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Sample GSM1267254 Query DataSets for GSM1267254
Status Public on Jul 29, 2014
Title JM15_1
Sample type SRA
 
Source name total RNA extracted from brain
Organism Nothobranchius furzeri
Characteristics age: 39 weeks
tissue: brain
strain: MZM 04/10
Extracted molecule total RNA
Extraction protocol The whole fish brains were dissected and transferred into 2 ml tubes with 1 ml cooled QIAzol (Qiagen, Hilden, Germany) and one 5 mm stainless steel bead (Qiagen) was added. Homogenization was performed using a TissueLyzer II (Qiagen) at 20 Hz for 2-3x 1 min. After incubation for 5 min at room temperature 200 µl chloroform was added. The tube was shaken for (at least) 15 s and incubated for 3 min at room temperature. Phase separation was achieved by centrifugation at 12,000x g for 20 min at 4°C. The aqueous phase was transferred into a fresh cup and 10 µg of Glycogen (Invitrogen, Darmstadt, Germany), 0.16x volume NaAc (2 M; pH 4.0) and 1.1x volume isopropanol were added, mixed thoroughly and incubated for 10 min at room temperature. The RNA was precipitated by a centrifugation step with 12,000 x g at 4°C for 20 min. The supernatant was removed and the pellet was washed with 80% Ethanol twice and air dried for 10 min. The RNA was resuspended in 20 µl DEPC-treated water by pipetting up and down, followed by incubation at 65°C for 5 min. The RNA was quantified with a NanoDrop 1000 (PeqLab, Erlangen, Germany) and stored at -80°C until use.
Sequencing procedure was done using Illumina methodology [Bentley et al, 2008]. Around 2.5 µg of total RNA was used for library preparation (Illumina, TruSeq™ RNA Sample Prep Kit v2) using the manufacturer’s description.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing GSE52462_Nfurzeri_MZM_brain_Normal_Ageing_counts_RPKM.xls - Illumina Casava software used for extraction of FASTQ files
GSE52462_Nfurzeri_MZM_brain_Normal_Ageing_counts_RPKM.xls - FASTQ files were mapped using Bowtie versus a transcriptome catalogue of N. furzeri containing 19,812 transcripts
GSE52462_Nfurzeri_MZM_brain_Normal_Ageing_counts_RPKM.xls - Uniquely mapped reads for each transcript were counted using R Statistical Language and Bioconductor.
GSE52462_Nfurzeri_MZM_brain_Normal_Ageing_counts_RPKM.xls - The read counts were normalized with respect to the size of the individual genes and to the total amount of mappable reads obtained in the sequencing process, resulting in RPKM-values (Mortazavi et al. 2008) for each gene.
GSE52462_Nfurzeri_MZM_brain_Normal_Ageing_counts_RPKM.xls - The transcripts were annotated additionally using Ensembl gene identifiers from D. rerio, while 13,561 shared a best bi-directional BLAST hit between both species.
GSE52462_Nfurzeri_MZM_brain_Normal_Ageing_counts_RPKM.xls - Genome_build: Transcriptome sequence published by Petzold et al. 2013 [PMID: 23496936]
GSE52462_Nfurzeri_MZM_brain_Normal_Ageing_counts_RPKM.xls - Supplementary_files_format_and_content: Excel file including raw counts and RPKM values for each sample
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GSE52462_counts_RPKMs_2015.xls - Illumina Casava software used for extraction of FASTQ files
GSE52462_counts_RPKMs_2015.xls - FASTQ files were mapped using Tophat (v2.0.6) to the N.furzeri genome.
GSE52462_counts_RPKMs_2015.xls - 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)
GSE52462_counts_RPKMs_2015.xls - RPKM values were computed using exon lengths provided by featureCounts as described in Mortazavi et al. 2008.
GSE52462_counts_RPKMs_2015.xls - Genome_build: genome v20150522 and annotation v20140422 can be downloaded from the Nothobranchius furzeri Information Network Genome Browser (http://nfingb.fli-leibniz.de/)
GSE52462_counts_RPKMs_2015.xls - Supplementary_files_format_and_content: Excel file includes raw counts and RPKM values
 
Submission date Nov 18, 2013
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)
GSE52462 RNA-seq of the brain of Nothobranchius furzeri at different time points
Relations
BioSample SAMN02404744
SRA SRX378355

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

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