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Sample GSM3106750 Query DataSets for GSM3106750
Status Public on Apr 20, 2018
Title OXR1A_F_3
Sample type SRA
 
Source name OXR1A-/- liver, female
Organism Mus musculus
Characteristics tissue: liver
age: 12 months
genotype: OXR1A-/-
Sex: female
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model BGISEQ-500
 
Description OXR1A_F_3
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 .
 
Submission date Apr 20, 2018
Last update date Apr 22, 2018
Contact name Mingyi Yang
E-mail(s) mingyiy@medisin.uio.no
Phone 004746613633
Organization name Oslo University Hospital
Department Department of Microbiology, Rikshospitalet
Street address Sognsvannsveien 20
City Oslo
ZIP/Postal code 0372
Country Norway
 
Platform ID GPL23479
Series (1)
GSE97024 OXR1A deficient male mouse displays fatty liver associated with impaired transcription regulation of hormone response and lipid metabolism
Relations
BioSample SAMN08964554
SRA SRX3981800

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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