run_metadata: 36751

This data as json

rowid	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.r4_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	tech_variant	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
36751	SRR850598	SRX277685	SRS420785	SRP022612	PRJNA203029	RNA seq of Danio rerio and Mus musculus skin for three different age groups	GSE46916	Other	Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month		pubmed:26620638		Nr70 danrer skin 24months rep1	GSM1141108		source name:total RNA extracted from skin\|strain:TuAB\|age:24 month\|tissue:skin	Nr70 danrer skin 24months rep1	Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample	total RNA extracted from skin		D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.		strain:TuAB\|age:24 month\|tissue:skin	GSM1141108	GSM1141108: Nr70 danrer skin 24months rep1; Danio rerio; RNA Seq	GSM1141108 1		1	D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.	GEO Accession:GSM1141108	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx		SRP022612			Nr70_2y.fastq.gz	fastq	2239190508.0	29463033.0	GSM1141108 r1	0:76	A:599665392;C:514113743;G:531871299;T:592730477;N:809597	76				599665392	514113743	531871299	592730477	809597	SRX277685	SRS420785	SRA076297	GEO	Leibniz Institute for Age Research - Fritz Lipmann Institute	1	0.89167		0.09031		0.73515		0.49129		76		B		usable mapping rate	illumina	early_illumina	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk		Germany	2013-05-14	Adult	Adult	Skin	Surface Structure