{"database": "metadata", "table": "run_metadata", "rows": [[36747, "SRR850602", "SRX277689", "SRS420755", "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", null, "pubmed:26620638", null, "Nr75 danrer skin 24months rep5", "GSM1141112", null, "source name:total RNA extracted from skin|strain:TuAB|age:24 month|tissue:skin", "Nr75 danrer skin 24months rep5", "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.\u00a0rerio: 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", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:24 month|tissue:skin", "GSM1141112", "GSM1141112: Nr75 danrer skin 24months rep5; Danio rerio; RNA Seq", "GSM1141112 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141112", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "Nr75_2y.fastq.gz", "fastq", 1000606196.0, 13165871.0, "GSM1141112 r1", "0:76", "A:270569436;C:233353660;G:238144829;T:258045669;N:492602", 76, null, null, null, 270569436, 233353660, 238144829, 258045669, 492602, "SRX277689", "SRS420755", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.8949, null, 0.07966, null, 0.7293, null, 0.47729, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["36747"], "units": {}, "query_ms": 9.41847499780124}