|
| Status |
Public on Jul 17, 2020 |
| Title |
DEN HFD -WT tumour 4 |
| Sample type |
SRA |
| |
|
| Source name |
Whole Liver Tissue
|
| Organism |
Mus musculus |
| Characteristics |
tissue: liver tumor
strain: C57BL/6J
genotype: Wild Type
Sex: male
treatment: DEN IP day 15 + 30 week HFD + SW -WT
|
| Treatment protocol |
Liver tissues were snap-frozen and stored at -80*C until RNA extraction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen tissue samples were lysed using Trizol (Sigma-Aldrich) and mRNA was extracted with the qiagen RBNA easy column. Concentrations and quality were assessed using the Agilent Pico 6000 kit on the Bioanalyzer 2100.
Sequencing library were constructed using Illumina mRNA library prep kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Time Point: 30 weeks after IP
T4
|
| Data processing |
Reads are mapped using STAR 2.5.0 to the mouse GRCm38 genome
Gene-level counts where generated using featureCounts (Subread 1.6.2) with Ensembl Transcript GTF V74
Genome_build: GRCm38
Supplementary_files_format_and_content: text file with counts
|
| |
|
| Submission date |
Nov 12, 2019 |
| Last update date |
Jul 17, 2020 |
| Contact name |
Peter Leary |
| E-mail(s) |
peter.leary@fgcz.ethz.ch
|
| Organization name |
ETH Zürich
|
| Department |
Functional Genomics Center Zürich
|
| Street address |
Winterthurerstrasse 190
|
| City |
Zürich |
| ZIP/Postal code |
8057 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE140243 |
Studying diet induced liver carcinogenesis |
|
| Relations |
| BioSample |
SAMN13264049 |
| SRA |
SRX7130068 |
