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| Status |
Public on Sep 08, 2021 |
| Title |
HA_CO_Rep2 |
| Sample type |
SRA |
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| Source name |
liver
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| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype: TiparpH532A
treatment: corn oil
tissue: liver
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| Treatment protocol |
Mice were injected with single intraperitoneal dose of 10ug/kg 2,3,7,8,-tetrachlorodibenzo-p-dioxin and the livers were harvested on day 6
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| Extracted molecule |
total RNA |
| Extraction protocol |
Livers were removed, flash frozen in liquid nitrogen, and frozen livers were homogenized in TRIZOL reagent (Life Technologies). Total RNA was isolated using the Aurum RNA isolation kits (BioRad).
Strand-specific TruSeqTM RNA-seq library prep according to 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 |
11-sample32_S80_L008
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| Data processing |
filtering with FastQC
remove adaptors with Trimmomatic 0.39
The reads were aligned with TopHat 2.0.14. using default parameters.
Peak calling using FeatureCounts 2.0.0.
Assembly of transcripts and differential gene expression analysis preformed using DESeq2 1.30.0.
Genome_build: mm10
Supplementary_files_format_and_content: Count matrix table with raw gene counts for every gene and every sample, CSV
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| Submission date |
Feb 22, 2021 |
| Last update date |
Jun 11, 2024 |
| Contact name |
Jason Matthews |
| E-mail(s) |
jason.matthews@medisin.uio.no
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| Phone |
+4797122798
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| Organization name |
University of Oslo
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| Department |
Nutrition
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| Street address |
Sognsvannsveien 9
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| City |
Oslo |
| ZIP/Postal code |
0372 |
| Country |
Norway |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE167205 |
2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)-inducible poly-ADP-ribose polymerase (TIPARP/PARP7) catalytic mutant mice (TiparpH532A) have increased sensitivity to TCDD-induced hepatotoxicity and lethality |
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| Relations |
| BioSample |
SAMN18025217 |
| SRA |
SRX10149110 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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