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Sample GSM1915478 Query DataSets for GSM1915478
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data is available on Series record

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