metadata: run_metadata: 4 rows where devstage_curation = "Gastrula" and experiment.library

4 rows where devstage_curation = "Gastrula" and experiment.library_selection = "RANDOM PCR"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	sample.title	sample.alias	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	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.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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
39629	39629	SRR1947863	SRX981062	SRS889614	SRP056748	PRJNA279991	Zebrafish Mespaa regulates miR 430 expression during gastrulation and initiates cardiac laterality	PRJNA279991	Other	Transcriptional events during initial vertebrate heart development in vivo remain poorly understood. Mesp1 a bHLH transcription factor has been described as the earliest transcriptional regulator of cardiac progenitors in multiple species and represents an excellent candidate for the investigation of relevant targets during cardiovascular development. We report here that both depletion and mutation of Mespaa the zebrafish homolog of mammalian Mesp1 lead to randomization of cardiac looping together with significant cardiac morphogenesis defects. These disruptions are preceded by a defect in cardiac left right asymmetry. Surprisingly the defect in asymmetry was found to occur independently of defects in the transient organ of laterality the Kupffer’s vesicle KV. We show that Mespaa regulates miR 430 expression during gastrulation to control the levels of Nodal signaling and that this regulation is required for asymmetric laterality signaling in the prospective heart field. Ectopic expression of miR 430 is sufficient to induce cardiac laterality defects and consistent with Mespaa over expression in this system the reduction of miR 430 leads to cardia bifida. This study reveals a novel transcriptional regulation of miR 430 by Mespaa and a role for this pathway in cardiac laterality during gastrulation.	Danio rerio injected with mespaa morpholino 5.5hpf	Zebrafish injected with mespaa morpholino	strain:Ekkwill\|dev stage:5.5hpf\|sex:pooled male and female\|tissue:whole embryo\|BioSampleModel:Model organism or animal	Zebrafish Mespaa regulates miR 430 expression during gastrulation and initiates cardiac laterality	Zebrafish injected with mespaa morpholino replicate 2	Zebrafish injected with mespaa morpholino replicate 2	1	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP056748	loader:latf load	Mespa-230413_TGTGAA_L008_R2.fastq.gz Mespa-230413_TGTGAA_L008_R1.fastq.gz	fastq fastq	7275994449.0	42132158.0	RNAseq Danio rerio 5.5hpf mespaa morpholino replicate2	0:101 1:101	A:2058072859;C:1476303521;G:1525105443;T:2088915957;N:127596669	101	101	2058072859	1476303521	1525105443	2088915957	127596669	SRX981062	SRS889614	SRA249481	Gladstone Institute\|Bioinformatics	Gladstone Institutes	2	0.86631	0.83649	0.14484	0.22396	0.78861	0.90727	0.65055	0.64516	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2015-04-07	Gastrula	Embryo	Whole Organism	All anatomical structures
39630	39630	SRR1947880	SRX981061	SRS895863	SRP056748	PRJNA279991	Zebrafish Mespaa regulates miR 430 expression during gastrulation and initiates cardiac laterality	PRJNA279991	Other	Transcriptional events during initial vertebrate heart development in vivo remain poorly understood. Mesp1 a bHLH transcription factor has been described as the earliest transcriptional regulator of cardiac progenitors in multiple species and represents an excellent candidate for the investigation of relevant targets during cardiovascular development. We report here that both depletion and mutation of Mespaa the zebrafish homolog of mammalian Mesp1 lead to randomization of cardiac looping together with significant cardiac morphogenesis defects. These disruptions are preceded by a defect in cardiac left right asymmetry. Surprisingly the defect in asymmetry was found to occur independently of defects in the transient organ of laterality the Kupffer’s vesicle KV. We show that Mespaa regulates miR 430 expression during gastrulation to control the levels of Nodal signaling and that this regulation is required for asymmetric laterality signaling in the prospective heart field. Ectopic expression of miR 430 is sufficient to induce cardiac laterality defects and consistent with Mespaa over expression in this system the reduction of miR 430 leads to cardia bifida. This study reveals a novel transcriptional regulation of miR 430 by Mespaa and a role for this pathway in cardiac laterality during gastrulation.	Danio rerio injected with negative control morpholino 5.5hpf	Zebrafish injected with untargeted negative control morpholino	strain:Ekkwill\|dev stage:5.5 hpf\|sex:pooled male and female\|tissue:whole embryo\|BioSampleModel:Model organism or animal	Zebrafish Mespaa regulates miR 430 expression during gastrulation and initiates cardiac laterality	Zebrafish injected with untargeted negative control morpholino replicate 2	Zebrafish injected with untargeted negative control morpholino replicate 2	1	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP056748	loader:latf load	Std-230413_GTGTTA_L008_R1.fastq.gz Std-230413_GTGTTA_L008_R2.fastq.gz	fastq fastq	10015452496.0	49581448.0	RNAseq Danio rerio 5.5hpf negative control morpholino replicate2	0:101 1:101	A:2883382922;C:1998043392;G:2046542450;T:2937071125;N:150412607	101	101	2883382922	1998043392	2046542450	2937071125	150412607	SRX981061	SRS895863	SRA249481	Gladstone Institute\|Bioinformatics	Gladstone Institutes	2	0.8766	0.85002	0.17158	0.25762	0.77167	0.89057	0.64584	0.66342	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2016-03-31	Gastrula	Embryo	Whole Organism	All anatomical structures
39631	39631	SRR1947876	SRX981011	SRS895863	SRP056748	PRJNA279991	Zebrafish Mespaa regulates miR 430 expression during gastrulation and initiates cardiac laterality	PRJNA279991	Other	Transcriptional events during initial vertebrate heart development in vivo remain poorly understood. Mesp1 a bHLH transcription factor has been described as the earliest transcriptional regulator of cardiac progenitors in multiple species and represents an excellent candidate for the investigation of relevant targets during cardiovascular development. We report here that both depletion and mutation of Mespaa the zebrafish homolog of mammalian Mesp1 lead to randomization of cardiac looping together with significant cardiac morphogenesis defects. These disruptions are preceded by a defect in cardiac left right asymmetry. Surprisingly the defect in asymmetry was found to occur independently of defects in the transient organ of laterality the Kupffer’s vesicle KV. We show that Mespaa regulates miR 430 expression during gastrulation to control the levels of Nodal signaling and that this regulation is required for asymmetric laterality signaling in the prospective heart field. Ectopic expression of miR 430 is sufficient to induce cardiac laterality defects and consistent with Mespaa over expression in this system the reduction of miR 430 leads to cardia bifida. This study reveals a novel transcriptional regulation of miR 430 by Mespaa and a role for this pathway in cardiac laterality during gastrulation.	Danio rerio injected with negative control morpholino 5.5hpf	Zebrafish injected with untargeted negative control morpholino	strain:Ekkwill\|dev stage:5.5 hpf\|sex:pooled male and female\|tissue:whole embryo\|BioSampleModel:Model organism or animal	Zebrafish Mespaa regulates miR 430 expression during gastrulation and initiates cardiac laterality	Zebrafish injected with untargeted negative control morpholino	Zebrafish injected with untargeted negative control morpholino replicate 1	1	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP056748	loader:latf load	Std-190413_ACACGA_L008_R2.fastq.gz Std-190413_ACACGA_L008_R1.fastq.gz	fastq fastq	10412449358.0	51546779.0	RNAseq Danio rerio 5.5hpf negative control morpholino replicate1	0:101 1:101	A:2998996009;C:2064995108;G:2125498634;T:3066600855;N:156358752	101	101	2998996009	2064995108	2125498634	3066600855	156358752	SRX981011	SRS895863	SRA249481	Gladstone Institute\|Bioinformatics	Gladstone Institutes	2	0.87394	0.84802	0.15672	0.23447	0.77072	0.89049	0.63241	0.65533	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2016-03-31	Gastrula	Embryo	Whole Organism	All anatomical structures
39632	39632	SRR1947862	SRX974390	SRS889614	SRP056748	PRJNA279991	Zebrafish Mespaa regulates miR 430 expression during gastrulation and initiates cardiac laterality	PRJNA279991	Other	Transcriptional events during initial vertebrate heart development in vivo remain poorly understood. Mesp1 a bHLH transcription factor has been described as the earliest transcriptional regulator of cardiac progenitors in multiple species and represents an excellent candidate for the investigation of relevant targets during cardiovascular development. We report here that both depletion and mutation of Mespaa the zebrafish homolog of mammalian Mesp1 lead to randomization of cardiac looping together with significant cardiac morphogenesis defects. These disruptions are preceded by a defect in cardiac left right asymmetry. Surprisingly the defect in asymmetry was found to occur independently of defects in the transient organ of laterality the Kupffer’s vesicle KV. We show that Mespaa regulates miR 430 expression during gastrulation to control the levels of Nodal signaling and that this regulation is required for asymmetric laterality signaling in the prospective heart field. Ectopic expression of miR 430 is sufficient to induce cardiac laterality defects and consistent with Mespaa over expression in this system the reduction of miR 430 leads to cardia bifida. This study reveals a novel transcriptional regulation of miR 430 by Mespaa and a role for this pathway in cardiac laterality during gastrulation.	Danio rerio injected with mespaa morpholino 5.5hpf	Zebrafish injected with mespaa morpholino	strain:Ekkwill\|dev stage:5.5hpf\|sex:pooled male and female\|tissue:whole embryo\|BioSampleModel:Model organism or animal	Zebrafish Mespaa regulates miR 430 expression during gastrulation and initiates cardiac laterality	RNAseq analysis of mespaa knockdown embryos	Zebrafish injected with mespaa morpholino replicate 1	1	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP056748	loader:latf load	Mespa-190413_CACACA_L008_R2.fastq.gz Mespa-190413_CACACA_L008_R1.fastq.gz	fastq fastq	715965164.0	3668538.0	RNAseq Danio rerio 5.5hpf mespaa morpholino replicate1	0:101 1:101	A:203464307;C:144071219;G:148845038;T:209200873;N:10383727	101	101	203464307	144071219	148845038	209200873	10383727	SRX974390	SRS889614	SRA249481	Gladstone Institute\|Bioinformatics	Gladstone Institutes	2	0.86222	0.8307	0.14165	0.17545	0.7624	0.84415	0.65454	0.64758	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2015-04-07	Gastrula	Embryo	Whole Organism	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");;