run_metadata: 36545

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
36545	SRR580556	SRX192118	SRS367416	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 p393–404 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.				vmat2:GFP 24h GFPminus control	GSM1015798		tissue:FACS sorted cells from whole embryo\|developmental stage:24 hpf line:ETvmat2:GFP\|facs sorting criteria:GFP negative cells	vmat2:GFP 24h GFPminus control	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 “Illumina pipline 1.5 to 1.7” 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.‘s 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 negative cells	GSM1015798	GSM1015798: vmat2:GFP 24h GFPminus control; Danio rerio; OTHER	GSM1015798 1		1		GEO Accession:GSM1015798	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx		SRP016009					109437330.0	3647911.0	GSM1015798 r1	0:30	A:22965140;C:22637764;G:44598580;T:19234832;N:1014	30				22965140	22637764	44598580	19234832	1014	SRX192118	SRS367416	SRA059310	GEO	Developmental Biology, Biology, University of Freiburg	1	0.79599		0.21065		0.90658		0.9542		30		B		usable mapping rate	illumina	early_illumina	unknown	poly_a	unknown	bulk	unknown	unknown		Germany	2012-10-05	Pharyngula	Embryo	Whole Organism	All anatomical structures