|
| Status |
Public on Oct 19, 2021 |
| Title |
MB_FLI_GR5.3_liver_RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Nothobranchius furzeri |
| Characteristics |
strain: GRZ
tissue: liver
age: 9 weeks
Sex: male
perturbation: Rotenone 15 pM
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction was done as described in Baumgart et al. 2012. (PMID:22487494)
Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequence information was extracted in FastQ format using CASAVA software 1.8.2 data processing step.
Reads were mapped using STAR (2.4.1d).
Reads per gene were counted using featureCounts (1.4.6-p4).
Counts were normalized to RPKM values as described in Mortazavi et al. (2008).
Genome_build: genome v20150522 and annotation v20150922 can be downloaded from the Nothobranchius furzeri Information Network Genome Browser (http://nfingb.fli-leibniz.de/)
Supplementary_files_format_and_content: The Excel files include raw counts (sample_counts.xls) and RPKM values (sample_rpkms.xls) of all genes for each sample.
|
| |
|
| Submission date |
Aug 25, 2017 |
| Last update date |
Oct 19, 2021 |
| Contact name |
JenAge Project |
| E-mail(s) |
geo-data@jenage.de
|
| Organization name |
Leibniz Institute for Age Research - Fritz Lipmann Institute
|
| Street address |
Beutenbergstr. 11
|
| City |
Jena |
| ZIP/Postal code |
D-07745 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17944 |
| Series (1) |
| GSE103138 |
Sequencing of Nothobranchius furzeri (strain: GRZ) liver from Rotenone treated animals |
|
| Relations |
| BioSample |
SAMN07561722 |
| SRA |
SRX3135407 |
