metadata: run_metadata: 2 rows where experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL", technology = "indrops" and tissue

2 rows where experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL", technology = "indrops" and tissue_curation = "Embryo Imprecise"

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
74458	74458	SRR23802705	SRX19634573	SRS17003744	SRP426627	PRJNA943249	Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Embryo Niche]	GSE227117	Transcriptome Analysis	We report single cell gene expression data for FACS isolated zebrafish kdrlflk1:mCherry and mrc1a.125:GFP double positive cells collected from whole embryos at 72 hpf. Overall design: kdrl:mCherry and mrc1a.125:GFP double positive transgenic embryos were homogenized filtered and then 25 000 GFP+ cells were FACS sorted into PBS. 3 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.	parent bioproject:PRJNA510836			kdrl:GFP+ mrc1a.125:GFP+ 72 hpf rep2	GSM7091919		source name:kdrl:GFP mrc1a.125:GFP transgenic zebrafish embryos wild type\|tissue:embryos\|genotype:wild type	kdrl:GFP+ mrc1a.125:GFP+ 72 hpf rep2	the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode	kdrl:GFP mrc1a.125:GFP transgenic zebrafish embryos wild type	No treatments	Approximately 3 000 kdrl:GFP+ and mrc1a.125:GFP+ cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops	Double transgenic kdrl:mCherry and mrc1a.125:GFP zebrafish embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf. Embryos were screened for transgene expression and then homogenized filtered and sorted using FACS into PBS collecting at least 25 000 cells.	tissue:embryos\|genotype:wild type	GSM7091919	GSM7091919: kdrl:GFP+ mrc1a.125:GFP+ 72 hpf rep2; Danio rerio; RNA Seq	GSM7091919 r1	GSM7091919	1	Approximately 3 000 kdrl:GFP+ and mrc1a.125:GFP+ cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP426627			GR4_Single_Cell_TCTTACGC.fastq.sorted.fastq.gz	fastq	13661225700.0	102550405.0	GSM7091919 r1	0:133.21	A:4263167363;C:2771561232;G:2605236063;T:4020689114;N:571928	133				4263167363	2771561232	2605236063	4020689114	571928	SRX19634573	SRS17003744			Oncology/Hematology, Boston Children's Hospital	1	0.64929		0.08349		0.80462		0.50638		149		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops		United States	2023-03-10	Larval	Larval	Embryo Imprecise	All anatomical structures
74459	74459	SRR23802706	SRX19634572	SRS17003743	SRP426627	PRJNA943249	Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Embryo Niche]	GSE227117	Transcriptome Analysis	We report single cell gene expression data for FACS isolated zebrafish kdrlflk1:mCherry and mrc1a.125:GFP double positive cells collected from whole embryos at 72 hpf. Overall design: kdrl:mCherry and mrc1a.125:GFP double positive transgenic embryos were homogenized filtered and then 25 000 GFP+ cells were FACS sorted into PBS. 3 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.	parent bioproject:PRJNA510836			kdrl:GFP+ mrc1a.125:GFP+ 72 hpf rep1	GSM7091918		source name:kdrl:GFP mrc1a.125:GFP transgenic zebrafish embryos wild type\|tissue:embryos\|genotype:wild type	kdrl:GFP+ mrc1a.125:GFP+ 72 hpf rep1	the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode	kdrl:GFP mrc1a.125:GFP transgenic zebrafish embryos wild type	No treatments	Approximately 3 000 kdrl:GFP+ and mrc1a.125:GFP+ cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops	Double transgenic kdrl:mCherry and mrc1a.125:GFP zebrafish embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf. Embryos were screened for transgene expression and then homogenized filtered and sorted using FACS into PBS collecting at least 25 000 cells.	tissue:embryos\|genotype:wild type	GSM7091918	GSM7091918: kdrl:GFP+ mrc1a.125:GFP+ 72 hpf rep1; Danio rerio; RNA Seq	GSM7091918 r1	GSM7091918	1	Approximately 3 000 kdrl:GFP+ and mrc1a.125:GFP+ cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP426627			GR_Single_Cell_AGGCTTAG.fastq.sorted.fastq.gz	fastq	15177402828.0	110023820.0	GSM7091918 r1	0:137.95	A:4661865038;C:2940634835;G:2919070311;T:4655218796;N:613848	137				4661865038	2940634835	2919070311	4655218796	613848	SRX19634572	SRS17003743			Oncology/Hematology, Boston Children's Hospital	1	0.73316		0.12888		0.79594		0.5247		127		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops		United States	2023-03-10	Larval	Larval	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");;