|
| Status |
Public on Jan 08, 2018 |
| Title |
NH_FLI_brain_101+102 |
| Sample type |
SRA |
| |
|
| Source name |
total RNA extracted from brain
|
| Organism |
Danio rerio |
| Characteristics |
strain: AB JxTu
age: 6 months
age category: young
tissue: brain
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from was extracted as described (Baumgart et al., 2012; PMID:22487494)
Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
NH_FLI_brain_101+102
|
| Data processing |
Illumina Casava v1.8.0 software used for extraction of FASTQ files
Reads were mapped using Tophat (v2.0.6) to the genome taken the annotation into account: tophat2 -p 24 -o OUTPUTDIR -g 1 --no-coverage-search --transcriptome-index=transcriptome_data/Danio_rerio.Zv9.73 Danio_rerio.Zv9.73
Counting of reads per gene was done using htseq-count: htseq-count --quiet --stranded=no --idattr=gene_id --mode=union SAMFILE Danio_rerio.Zv9.73.gtf > OUTPUTFILE
Counts were normalized to RPKM values as described in Mortazavi et al. (2008). Gene were excluded from dataset if at least one sample has a RPKM of 0.
Genome_build: Ensemble Zv9.73
Supplementary_files_format_and_content: Excel file includes raw counts and RPKM values for each sample
|
| |
|
| Submission date |
Oct 21, 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 |
GPL14875 |
| Series (1) |
| GSE74244 |
Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues (brain, liver, skin) |
|
| Relations |
| BioSample |
SAMN04201863 |
| SRA |
SRX1362042 |
