{"database": "metadata", "table": "run_metadata", "rows": [[36544, "SRR580557", "SRX192119", "SRS367417", "SRP016009", "PRJNA176710", "Zebrafish Danio rerio catecholaminergic neuron RNA seq based transcript profiles", "GSE41373", "Transcriptome Analysis", "This project aimed at identifying developmental stage specific transcript profiles for catecholaminergic neurons in embryos and early larvae of zebrafish Danio rerio. Catecholaminergic neurons were labeled using transgenic zebrafish strains to drive expression of GFP. At stages 24  36  72 hpf and 96 hpf  embryos were dissociated and GFP expressing cells sorted by FACS. Isolated RNAs were processed using either polyA selection and libray generation or NanoCAGE. This is the first effort to determine stage specific mRNA profiles of catecholaminergic neurons in zebrafish. Overall design: Catecholaminergic neurons were labeled by four different strategies: 1 24 hrs old embryos: we used the ETvmat2:GFP transgenic line Wen et al. 2007. Visualization of monoaminergic neurons and neurotoxicity of MPTP in live transgenic zebrafish. Dev Biol. 2008 Vol 314 p84 92 which at this early stage labels catecholaminergic neurons in posterior tuberculum and locus coeruleus; 2 24 hrs old embryos: we used Tgotpb.A:egfpzc48 transgenic line Fujimoto et al. Identification of a dopaminergic enhancer indicates complexity in vertebrate dopamine neuron phenotype specification. Dev Biol 2011  Vol 352  p393\u2013404 which at this stage label ventral diencephalic dopaminergic neurons and some preoptic neurons. 3 For 72 and 96 hrs old zebrafish larvae we used a th:GFP BAC transgenic lines that labels catecholaminergic neurons Tay et al.  Comprehensive catecholaminergic projectome analysis reveals single neuron integration of zebrafish ascending and descending dopaminergic systems. Nat Comms 2011 Vol 2  171; also: T. Leng and W. Driever  unpublished. 4 for the 36 and 48 hrs old zebrafish larvae we used a th:Gal4VP16 driver and UAS:EGFP responder transgenic line system to label catecholaminergic cells Fernandes et al.  Deep brain photoreceptors control light seeking behavior in zebrafish larvae. Curr Biol. 2012 Vol 22  DOI 10.1016/j.cub.2012.08.016. We used the different transgenic lines  because lines 3 and 4 do not efficiently label catecholaminergic neurons at early stages  while lines 1 and 2 also have GFP expression in several other non catecholaminergic populations at later stages of development. Embryos were dissociated and catecholaminergic neurons were FACS sorted from GFP tagged zebrafish Manoli and Driever  2012  Cold Spring Harbor Protoc. DOI 10.1101/pdb.prot069633. RNA was either processed for NanoCAGE  or mRNA was isolated and amplified. cDNA was sequenced by Illumina technique. This data submission is a series of data files consisting of three independent experiments with diffrent RNA Seq depth: Samples 1 4 NanoCage: Samples 5 8 RNA Seq high read numbers  and SAmples 9 12 RNA Seq low read numbers.", null, null, null, "vmat2:GFP 24h GFPplus sorted catecholaminergic neurons", "GSM1015799", null, "tissue:FACS sorted cells from whole embryo|developmental stage:24 hpf line:ETvmat2:GFP|facs sorting criteria:GFP positive cells", "vmat2:GFP 24h GFPplus sorted catecholaminergic neurons", "Library strategy: RNA Seq NanoCAGE Illumina Casava1.7 software used for basecalling. Samples 1 through 4: sequence data are in read files from two lanes using bar codes vmatGFPminus   ATCGTG; vmatGFPplus   AGTATA; otpGFPminus   AGTAGC; otpGFPplus   AGTACG; Samples 5 though 12 sequence data are in separate read files each Fastq sequencing data  were imported with NGS Illumina import. For this import the quality score was set to \u201cIllumina pipline 1.5 to 1.7\u201d Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using CLC Genomics Workbench v4.8 Sequences were mapped to genome with CLC Genomics Workbench v4.8 built48014 using menue \"high thriughput sequencing\" and mapping settings minimal fraction length 0.9  minimum similarity fraction 0.8  maximum number of hitts for read 10 Expression values were calculated as RPKM using CLC Genomics Workbench v4.8 Statistical analysis were performed using the Test on proportions => Kal et al.\u2018s test Z test using CLC Genomics Workbench v4.8 Genome build: Zebrafish reference genome ZV9.66 Supplementary files format and content: Excel spreadsheets with output generated from CLC Genomics Workbench v4.8; each spreadsheet  provides data analysis for comparison of one GFP plus experimental and one GFP minus control sample", "FACS sorted cells from whole embryo", "Cells were dissociated and FACS sorted as described in: Manoli and Driever  2012  Cold Spring Harbor Protoc. DOI 10.1101/pdb.prot069633", "RNA was extracted from FACS sorted cells as descried in: Manoli and Driever  2012  Cold Spring Harbor Protoc. DOI 10.1101/pdb.prot069633 Samples 1 through 4 were processed for NanoCAGE Salmullah et al.  CSH Protocols 2011  DOI 10.1101/pdb.prot5559; Samples 5 through 12 were processed for mRNA Seq Manoli and Driever  2012  Cold Spring Harbor Protoc. DOI 10.1101/pdb.prot069633 including an amplification step using Ambion RNA amp kit as described in CSH Protocol.", "Zebrafish were gown under standard condition 28 Celsius", "developmental stage:24 hpf line:ETvmat2:GFP|facs sorting criteria:GFP positive cells", "GSM1015799", "GSM1015799: vmat2:GFP 24h GFPplus sorted catecholaminergic neurons; Danio rerio; OTHER", "GSM1015799 1", null, "1", null, "GEO Accession:GSM1015799", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP016009", null, null, null, null, 89312790.0, 2977093.0, "GSM1015799 r1", "0:30", "A:19953403;C:17739114;G:34684963;T:16934433;N:877", 30, null, null, null, 19953403, 17739114, 34684963, 16934433, 877, "SRX192119", "SRS367417", "SRA059310", "GEO", "Developmental Biology, Biology, University of Freiburg", 1, 0.66653, null, 0.18449, null, 0.87623, null, 0.81483, null, 30, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2012-10-05", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"]], "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": ["36544"], "units": {}, "query_ms": 10.568375000730157}