|
| Status |
Public on Dec 03, 2015 |
| Title |
JM12.5 |
| Sample type |
SRA |
| |
|
| Source name |
total RNA extracted from skin
|
| Organism |
Nothobranchius furzeri |
| Characteristics |
strain/background: MZM-0410
tissue: skin
age: 39 weeks
FISH id: JM12.5
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction was done as described in Baumgart et al. 2012 (PMID: 22487494).
For library preparation, an amount of around 2.5 μg of total RNA per sample was processed using Illumina's TruSeq RNA Sample Prep Kit v2 following the manufacturer's instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Processed data file: counts_RPKMs.txt
|
| Data processing |
Sequence information was extracted in FastQ format using Illumina's Casava software v1.8.4.
Reads were mapped using Tophat (v2.0.6) to the N. furzeri genome (tophat2 -p 24 -o OUTPUT --no-coverage-search -g 1 GENOME INPUT.FASTQ).
Uniquely mapped reads were counted for each gene_id using featureCounts v1.4.3-p1 (featureCounts -T 8 -a ANNOTATION.GTF -s 0 -t exon -g gene_id -o COUNTS.CSV INPUT.SAM).
Counts were normalized to RPKM values as described in Mortazavi et al. (2008) using the length of the regarding transcript as reported by featureCounts.
Genome_build: genome v20150522 and annotation v20140422 can be downloaded from the Nothobranchius furzeri Information Network Genome Browser (http://nfingb.fli-leibniz.de/)
Supplementary_files_format_and_content: counts_RPKMs.txt: Tab-delimited text file includes raw counts and RPKM values of all genes for each sample.
|
| |
|
| Submission date |
Sep 01, 2015 |
| Last update date |
May 15, 2019 |
| 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 |
GPL19871 |
| Series (1) |
| GSE72584 |
RNA-seq of the killifish Nothobranchius furzeri strain MZM-0410 |
|
| Relations |
| BioSample |
SAMN04025442 |
| SRA |
SRX1176835 |
