metadata: run_metadata: 2 rows where devstage_curation = "Cleavage" and experiment.library

2 rows where devstage_curation = "Cleavage" and experiment.library_strategy = "FL-cDNA"

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
8055	8055	ERR022484	ERX008924	ERS017427	ERP000400	PRJEB2333	Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	E-MTAB-434	Other					E MTAB 434:ZF 2cells	SAMEA898400	Wellcome Sanger Institute	Alias:E MTAB 434:ZF 2cells\|Broker name:ArrayExpress\|Description:Protocols: Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 250 to 300 bp.\|DevelopmentalStage:embryo\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2011 03 10T17:55:05Z\|INSDC last update:2018 03 08T15:25:14Z\|INSDC status:public\|SRA accession:ERS017427\|Sample Name:ERS017427\|Sex:mixed\|StrainOrLine:Tuebingen\|Title:ZF 2cells									Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	E MTAB 434:sequencing of Zebrafish embryo 2cells	RNA from Zebrafish embryo 2cells	Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 250 to 300 bp.	Experimental Factor: DEVELPOMENTAL STAGE:embryo\|Experimental Factor: ORGANISM PART:cell	FL-cDNA	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina Genome Analyzer II		ERP000400	Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	ENA FIRST PUBLIC:2011 03 10\|ENA LAST UPDATE:2018 11 16	4946_5.srf	srf	3947547008.0	25970704.0	E MTAB 434:4946 5.srf	0:76 1:76	A:1069302461;C:914233601;G:902631356;T:1055986090;N:5393500	76	76			1069302461	914233601	902631356	1055986090	5393500	ERX008924	ERS017427	ERA015179	SC\|Wellcome Trust Sanger Institute	SC\|Wellcome Trust Sanger Institute	2	0.93356	0.93346	0.03988	0.04022	0.79135	0.79198	0.48864	0.48464	76	76	B	B	biological fallback assumption	illumina	early_illumina	unknown	poly_a	unknown	bulk	unknown	unknown		United Kingdom	2011-03-10	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
75469	75469	SRR24682224	SRX20461649	SRS17774520	SRP438861	PRJNA973729	Danio rerio strain:AB Raw sequence reads	PRJNA973729	Other	Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.					2 cell		strain:AB\|dev stage:2 cell\|sex:not determined\|tissue:embryo\|BioSampleModel:Model organism or animal									full length transcriptome of Danio rerio: 2 cell	2 cell	2 cell	The RNA of each sample was reversely transcribed into cDNA using a SMARTer PCR cDNA Synthesis Kit. Prime STAR GXL DNA Polymerase Kit was used to PCR amplify the full length cDNA. The SMARTbell libraries were constructed with the SMARTbell template prep kit. Conduct damage repair and end repair. The stem loop sequencing adaptors were linked to both ends of the DNA fragment and used to remove the failed fragment using exonuclease.			FL-cDNA	TRANSCRIPTOMIC	cDNA	SINGLE	PACBIO_SMRT	Sequel		SRP438861		assembly:GRCz11	P02TYR22604097_1_r64053_20220510_083113_3_G01.ccs.bam	bam	2615775919.0	929356.0	P02TYR22604097 1 r64053 20220510 083113 3 G01.ccs.bam	0:2814.61	A:735214781;C:591950532;G:624727601;T:663883005;N:0	2814				735214781	591950532	624727601	663883005	0	SRX20461649	SRS17774520	SRA1641718	Institute of hydrobiology, chinese academy od sciences\|Aquatic Biodiversity and Resource Conservation Res	Institute of hydrobiology, chinese academy od sciences	1	0.58166		0.00058		0.82933		0.48648		1706		T		long read	pacbio	pacbio_modern	full_length	cdna_unspecified	smarter	bulk	unknown	unknown		China	2023-05-21	Cleavage	Embryo	Embryo Imprecise	All anatomical structures

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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");;