|
| Status |
Public on Dec 03, 2015 |
| Title |
brain MR28 27weeks rotenone |
| Sample type |
SRA |
| |
|
| Source name |
total RNA extracted from brain
|
| Organism |
Nothobranchius furzeri |
| Characteristics |
tissue: brain
age: 27 weeks
age at death: 27 weeks
treatment: 15pM rotenone
FISH id: MR28
|
| Treatment protocol |
Rotenone dissolved in DMSO or equal amounts of pure DMSO was added to final concentrations of 15 pM. Treatment started when the fish reached the age of 5 weeks (young group) or 23 weeks (old group). For cleaning purpose and renewal 30% water was changed twice per week and fresh Rotenone and DMSO was added to the tanks. After 4 weeks 5 animals of each treatment group were sacrificed and RNA was extracted from brain, liver and skin tissues.
|
| Growth protocol |
Animal maintenance was performed as described by Terzebasi et al., 2008 and 2009.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For library preparation an amount of around 2.5 μg of total RNA per sample was processed using Illumina’s TruSeqTM RNA Sample Prep Kit (Illumina; San Diego; CA, USA) following the manufacturer’s instruction.
Total RNA was isolated using QIAzol (Qiagen, Hilden, Germany) based on the phenol/chloroform extraction method. Afterwards the RNA was quantified photometrically with a NanoDrop 1000 (PeqLab, Erlangen, Germany) and stored at -80 °C until use.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
MR28_1
|
| Data processing |
FASTQ files were extracted using Illumina CASAVA v1.8.0 (Sample 1-50), CASAVA v1.8.2 (Sample 51-95) or bcl2fastq v1.8.4 (Sample 96-185) software.
FASTQ files were mapped using Tophat (v2.0.6) vs. the N. furzeri genome.
Uniquely mapped reads were counted for each gene_id using featureCounts v1.4.3-p1 (featureCounts -T 8 -a $GTF -s 0 -t exon -g gene_id -o featureCounts_gene.txt $SAMFILE) .
RPKM values were computed using exon lengths provided by featureCounts and the sum of all mapped reads per sample according to Mortazavi et al. (2008).
Genome build: Genome v20150522 and annotation v20140422 can be downloaded from the Nothobranchius furzeri Information Network Genome Browser (http://nfingb.fli-leibniz.de/). In addition, 18 mitochondrial genes were included.
Supplementary_files_format_and_content: Text files including raw counts and RPKM values of each sample.
|
| |
|
| Submission date |
Mar 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
JenAge Project |
| E-mail(s) |
[email protected]
|
| 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) |
| GSE66712 |
RNA-seq of the killifish N.furzeri during normal aging (cross-sectional and longitudinal study) and treatment with rotenone |
|
| Relations |
| BioSample |
SAMN03396520 |
| SRA |
SRX915096 |
