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| Status |
Public on Apr 20, 2018 |
| Title |
OXR1A_M_2 |
| Sample type |
SRA |
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| Source name |
OXR1A-/- liver, male
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| Organism |
Mus musculus |
| Characteristics |
tissue: liver
age: 12 months
genotype: OXR1A-/-
Sex: male
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| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was isolated from mice liver using a RNeasy kit from Qiagen.
The mRNA was separated from total RNA by Oligo(dT) magnetic beads, and cDNA synthesized by reverse transcription with N6 primer. Adaptors were ligated to the sticky 3' end of the cDNA. Two specific primers were used in PCR to amplify the ligation products. Denature the PCR product by heating and the single strand DNA is cyclized by splint oligo and DNA ligase.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
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| Description |
OXR1A_M_2
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| Data processing |
Sequencing: The library products are ready for sequencing via SE50 instrument.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The clean reads were mapped to human reference sequences and/or reference gene set using TopHat2(Kim et al, 2013). FPKM(Fragments Per Kilo bases per Million reads) is used to estimate gene expression level. Readcount was adjusted by TMM, then differential expression analysis was performed by using the DEGseq R package.
The software GOseq (Young et al., 2010) was used for Gene Ontology (OG) enrichment analysis.
Annotating to the KEGG database by BLAST(-p blastx -e 1e-5 -m 8).
Genome_build: standard reference of mouse genome mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample .
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| Submission date |
Apr 20, 2018 |
| Last update date |
Apr 22, 2018 |
| Contact name |
Mingyi Yang |
| E-mail(s) |
[email protected]
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| Phone |
004746613633
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| Organization name |
Oslo University Hospital
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| Department |
Department of Microbiology, Rikshospitalet
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| Street address |
Sognsvannsveien 20
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| City |
Oslo |
| ZIP/Postal code |
0372 |
| Country |
Norway |
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| Platform ID |
GPL23479 |
| Series (1) |
| GSE97024 |
OXR1A deficient male mouse displays fatty liver associated with impaired transcription regulation of hormone response and lipid metabolism |
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| Relations |
| BioSample |
SAMN08964556 |
| SRA |
SRX3981796 |
| 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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