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| Status |
Public on Nov 03, 2021 |
| Title |
KO_3d_full liver [022_2] |
| Sample type |
SRA |
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| Source name |
KO_3d_full liver
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| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6JBomTac (PMID 31320478)
genotype/variation: hepatocyte-specific NAMPT knockout (KO)
Sex: female
age: 3 days
tissue: whole liver
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNeasy mini kit (Qiagen) according to the manufacturer’s protocol. Total RNA sequencing libraries were prepared using the Illumina TruSeq Stranded total RNA Gold protocol (Illumina). The total RNA (500ng) was depleted of rRNA by RiboZero beads, fragmented, and cDNA was synthesized using SuperScript III Reverse Transcriptase (Thermo Fisher Scientific). cDNA was adenylated to prime for adapter ligation and after a clean-up using AMPure beads (Beckman coulter), DNA fragments were amplified using PCR followed by a final clean-up.
Libraries were quality-controlled using a Bioanalyzer instrument (Agilent Technologies) and subjected to 51-bp paired-end sequencing on a NovaSeq 6000 system (Illumina). A total of 1.1 billion reads were generated.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
022_2_S2
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| Data processing |
STAR v2.7.2b was used to align sequence reads onto the GRCm38 mouse genome assembly, with the GENCODE version M22 gene model
reads were summarized onto genes by featureCounts v1.6.4 with the same gene model as when mapping, counting only fragments where both ends of the fragment were aligned
The quasi-likelihood tests found in the R package edgeR v3.26.0Â was used for differential expression testing, using a two-way model of the form expression ~ Genotype * Age
Gene Ontology and Reactome enrichments were found by CAMERA
Genome_build: mm10
Supplementary_files_format_and_content: CSV file with counts of GENCODE vM22 genes
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| Submission date |
Jan 29, 2020 |
| Last update date |
Nov 03, 2021 |
| Contact name |
Lars Roed Ingerslev |
| E-mail(s) |
ingerslev@sund.ku.dk
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| Organization name |
Copenhagen University
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| Department |
NNF Center for Basic Metabolic Research
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| Lab |
Integrative Physiology
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| Street address |
Blegdamsvej 3B
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| City |
Copenhagen |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE144443 |
Hepatocyte-specific knockout of Nicotinamide phosphoribosyltransferase increases susceptibility for liver fibrosis in mice |
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| Relations |
| BioSample |
SAMN13940003 |
| SRA |
SRX7646095 |
| 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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