte
genotype: control
Sex: Male
strain: C57BL/6
treatment: Dox OFF at 3 weeks during 2 months
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
LB03009
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| 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
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| Submission date |
Mar 06, 2024 |
| Last update date |
Apr 22, 2024 |
| Contact name |
Latifa Bakiri |
| Organization name |
Medical University of Vienna
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| Department |
Laboratory Medicine
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| Street address |
Lazarettgasse 14, BT25/2, 6th floor Lab 2
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| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE261005 |
Liver cancer development driven by the AP-1/c-Jun~Fra2 dimer through c-Myc |
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| Relations |
| BioSample |
SAMN40283145 |
| SRA |
SRX23855574 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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