run_metadata: 55530

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
55530	SRR10527609	SRX7212100	SRS5714969	SRP233088	PRJNA591638	dmh4/+ severe scoliosis brain RNA sequencing	PRJNA591638	Other	RNA sequencing preformed on brains dissected from dmh4/+ zebrafish with severe scoliosis to identify gene expression involved in idiopathic scoliosis.					wildtype		strain:not applicable\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:21 dpf\|dev stage:juvenile\|sex:not applicable\|tissue:whole brain\|phenotype:straight spine\|BioSampleModel:Model organism or animal									RNA seq of scoliotic zebrafish brains: wildtype sibling with straight spine	wt H	wt H	3 brains were pooled from 21 dpf fish and RNA extracted with an RNA extraction kit. RNA sample quality was assessed using an Agilent Bioanalyzer. Library prep and subsequent sequencing was performed by The Centre for Applied Genomics at The Hospital for Sick Children SickKids using the NEBNext stranded RNA.			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP233088		loader:fastq load.py	wt_CPGFP_3brains_H_R1.fastq.gz wt_CPGFP_3brains_H_R2.fastq.gz	fastq fastq	22816701936.0	90542468.0	wt CPGFP 3brains H R1.fastq.gz	0:126 1:126	A:6403495683;C:4996055352;G:4989237508;T:6421208778;N:6704615	126	126			6403495683	4996055352	4989237508	6421208778	6704615	SRX7212100	SRS5714969	SRA1002469	The Hospital for Sick Children\|Developmental and Stem Cell Biology	The Hospital for Sick Children	2	0.95628	0.95875	0.14601	0.14507	0.69035	0.69065	0.48565	0.48768	126	126	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown		Canada	2019-11-27	Multi-stage	Multi-stage	Brain	Nervous System