|
| Status |
Public on Sep 26, 2022 |
| Title |
High fat diet fed (ad libitum) liver_sample3 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
weeks on diet: 16
strain: C56B6/J
treatment: High fat diet fed (ad libitum)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Livers were removed and flash frozen in liquid nitrogen RNA was harvested using TRIzol and the Qiagen RNAeasy kit with Dnase treatment. RNA was quanified by Agilent 2100 bioanalsyer.
PolyA enrichment was performed using NEBNext Poly(A) mRNA magnetic Isolation and libraries prepared using NEBNext Ultra II RNA Library Prep kit for Illumina
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
HFD_Fed_Liver_3
|
| Data processing |
Illumina CASAVA 1.8.4 software used for basecalling.
Reads were mapped to mm10 whole genome using tophat2 (2.0.11) with argument “--library-type fr-firststrand"
Gene annotations were obtained from iGenome GRCm38. Gene-based read count were obtained using featureCounts function from Rsubread Bioconductor package
Genome_build: mm10
Supplementary_files_format_and_content: csv file includes Gene counts for each Sample
|
| |
|
| Submission date |
Jun 03, 2020 |
| Last update date |
Sep 26, 2022 |
| Contact name |
LMS Bioinformatics Core |
| E-mail(s) |
bioinformatics@lms.mrc.ac.uk
|
| Organization name |
MRC London Institute of Medical Sciences
|
| Department |
Bioinformatics Core
|
| Street address |
Hammersmith Hospital Campus, Du Cane Road
|
| City |
London |
| ZIP/Postal code |
W12 0NN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE151750 |
RNAseq of liver of CD and HFD fed mice in fed or fasted conditions |
| GSE151753 |
Characterization of the role of RBFOX2 in the liver |
|
| Relations |
| BioSample |
SAMN15096541 |
| SRA |
SRX8466189 |
