metadata: run_metadata: 2 rows where experiment.library_source = "TRANSCRIPTOMIC", experiment.library_strategy = "ATAC-seq" and tissue_curation

2 rows where experiment.library_source = "TRANSCRIPTOMIC", experiment.library_strategy = "ATAC-seq" and tissue_curation_coarse = "All anatomical structures"

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
66926	66926	SRR16832335	SRX13025545	SRS10963312	SRP344879	PRJNA778402	Atlas of lymphangiogenesis [scATAC Seq]	GSE188340	Other	During development lymphatic vasculature forms as a second and distinct network that derives from embryonic blood vessels. Transdifferentiation of venous endothelial cells into specified lymphatic endothelial cells LECs is the first step in this process. Transdifferentiation and specification of LEC fate requires Prox1 but how Prox1 regulates transdifferentiation and differentiation is not fully understood. We present a single cell transcriptomic atlas of lymphangiogenesis spanning four key developmental stages that reveals new markers and functional regulators of lymphatic development. We extend this to comprehensively profile single cell transcriptomic and chromatin changes controlled by Prox1 using zygotic prox1a mutants which form lymphatics that then dedifferentiate. Combining this with single cell analysis of Prox1 null double prox1a/prox1b maternal zygotic mutants we reveal in depth the role of Prox1 in control of LEC fate specification and differentiation. This resource reveals dual and progressive functions for Prox1 blocking blood vascular and hematopoietic fate while simultaneously up regulating a small number of early acting genes that include tspan18a/b and lgals3a/b which are essential for lymphangiogenesis. This embryonic developmental resource will serve as a baseline to better understand both developmental and pathological lymphangiogenesis in the future. [Citations in sample metadata correspond to reference numbers in the associated publication.] Overall design: Single cell ATAC profiles of endothelial cells from developing zebrafish at 4dpf in Zprox / mutant and matched WT siblings. All code associated with this data and publication are publicly available under an open source software license at: https://atlassian.petermac.org.au/bitbucket/users/tyrone.chen/repos/hogan lab/browse/2022 Grimm Mason et al PROX1 NatCellBiol/	parent bioproject:PRJNA778399	pubmed:36912146		20158: Zprox1ab 4dpf scATAC seq	GSM5677991		source name:embryo\|tissue:embryo\|transgenic:Tgfli1a:negfp;Tg 5.2lyve1b:dsRed\|facs:nEGFP and dsRed2 double positive\|Stage:4dpf\|genotype:Zprox1ab mutant\|platform:10X Chromium scATAC\|facility:Peter Mac Molecular Genomics\|cellranger atac pipeline:2.0.0\|r version:4.0.5\|internal id:20158\|gap study version:ATAC 1.1	20158: Zprox1ab 4dpf scATAC seq	Where necessary fastq files were made using Cell Ranger [14] version 3.1.0 or 3.0.2 mkfastq. Sequencing QC was assessed using FastQC 0.11.6 and MultiQC viewer for aggregated reports. Cell Ranger count and aggr were used to generate aggregated count files mapped to GRCz11 Ensembl 101 without xxx normalisation. Doublets were identified from the filtered aggregated count files using Scrublet [15] in Python version 3.6 and filtered from subsequent analyses. For the MZprox1 / mutant and Zprox1 / mutant datasets filtered aggregated count files were processed sc transform normalised filtered and clustered louvain using Seurat version 2.0 [16] and 3.0 [17] respectively for R statistical software version 4.0.2. QC was evaluated before and post normalisation using plot functions in Seurat and scater 1.20.1 [18] and all thresholds and settings are described in scripting. Cluster solutions were evaluated using ClusTree [19]. Datasets used in the atlas of lymphangiogenesis were processed filtered merged and log normalised using Seurat version 3.0 [17] with QC and settings as above. Merged data was clustered and normalised using CSS simspec [20] and clustering and cluster evaluation performed on this object only as described above. For all scRNA seq datasets cluster phenotype was determined using the expression of key markers Supplementary Table with the aid of CellXGene visualisation software [21]. All downstream analysis and plotting were performed using Seurat version 3.0 [17] using default settings. For velocity analysis loom files containing RNA velocity information were first generated from the 10X data associated with each sample using velocyto.R 0.6. Relevant sample subsets were then combined with loompy 3.0.6. From pre computed Seurat UMAPs in scRNA seq processing and analysis cell barcode and associated metadata were obtained and combined with the loom files. With the combined velocity scores and cell metadata velocity maps were plotted with velocyto.R 0.6 and overlaid on the UMAPs. Genome build: …	embryo	All injections were performed as previously described [10]. CRISPR genome editing for tspan18a/b was performed as previously described [11] and all genotyping confirmed using PCR [12]. slc7a7aBAC:slc7a7a Citrineuom10 and fabp11aBAC:fabp11a Citrineuom10 recombineering was performed as previously described.	Single cell suspensions were sorted by FACS and prepared for nuclei isolation as previously described by 10x Genomics Demonstrated Protocol for Single Cell ATAC Sequencing CG000169 Rev D. Cell suspensions were pelleted 300 x g for 5 minutes and rinsed with PBS + 0.04% BSA. Cells were resuspended in 95uL of freshly prepared lysis buffer 10mM Tris HCl pH 7.4 10 mM NaCl 3 mM MgCl2 0.1% Tween 20 0.1% NP40 Substitute 0.01% Digitonin and 1% BSA and incubated on ice for 1 minute. 100uL of chilled wash buffer 10 mM Tris HCl pH 7.4 10 mM NaCl 3 mM MgCl2 0.1% Tween 20 1% BSA was used to neutralise the reaction before the nuclei were pelleted 500 x g for 5 minutes and resuspended again in 7uL of 1x Nuclei Buffer 10X Genomics Cat# PN 2000153/2000207. Presence of healthy and intact nuclei was assessed by visual inspection on a brightfield microscope using Trypan Blue staining Thermo Fisher Cat# T10282 and Countess Cell Counting Chamber Slides Thermo Fisher Cat# C10228. Single nuclei suspensions were resuspended at approximately 5000 nuclei per L before undergoing tagmentation for 60min at 37C. post tagmentation nuclei were partitioned and barcoded using the 10X Genomics Chromium Controller 10X Genomics and the Single Cell ATAC Reagent Kit V1.1; 10X Genomics; PN 1000176 . Tagmented nuclei were loaded onto the Chromium Single Cell Chip H 10X Genomics; PN 1000162 GEM generation barcoding and library construction was performed according to the 10X Genomics Chromium User Guide. The resulting single cell ATAC libraries contained unique sample indices for each sample. The libraries were quantified on the Agilent BioAnalyzer 2100 using the High Sensitivity DNA Kit Agilent 5067 4626 and pooled in equimolar ratios. Sequencing was performed on an Illumina NextSeq 500 using a 150 cycle High Output Kit as follows: 50bp Read1 8bp i7 index 16bp i5 index 50bp Read2 achieving a read depth of 25 000 read pairs per nucleus.	Zebrafish work was conducted in compliance with animal ethics committees at University of Queensland and Peter MacCallum Cancer Centre. The uq52bh dut mutant was isolated in a previously described genetic screen [7]. The genetic mapping approach was performed as previously described [8 9].	tissue:embryo\|transgenic:Tgfli1a:negfp;Tg 5.2lyve1b:dsRed\|facs:nEGFP and dsRed2 double positive\|Stage:4dpf\|genotype:Zprox1ab mutant\|platform:10X Chromium scATAC\|version:ATAC 1.1\|facility:Peter Mac Molecular Genomics\|cellranger atac pipeline:2.0.0\|r version:4.0.5\|internal id:20158	GSM5677991	GSM5677991: 20158: Zprox1ab 4dpf scATAC seq; Danio rerio; ATAC seq	GSM5677991 r1	GSM5677991	1	Single cell suspensions were sorted by FACS and prepared for nuclei isolation as previously described by 10x Genomics Demonstrated Protocol for Single Cell ATAC Sequencing CG000169 Rev D. Cell suspensions were pelleted 300 x g for 5 minutes and rinsed with PBS + 0.04% BSA. Cells were resuspended in 95uL of freshly prepared lysis buffer 10mM Tris HCl pH 7.4 10 mM NaCl 3 mM MgCl2 0.1% Tween 20 0.1% NP40 Substitute 0.01% Digitonin and 1% BSA and incubated on ice for 1 minute. 100uL of chilled wash buffer 10 mM Tris HCl pH 7.4 10 mM NaCl 3 mM MgCl2 0.1% Tween 20 1% BSA was used to neutralise the reaction before the nuclei were pelleted 500 x g for 5 minutes and resuspended again in 7uL of 1x Nuclei Buffer 10X Genomics Cat# PN 2000153/2000207. Presence of healthy and intact nuclei was assessed by visual inspection on a brightfield microscope using Trypan Blue staining Thermo Fisher Cat# T10282 and Countess Cell Counting Chamber Slides Thermo Fisher Cat# C10228. Single nuclei suspensions were resuspended at approximately 5000 nuclei per L before undergoing tagmentation for 60min at 37C. post tagmentation nuclei were partitioned and barcoded using the 10X Genomics Chromium Controller 10X Genomics and the Single Cell ATAC Reagent Kit V1.1; 10X Genomics; PN 1000176 . Tagmented nuclei were loaded onto the Chromium Single Cell Chip H 10X Genomics; PN 1000162 GEM generation barcoding and library construction was performed according to the 10X Genomics Chromium User Guide. The resulting single cell ATAC libraries contained unique sample indices for each sample. The libraries were quantified on the Agilent BioAnalyzer 2100 using the High Sensitivity DNA Kit Agilent 5067 4626 and pooled in equimolar ratios. Sequencing was performed on an Illumina NextSeq 500 using a 150 cycle High Output Kit as follows: 50bp Read1 8bp i7 index 16bp i5 index 50bp Read2 achieving a read depth of 25 000 read pairs per nucleus.		ATAC-seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		SRP344879		loader:fastq load.py\|options: readTypes=BTB read1PairFiles=20158 Prox Mut S7 R1 001.fastq.gz read2PairFiles=20158 Prox Mut S7 R2 001.fastq.gz read3PairFiles=20158 Prox Mut S7 R3 001.fastq.gz	20158_Prox-Mut_S7_R1_001.fastq.gz 20158_Prox-Mut_S7_R2_001.fastq.gz 20158_Prox-Mut_S7_R3_001.fastq.gz	fastq fastq fastq	10416417336.0	65926692.0	GSM5677991 r1	0:71 1:16 2:71	A:2269946152;C:2457596815;G:2197719841;T:2435900098;N:427358	71	16	71		2269946152	2457596815	2197719841	2435900098	427358	SRX13025545	SRS10963312	SRA1327178	Computational Biology Lab, School of Biological Sciences, Monash University	Computational Biology Lab, School of Biological Sciences, Monash University	2	0.39271	0.39125	0.30282	0.30048	0.79829	0.79803	0.52845	0.52503	71	71	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	sc	single_cell_droplet	10x		Australia	2021-11-06	Larval	Larval	Embryo Imprecise	All anatomical structures
66927	66927	SRR16832336	SRX13025544	SRS10963311	SRP344879	PRJNA778402	Atlas of lymphangiogenesis [scATAC Seq]	GSE188340	Other	During development lymphatic vasculature forms as a second and distinct network that derives from embryonic blood vessels. Transdifferentiation of venous endothelial cells into specified lymphatic endothelial cells LECs is the first step in this process. Transdifferentiation and specification of LEC fate requires Prox1 but how Prox1 regulates transdifferentiation and differentiation is not fully understood. We present a single cell transcriptomic atlas of lymphangiogenesis spanning four key developmental stages that reveals new markers and functional regulators of lymphatic development. We extend this to comprehensively profile single cell transcriptomic and chromatin changes controlled by Prox1 using zygotic prox1a mutants which form lymphatics that then dedifferentiate. Combining this with single cell analysis of Prox1 null double prox1a/prox1b maternal zygotic mutants we reveal in depth the role of Prox1 in control of LEC fate specification and differentiation. This resource reveals dual and progressive functions for Prox1 blocking blood vascular and hematopoietic fate while simultaneously up regulating a small number of early acting genes that include tspan18a/b and lgals3a/b which are essential for lymphangiogenesis. This embryonic developmental resource will serve as a baseline to better understand both developmental and pathological lymphangiogenesis in the future. [Citations in sample metadata correspond to reference numbers in the associated publication.] Overall design: Single cell ATAC profiles of endothelial cells from developing zebrafish at 4dpf in Zprox / mutant and matched WT siblings. All code associated with this data and publication are publicly available under an open source software license at: https://atlassian.petermac.org.au/bitbucket/users/tyrone.chen/repos/hogan lab/browse/2022 Grimm Mason et al PROX1 NatCellBiol/	parent bioproject:PRJNA778399	pubmed:36912146		20157: WT 4dpf scATAC seq	GSM5677990		source name:embryo\|tissue:embryo\|transgenic:Tgfli1a:negfp;Tg 5.2lyve1b:dsRed\|facs:nEGFP and dsRed2 double positive\|Stage:4dpf\|genotype:WT\|platform:10X Chromium scATAC\|facility:Peter Mac Molecular Genomics\|cellranger atac pipeline:2.0.0\|r version:4.0.5\|internal id:20157\|gap study version:ATAC 1.1	20157: WT 4dpf scATAC seq	Where necessary fastq files were made using Cell Ranger [14] version 3.1.0 or 3.0.2 mkfastq. Sequencing QC was assessed using FastQC 0.11.6 and MultiQC viewer for aggregated reports. Cell Ranger count and aggr were used to generate aggregated count files mapped to GRCz11 Ensembl 101 without xxx normalisation. Doublets were identified from the filtered aggregated count files using Scrublet [15] in Python version 3.6 and filtered from subsequent analyses. For the MZprox1 / mutant and Zprox1 / mutant datasets filtered aggregated count files were processed sc transform normalised filtered and clustered louvain using Seurat version 2.0 [16] and 3.0 [17] respectively for R statistical software version 4.0.2. QC was evaluated before and post normalisation using plot functions in Seurat and scater 1.20.1 [18] and all thresholds and settings are described in scripting. Cluster solutions were evaluated using ClusTree [19]. Datasets used in the atlas of lymphangiogenesis were processed filtered merged and log normalised using Seurat version 3.0 [17] with QC and settings as above. Merged data was clustered and normalised using CSS simspec [20] and clustering and cluster evaluation performed on this object only as described above. For all scRNA seq datasets cluster phenotype was determined using the expression of key markers Supplementary Table with the aid of CellXGene visualisation software [21]. All downstream analysis and plotting were performed using Seurat version 3.0 [17] using default settings. For velocity analysis loom files containing RNA velocity information were first generated from the 10X data associated with each sample using velocyto.R 0.6. Relevant sample subsets were then combined with loompy 3.0.6. From pre computed Seurat UMAPs in scRNA seq processing and analysis cell barcode and associated metadata were obtained and combined with the loom files. With the combined velocity scores and cell metadata velocity maps were plotted with velocyto.R 0.6 and overlaid on the UMAPs. Genome build: …	embryo	All injections were performed as previously described [10]. CRISPR genome editing for tspan18a/b was performed as previously described [11] and all genotyping confirmed using PCR [12]. slc7a7aBAC:slc7a7a Citrineuom10 and fabp11aBAC:fabp11a Citrineuom10 recombineering was performed as previously described.	Single cell suspensions were sorted by FACS and prepared for nuclei isolation as previously described by 10x Genomics Demonstrated Protocol for Single Cell ATAC Sequencing CG000169 Rev D. Cell suspensions were pelleted 300 x g for 5 minutes and rinsed with PBS + 0.04% BSA. Cells were resuspended in 95uL of freshly prepared lysis buffer 10mM Tris HCl pH 7.4 10 mM NaCl 3 mM MgCl2 0.1% Tween 20 0.1% NP40 Substitute 0.01% Digitonin and 1% BSA and incubated on ice for 1 minute. 100uL of chilled wash buffer 10 mM Tris HCl pH 7.4 10 mM NaCl 3 mM MgCl2 0.1% Tween 20 1% BSA was used to neutralise the reaction before the nuclei were pelleted 500 x g for 5 minutes and resuspended again in 7uL of 1x Nuclei Buffer 10X Genomics Cat# PN 2000153/2000207. Presence of healthy and intact nuclei was assessed by visual inspection on a brightfield microscope using Trypan Blue staining Thermo Fisher Cat# T10282 and Countess Cell Counting Chamber Slides Thermo Fisher Cat# C10228. Single nuclei suspensions were resuspended at approximately 5000 nuclei per L before undergoing tagmentation for 60min at 37C. post tagmentation nuclei were partitioned and barcoded using the 10X Genomics Chromium Controller 10X Genomics and the Single Cell ATAC Reagent Kit V1.1; 10X Genomics; PN 1000176 . Tagmented nuclei were loaded onto the Chromium Single Cell Chip H 10X Genomics; PN 1000162 GEM generation barcoding and library construction was performed according to the 10X Genomics Chromium User Guide. The resulting single cell ATAC libraries contained unique sample indices for each sample. The libraries were quantified on the Agilent BioAnalyzer 2100 using the High Sensitivity DNA Kit Agilent 5067 4626 and pooled in equimolar ratios. Sequencing was performed on an Illumina NextSeq 500 using a 150 cycle High Output Kit as follows: 50bp Read1 8bp i7 index 16bp i5 index 50bp Read2 achieving a read depth of 25 000 read pairs per nucleus.	Zebrafish work was conducted in compliance with animal ethics committees at University of Queensland and Peter MacCallum Cancer Centre. The uq52bh dut mutant was isolated in a previously described genetic screen [7]. The genetic mapping approach was performed as previously described [8 9].	tissue:embryo\|transgenic:Tgfli1a:negfp;Tg 5.2lyve1b:dsRed\|facs:nEGFP and dsRed2 double positive\|Stage:4dpf\|genotype:WT\|platform:10X Chromium scATAC\|version:ATAC 1.1\|facility:Peter Mac Molecular Genomics\|cellranger atac pipeline:2.0.0\|r version:4.0.5\|internal id:20157	GSM5677990	GSM5677990: 20157: WT 4dpf scATAC seq; Danio rerio; ATAC seq	GSM5677990 r1	GSM5677990	1	Single cell suspensions were sorted by FACS and prepared for nuclei isolation as previously described by 10x Genomics Demonstrated Protocol for Single Cell ATAC Sequencing CG000169 Rev D. Cell suspensions were pelleted 300 x g for 5 minutes and rinsed with PBS + 0.04% BSA. Cells were resuspended in 95uL of freshly prepared lysis buffer 10mM Tris HCl pH 7.4 10 mM NaCl 3 mM MgCl2 0.1% Tween 20 0.1% NP40 Substitute 0.01% Digitonin and 1% BSA and incubated on ice for 1 minute. 100uL of chilled wash buffer 10 mM Tris HCl pH 7.4 10 mM NaCl 3 mM MgCl2 0.1% Tween 20 1% BSA was used to neutralise the reaction before the nuclei were pelleted 500 x g for 5 minutes and resuspended again in 7uL of 1x Nuclei Buffer 10X Genomics Cat# PN 2000153/2000207. Presence of healthy and intact nuclei was assessed by visual inspection on a brightfield microscope using Trypan Blue staining Thermo Fisher Cat# T10282 and Countess Cell Counting Chamber Slides Thermo Fisher Cat# C10228. Single nuclei suspensions were resuspended at approximately 5000 nuclei per L before undergoing tagmentation for 60min at 37C. post tagmentation nuclei were partitioned and barcoded using the 10X Genomics Chromium Controller 10X Genomics and the Single Cell ATAC Reagent Kit V1.1; 10X Genomics; PN 1000176 . Tagmented nuclei were loaded onto the Chromium Single Cell Chip H 10X Genomics; PN 1000162 GEM generation barcoding and library construction was performed according to the 10X Genomics Chromium User Guide. The resulting single cell ATAC libraries contained unique sample indices for each sample. The libraries were quantified on the Agilent BioAnalyzer 2100 using the High Sensitivity DNA Kit Agilent 5067 4626 and pooled in equimolar ratios. Sequencing was performed on an Illumina NextSeq 500 using a 150 cycle High Output Kit as follows: 50bp Read1 8bp i7 index 16bp i5 index 50bp Read2 achieving a read depth of 25 000 read pairs per nucleus.		ATAC-seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		SRP344879		loader:fastq load.py\|options: readTypes=BTB	20157_Wild-Type_S6_R1_001.fastq.gz 20157_Wild-Type_S6_R2_001.fastq.gz 20157_Wild-Type_S6_R3_001.fastq.gz	fastq fastq fastq	9771147706.0	61842707.0	GSM5677990 r1	0:71 1:16 2:71	A:2361071727;C:2051725100;G:1909318228;T:2459149367;N:399972	71	16	71		2361071727	2051725100	1909318228	2459149367	399972	SRX13025544	SRS10963311	SRA1327178	Computational Biology Lab, School of Biological Sciences, Monash University	Computational Biology Lab, School of Biological Sciences, Monash University	2	0.83384	0.83194	0.67607	0.67264	0.68014	0.67992	0.50904	0.50945	71	71	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	sc	single_cell_droplet	10x		Australia	2021-11-06	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");;