|
| Status |
Public on Sep 15, 2019 |
| Title |
NASH 5 |
| Sample type |
SRA |
| |
|
| Source name |
wistar rat hepatic tissue
|
| Organism |
Rattus norvegicus |
| Characteristics |
group: NASH
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAqueous-Micro kit (Ambion)
TruSeq Stranded mRNA Sample Preparation Guide (Part # 15031047 Rev. E)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Raw reads data were converted into FASTQ format and quality control was performed using the FASTQC software (Babraham Bioinformatics).
After trimming for adapters using trim_galore (Babraham Bioinformatics), mapping of the reads were obtained using the STAR program against rattus norvegicus genome (Rnor.6) and the quantification of genes and transcripts were done with the RSEM program using ensembl annotation (Rattus_norvegicus.Rnor_6.0.91.chr.gtf)
We use TMM method and limma-voom transformation from rounded expected counts to normalize the non biological variability
Genome_build: Rnor6
Supplementary_files_format_and_content: RSEM expected counts
|
| |
|
| Submission date |
Apr 09, 2019 |
| Last update date |
Sep 15, 2019 |
| Contact name |
Juanjo Lozano |
| E-mail(s) |
juanjo.lozano@ciberehd.org
|
| Organization name |
CIBEREHD
|
| Department |
Plataforma de Bioinformatica
|
| Street address |
C/ Rosselló 153
|
| City |
Barcelona |
| ZIP/Postal code |
08036 |
| Country |
Spain |
| |
|
| Platform ID |
GPL22396 |
| Series (1) |
| GSE129525 |
Introducing a new pre-clinical rat model of advanced NASH by combining carbon tetrachloride with high fat & cholesterol diet |
|
| Relations |
| BioSample |
SAMN11372033 |
| SRA |
SRX5657233 |
