run_metadata: 38301

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
38301	SRR1648854	SRX757981	SRS743128	SRP049716	PRJNA266970	RNA sequencing of the developing zebrafish head	GSE63191	Transcriptome Analysis	We sequenced strand specific mRNA from the heads of 3 groups of wild type zebrafish Danio rerio 5 dpf Overall design: Examination of the relative expression of genes in the developing zebrafish brain		pubmed:25561519		Wildtype Replicate 1	GSM1543672		source name:whole head\|develolpmental stage:5 dpf embryo\|tissue:whole head	Wildtype Replicate 1	Basecalls performed using CASAVA version 1.5 Alignment was performed with Gsnap v2012 07 20 using default parameters and the zv9 genome/transcriptome from Ensembl Accurate dose response was verified with custom analysis tools and the included ERCC RNA spike ins Aligned reads were quantified with Cufflinks v2.1.0 using default parameters and the zv9 transcriptome from Ensembl Genome build: zv9 Supplementary files format and content: Cufflinks v2.1.0 genes.fpkm tracking	whole head		TRIzol Invitrogen extraction per manufactor's instructions Strand specific polyA selected RNA Seq libraries were constructed using a custom dUTP method similar to the standard Illumina protocols with the addition of 1ul of a 1:10 dilution of ERCC RNA spike ins prior to polyA selection.	Zebrafish embryos from natural matings were maintained at 28C in 6 or 10cm dishes. 5 dpf the heads of 80 100 embryos per replicate were obtained for RNA extraction.	develolpmental stage:5 dpf embryo\|tissue:whole head	GSM1543672	GSM1543672: Wildtype Replicate 1; Danio rerio; RNA Seq	GSM1543672		1	TRIzol Invitrogen extraction per manufactor's instructions Strand specific polyA selected RNA Seq libraries were constructed using a custom dUTP method similar to the standard Illumina protocols with the addition of 1ul of a 1:10 dilution of ERCC RNA spike ins prior to polyA selection.	GEO Accession:GSM1543672	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP049716			uninjected_rep1_zebrafish_121230_AC1BMGACXX_Illumina2_1.fastq.gz uninjected_rep1_zebrafish_121230_AC1BMGACXX_Illumina2_2.fastq.gz	fastq fastq	5994627800.0	59946278.0	GSM1543672 r1	0:50 1:50	A:1649718236;C:1309696705;G:1340401079;T:1694576298;N:235482	50	50			1649718236	1309696705	1340401079	1694576298	235482	SRX757981	SRS743128	SRA200859	GEO	Center for Human Genetic Research, Massachusetts General Hospital	2	0.9191	0.92223	0.18431	0.18241	0.68889	0.68793	0.48942	0.48534	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown		United States	2014-11-12	Larval	Larval	Head	Nervous System