metadata: run_metadata: 2 rows where experiment.library_selection = "size fractionation", experiment.library_strategy = "RNA-Seq" and tissue

2 rows where experiment.library_selection = "size fractionation", experiment.library_strategy = "RNA-Seq" and tissue_curation = "Eye"

descending

Link	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
49091	49091	SRR7666344	SRX4527573	SRS3645455	SRP157045	PRJNA485433	Diurnal transcriptome of adult zebrafish eye	PRJNA485433	Other	Circadian rhythms orchestrate organism physiology to rhythmic changes in the environment with the daily day and night cycle being the most prominent cyclic change occurring. In this regard retina being a light responsive organ shows its vital physiological processes to be regulated by the clock. Here we report the diurnal transcriptome of zebrafish retina at Zt4day and Zt16night. We found 39% and 31% of the known genes to be expressed in retina at Zt4 and Zt16 respectively Reference genome Zv9. Also by applying stringent cutoff of 5FPKM we identified 123 transcripts to be expressed differentially between the two time points which contains few novel transcripts. In future this study will contribute to the understanding of organ and species specific regulation of circadian rhythms and will also provide novel genes involved in the circadian regulation of retina.					ZT4		strain:Assam wild type\|age:>3 month\|dev stage:adult\|sex:pooled male and female\|tissue:eye\|BioSampleModel:Model organism or animal									diurnal trancriptome of retina	ZT4 101nt	ZT4 101nt	total transcriptome with Truseq stranded library			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP157045			ZF_Eye_CT4_gt50_R1_P.fastq ZF_Eye_CT4_gt50_R2_P.fastq	fastq fastq	4550334348.0	22527137.0	ZF Eye CT4 gt50 R1 P.fastq	0:101.00 1:101.00	A:1196463938;C:1068045211;G:1064853438;T:1220233324;N:738437	101	101			1196463938	1068045211	1064853438	1220233324	738437	SRX4527573	SRS3645455	SRA756783	CSIR Insitute of Genomics and Integrative Biology\|Functional Genomics	CSIR Insitute of Genomics and Integrative Biology	2	0.92663	0.92909	0.33125	0.32333	0.70197	0.7013	0.55991	0.52684	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown		India	2018-12-27	Adult	Adult	Eye	Sensory System
49092	49092	SRR7666345	SRX4527572	SRS3645456	SRP157045	PRJNA485433	Diurnal transcriptome of adult zebrafish eye	PRJNA485433	Other	Circadian rhythms orchestrate organism physiology to rhythmic changes in the environment with the daily day and night cycle being the most prominent cyclic change occurring. In this regard retina being a light responsive organ shows its vital physiological processes to be regulated by the clock. Here we report the diurnal transcriptome of zebrafish retina at Zt4day and Zt16night. We found 39% and 31% of the known genes to be expressed in retina at Zt4 and Zt16 respectively Reference genome Zv9. Also by applying stringent cutoff of 5FPKM we identified 123 transcripts to be expressed differentially between the two time points which contains few novel transcripts. In future this study will contribute to the understanding of organ and species specific regulation of circadian rhythms and will also provide novel genes involved in the circadian regulation of retina.					ZT16		strain:Assam wild type\|age:>3months\|dev stage:adult\|sex:pooled male and female\|tissue:eye\|BioSampleModel:Model organism or animal									diurnal transcriptome of retina	ZT16 101nt	ZT16 101nt	total transcriptome with Truseq stranded library			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP157045			ZF_Eye_CT016_gt50_R1_P.fastq ZF_Eye_CT016_gt50_R2_P.fastq	fastq fastq	14656436974.0	72560331.0	ZF Eye CT016 gt50 R1 P.fastq	0:100.99 1:100.99	A:3573626926;C:3724443056;G:3714836422;T:3641178568;N:2352002	100	100			3573626926	3724443056	3714836422	3641178568	2352002	SRX4527572	SRS3645456	SRA756783	CSIR Insitute of Genomics and Integrative Biology\|Functional Genomics	CSIR Insitute of Genomics and Integrative Biology	2	0.917	0.91899	0.27178	0.261	0.72135	0.72082	0.63885	0.63571	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown		India	2018-08-10	Adult	Adult	Eye	Sensory System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;