metadata: run_metadata: 11 rows where devstage_curation = "Segmentation" and tissue

11 rows where devstage_curation = "Segmentation" and tissue_curation = "Multi-tissue"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	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.study_ref	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
34551	34551	SRR32104356	SRX27449954	SRS23876475	SRP559533	PRJNA1214751	Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq]	GSE287815	Transcriptome Analysis	During vertebrate development the heart primarily arises from mesoderm with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives. Here by integrating bulk and single cell RNAseq with ATAC seq we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1 sox9a tfap2a and ets1. Notably we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.		17hpf Positive CNC 3	GSM8751787	source name:cardiac neural crest from midbrain hindbrain boundary to somite 6\|tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6\|cell type:migratory cardiac neural crest\|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP\|age:16 somite stage 17hpf\|fluorophore:mcherry +\|geo loc name:missing\|collection date:missing	17hpf Positive CNC 3	Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples	cardiac neural crest from midbrain hindbrain boundary to somite 6	mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.	tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6\|cell type:migratory cardiac neural crest\|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP\|age:16 somite stage 17hpf\|fluorophore:mcherry +	GSM8751787	GSM8751787: 17hpf Positive CNC 3; Danio rerio; RNA Seq	GSM8751787 r1	GSM8751787	1	mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP559533	Sox10_pos_17hpf_CNC_3_22028_combined_filtered.fastq.gz	fastq	5836253400.0	58362534.0	GSM8751787 r1	0:100	A:1666874971;C:1250406201;G:1263794016;T:1655113176;N:65036	100		1666874971	1250406201	1263794016	1655113176	65036	SRX27449954	SRS23876475	SRA2058978	Martik Lab, Molecular and Cell Biology, University of California Berkeley	Martik Lab, Molecular and Cell Biology, University of California Berkeley												B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2025-01-23	Segmentation	Embryo	Multi-tissue	Multi-system
34552	34552	SRR32104357	SRX27449953	SRS23876474	SRP559533	PRJNA1214751	Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq]	GSE287815	Transcriptome Analysis	During vertebrate development the heart primarily arises from mesoderm with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives. Here by integrating bulk and single cell RNAseq with ATAC seq we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1 sox9a tfap2a and ets1. Notably we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.		17hpf Positive CNC 2	GSM8751786	source name:cardiac neural crest from midbrain hindbrain boundary to somite 6\|tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6\|cell type:migratory cardiac neural crest\|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP\|age:16 somite stage 17hpf\|fluorophore:mcherry +\|geo loc name:missing\|collection date:missing	17hpf Positive CNC 2	Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples	cardiac neural crest from midbrain hindbrain boundary to somite 6	mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.	tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6\|cell type:migratory cardiac neural crest\|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP\|age:16 somite stage 17hpf\|fluorophore:mcherry +	GSM8751786	GSM8751786: 17hpf Positive CNC 2; Danio rerio; RNA Seq	GSM8751786 r1	GSM8751786	1	mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP559533	Sox10_pos_17hpf_CNC_2_21338_combined_filtered.fastq.gz	fastq	2444486550.0	48889731.0	GSM8751786 r1	0:50	A:706384494;C:515182895;G:525593789;T:697319091;N:6281	50		706384494	515182895	525593789	697319091	6281	SRX27449953	SRS23876474	SRA2058978	Martik Lab, Molecular and Cell Biology, University of California Berkeley	Martik Lab, Molecular and Cell Biology, University of California Berkeley												B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2025-01-23	Segmentation	Embryo	Multi-tissue	Multi-system
34553	34553	SRR32104358	SRX27449952	SRS23876472	SRP559533	PRJNA1214751	Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq]	GSE287815	Transcriptome Analysis	During vertebrate development the heart primarily arises from mesoderm with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives. Here by integrating bulk and single cell RNAseq with ATAC seq we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1 sox9a tfap2a and ets1. Notably we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.		17hpf Positive CNC 1	GSM8751785	source name:cardiac neural crest from midbrain hindbrain boundary to somite 6\|tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6\|cell type:migratory cardiac neural crest\|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP\|age:16 somite stage 17hpf\|fluorophore:mcherry +\|geo loc name:missing\|collection date:missing	17hpf Positive CNC 1	Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples	cardiac neural crest from midbrain hindbrain boundary to somite 6	mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.	tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6\|cell type:migratory cardiac neural crest\|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP\|age:16 somite stage 17hpf\|fluorophore:mcherry +	GSM8751785	GSM8751785: 17hpf Positive CNC 1; Danio rerio; RNA Seq	GSM8751785 r1	GSM8751785	1	mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP559533	Sox10_pos_17hpf_CNC_1_21309_combined_filtered.fastq.gz	fastq	3136080950.0	62721619.0	GSM8751785 r1	0:50	A:867446661;C:707750289;G:716376649;T:844460193;N:47158	50		867446661	707750289	716376649	844460193	47158	SRX27449952	SRS23876472	SRA2058978	Martik Lab, Molecular and Cell Biology, University of California Berkeley	Martik Lab, Molecular and Cell Biology, University of California Berkeley												B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2025-01-23	Segmentation	Embryo	Multi-tissue	Multi-system
60451	60451	SRR12283718	SRX8787097	SRS7055744	SRP273008	PRJNA647599	Transcriptome of nkx2.2a+ olig2+ dbx1b+ cells from 14hpf zebrafish embryo	GSE154885	Transcriptome Analysis	cDNA extracted from FACS sorted GFP positive cells taken from trunk region of 14hpf zebrafish embryo with transgenic reporter TgBACnkx2.2a:memGFP TgBAColig2:GFP or TgBACdbx1b:GFP Overall design: transcriptome of nkx2.2a+ olig2+ dbx1b+ cells from 14hpf zebrafish embryo	pubmed:33004519	TgBACdbx1b:GFP positive cells 2	GSM4681846	tissue:FACS sorted dbx1b + neural progenitors\|age:14hpf\|genotype:WT	TgBACdbx1b:GFP positive cells 2	Sequenced reads were filtered by fastqc 0.11.3 then mapped to GRCz10 whole genome using bowtie 1.1.1 with parameters q n 2 l 28 e 1000 I 0 X 1000 k 1 m 200 Reads Per Kilobase of exon per Megabase of library size RPKM were calculated. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include gene names gene length mapped count unmapped count Supplementary files format and content: excel spreadsheet with gene names and transcript count in each sample	FACS sorted dbx1b + neural progenitors	14hpf zebrafish embryos were dissected to remove the brain and tail region. The trunk region is dissociated by mechanical pipetting in FACSMax solution. The dissociated cells are resuspended in PBS FACS sorted for GFP positive cells. The sorted cells are spun down and the pellet was flash frozen in Trizol for RNA extraction. RNA libraries were prepared for sequencing using standard Illumina protocols	age:14hpf\|genotype:WT	GSM4681846	GSM4681846: TgBACdbx1b:GFP positive cells 2; Danio rerio; RNA Seq	GSM4681846		1	14hpf zebrafish embryos were dissected to remove the brain and tail region. The trunk region is dissociated by mechanical pipetting in FACSMax solution. The dissociated cells are resuspended in PBS FACS sorted for GFP positive cells. The sorted cells are spun down and the pellet was flash frozen in Trizol for RNA extraction. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4681846	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP273008	LIB018768_TRA00046531_S8_L002_R1.fastq LIB018768_TRA00046531_S8_L002_R2.fastq	fastq fastq	2333457800.0	23334578.0	GSM4681846 r1	0:50 1:50	A:665714687;C:482177371;G:502528257;T:682738013;N:299472	50	50	665714687	482177371	502528257	682738013	299472	SRX8787097	SRS7055744	SRA1102160	GEO	Sean Megason, Systems Biology, Harvard Medical School	2	0.84752	0.83215	0.23085	0.22303	0.76635	0.76997	0.6427	0.65075	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2020-07-22	Segmentation	Embryo	Multi-tissue	Multi-system
60452	60452	SRR12283717	SRX8787096	SRS7055743	SRP273008	PRJNA647599	Transcriptome of nkx2.2a+ olig2+ dbx1b+ cells from 14hpf zebrafish embryo	GSE154885	Transcriptome Analysis	cDNA extracted from FACS sorted GFP positive cells taken from trunk region of 14hpf zebrafish embryo with transgenic reporter TgBACnkx2.2a:memGFP TgBAColig2:GFP or TgBACdbx1b:GFP Overall design: transcriptome of nkx2.2a+ olig2+ dbx1b+ cells from 14hpf zebrafish embryo	pubmed:33004519	TgBACdbx1b:GFP positive cells 1	GSM4681845	tissue:FACS sorted dbx1b + neural progenitors\|age:14hpf\|genotype:WT	TgBACdbx1b:GFP positive cells 1	Sequenced reads were filtered by fastqc 0.11.3 then mapped to GRCz10 whole genome using bowtie 1.1.1 with parameters q n 2 l 28 e 1000 I 0 X 1000 k 1 m 200 Reads Per Kilobase of exon per Megabase of library size RPKM were calculated. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include gene names gene length mapped count unmapped count Supplementary files format and content: excel spreadsheet with gene names and transcript count in each sample	FACS sorted dbx1b + neural progenitors	14hpf zebrafish embryos were dissected to remove the brain and tail region. The trunk region is dissociated by mechanical pipetting in FACSMax solution. The dissociated cells are resuspended in PBS FACS sorted for GFP positive cells. The sorted cells are spun down and the pellet was flash frozen in Trizol for RNA extraction. RNA libraries were prepared for sequencing using standard Illumina protocols	age:14hpf\|genotype:WT	GSM4681845	GSM4681845: TgBACdbx1b:GFP positive cells 1; Danio rerio; RNA Seq	GSM4681845		1	14hpf zebrafish embryos were dissected to remove the brain and tail region. The trunk region is dissociated by mechanical pipetting in FACSMax solution. The dissociated cells are resuspended in PBS FACS sorted for GFP positive cells. The sorted cells are spun down and the pellet was flash frozen in Trizol for RNA extraction. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4681845	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP273008	LIB018768_TRA00046530_S7_L002_R1.fastq LIB018768_TRA00046530_S7_L002_R2.fastq	fastq fastq	1766472900.0	17664729.0	GSM4681845 r1	0:50 1:50	A:494774427;C:378835123;G:387031562;T:505606249;N:225539	50	50	494774427	378835123	387031562	505606249	225539	SRX8787096	SRS7055743	SRA1102160	GEO	Sean Megason, Systems Biology, Harvard Medical School	2	0.86013	0.84612	0.18313	0.17713	0.77015	0.77532	0.64231	0.56308	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2020-07-22	Segmentation	Embryo	Multi-tissue	Multi-system
60453	60453	SRR12283716	SRX8787095	SRS7055742	SRP273008	PRJNA647599	Transcriptome of nkx2.2a+ olig2+ dbx1b+ cells from 14hpf zebrafish embryo	GSE154885	Transcriptome Analysis	cDNA extracted from FACS sorted GFP positive cells taken from trunk region of 14hpf zebrafish embryo with transgenic reporter TgBACnkx2.2a:memGFP TgBAColig2:GFP or TgBACdbx1b:GFP Overall design: transcriptome of nkx2.2a+ olig2+ dbx1b+ cells from 14hpf zebrafish embryo	pubmed:33004519	TgBAColig2:GFP positive cells 2	GSM4681844	tissue:FACS sorted olig2 + neural progenitors\|age:14hpf\|genotype:WT	TgBAColig2:GFP positive cells 2	Sequenced reads were filtered by fastqc 0.11.3 then mapped to GRCz10 whole genome using bowtie 1.1.1 with parameters q n 2 l 28 e 1000 I 0 X 1000 k 1 m 200 Reads Per Kilobase of exon per Megabase of library size RPKM were calculated. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include gene names gene length mapped count unmapped count Supplementary files format and content: excel spreadsheet with gene names and transcript count in each sample	FACS sorted olig2 + neural progenitors	14hpf zebrafish embryos were dissected to remove the brain and tail region. The trunk region is dissociated by mechanical pipetting in FACSMax solution. The dissociated cells are resuspended in PBS FACS sorted for GFP positive cells. The sorted cells are spun down and the pellet was flash frozen in Trizol for RNA extraction. RNA libraries were prepared for sequencing using standard Illumina protocols	age:14hpf\|genotype:WT	GSM4681844	GSM4681844: TgBAColig2:GFP positive cells 2; Danio rerio; RNA Seq	GSM4681844		1	14hpf zebrafish embryos were dissected to remove the brain and tail region. The trunk region is dissociated by mechanical pipetting in FACSMax solution. The dissociated cells are resuspended in PBS FACS sorted for GFP positive cells. The sorted cells are spun down and the pellet was flash frozen in Trizol for RNA extraction. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4681844	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP273008	LIB018768_TRA00046535_S12_L002_R1.fastq LIB018768_TRA00046535_S12_L002_R2.fastq	fastq fastq	1883562500.0	18835625.0	GSM4681844 r1	0:50 1:50	A:538880974;C:389273777;G:399233943;T:555933855;N:239951	50	50	538880974	389273777	399233943	555933855	239951	SRX8787095	SRS7055742	SRA1102160	GEO	Sean Megason, Systems Biology, Harvard Medical School	2	0.83434	0.81762	0.28607	0.27612	0.77804	0.78137	0.67234	0.67724	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2020-07-22	Segmentation	Embryo	Multi-tissue	Multi-system
60454	60454	SRR12283715	SRX8787094	SRS7055741	SRP273008	PRJNA647599	Transcriptome of nkx2.2a+ olig2+ dbx1b+ cells from 14hpf zebrafish embryo	GSE154885	Transcriptome Analysis	cDNA extracted from FACS sorted GFP positive cells taken from trunk region of 14hpf zebrafish embryo with transgenic reporter TgBACnkx2.2a:memGFP TgBAColig2:GFP or TgBACdbx1b:GFP Overall design: transcriptome of nkx2.2a+ olig2+ dbx1b+ cells from 14hpf zebrafish embryo	pubmed:33004519	TgBAColig2:GFP positive cells 1	GSM4681843	tissue:FACS sorted olig2 + neural progenitors\|age:14hpf\|genotype:WT	TgBAColig2:GFP positive cells 1	Sequenced reads were filtered by fastqc 0.11.3 then mapped to GRCz10 whole genome using bowtie 1.1.1 with parameters q n 2 l 28 e 1000 I 0 X 1000 k 1 m 200 Reads Per Kilobase of exon per Megabase of library size RPKM were calculated. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include gene names gene length mapped count unmapped count Supplementary files format and content: excel spreadsheet with gene names and transcript count in each sample	FACS sorted olig2 + neural progenitors	14hpf zebrafish embryos were dissected to remove the brain and tail region. The trunk region is dissociated by mechanical pipetting in FACSMax solution. The dissociated cells are resuspended in PBS FACS sorted for GFP positive cells. The sorted cells are spun down and the pellet was flash frozen in Trizol for RNA extraction. RNA libraries were prepared for sequencing using standard Illumina protocols	age:14hpf\|genotype:WT	GSM4681843	GSM4681843: TgBAColig2:GFP positive cells 1; Danio rerio; RNA Seq	GSM4681843		1	14hpf zebrafish embryos were dissected to remove the brain and tail region. The trunk region is dissociated by mechanical pipetting in FACSMax solution. The dissociated cells are resuspended in PBS FACS sorted for GFP positive cells. The sorted cells are spun down and the pellet was flash frozen in Trizol for RNA extraction. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4681843	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP273008	LIB018768_TRA00046532_S9_L002_R1.fastq LIB018768_TRA00046532_S9_L002_R2.fastq	fastq fastq	1679123300.0	16791233.0	GSM4681843 r1	0:50 1:50	A:483066027;C:337334552;G:356429892;T:502080995;N:211834	50	50	483066027	337334552	356429892	502080995	211834	SRX8787094	SRS7055741	SRA1102160	GEO	Sean Megason, Systems Biology, Harvard Medical School	2	0.82763	0.8109	0.27206	0.26478	0.78526	0.78851	0.70765	0.7123	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2020-07-22	Segmentation	Embryo	Multi-tissue	Multi-system
60455	60455	SRR12283714	SRX8787093	SRS7055740	SRP273008	PRJNA647599	Transcriptome of nkx2.2a+ olig2+ dbx1b+ cells from 14hpf zebrafish embryo	GSE154885	Transcriptome Analysis	cDNA extracted from FACS sorted GFP positive cells taken from trunk region of 14hpf zebrafish embryo with transgenic reporter TgBACnkx2.2a:memGFP TgBAColig2:GFP or TgBACdbx1b:GFP Overall design: transcriptome of nkx2.2a+ olig2+ dbx1b+ cells from 14hpf zebrafish embryo	pubmed:33004519	TgBACnkx2.2a:memGFP positive cells 2	GSM4681842	tissue:FACS sorted nkx2.2a + neural progenitors\|age:14hpf\|genotype:WT	TgBACnkx2.2a:memGFP positive cells 2	Sequenced reads were filtered by fastqc 0.11.3 then mapped to GRCz10 whole genome using bowtie 1.1.1 with parameters q n 2 l 28 e 1000 I 0 X 1000 k 1 m 200 Reads Per Kilobase of exon per Megabase of library size RPKM were calculated. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include gene names gene length mapped count unmapped count Supplementary files format and content: excel spreadsheet with gene names and transcript count in each sample	FACS sorted nkx2.2a + neural progenitors	14hpf zebrafish embryos were dissected to remove the brain and tail region. The trunk region is dissociated by mechanical pipetting in FACSMax solution. The dissociated cells are resuspended in PBS FACS sorted for GFP positive cells. The sorted cells are spun down and the pellet was flash frozen in Trizol for RNA extraction. RNA libraries were prepared for sequencing using standard Illumina protocols	age:14hpf\|genotype:WT	GSM4681842	GSM4681842: TgBACnkx2.2a:memGFP positive cells 2; Danio rerio; RNA Seq	GSM4681842		1	14hpf zebrafish embryos were dissected to remove the brain and tail region. The trunk region is dissociated by mechanical pipetting in FACSMax solution. The dissociated cells are resuspended in PBS FACS sorted for GFP positive cells. The sorted cells are spun down and the pellet was flash frozen in Trizol for RNA extraction. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4681842	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP273008	LIB018768_TRA00046534_S11_L002_R1.fastq LIB018768_TRA00046534_S11_L002_R2.fastq	fastq fastq	1829250400.0	18292504.0	GSM4681842 r1	0:50 1:50	A:519439919;C:375677698;G:393002097;T:540898141;N:232545	50	50	519439919	375677698	393002097	540898141	232545	SRX8787093	SRS7055740	SRA1102160	GEO	Sean Megason, Systems Biology, Harvard Medical School	2	0.83765	0.81845	0.28167	0.27377	0.79271	0.79563	0.73414	0.73464	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2020-07-22	Segmentation	Embryo	Multi-tissue	Multi-system
60456	60456	SRR12283713	SRX8787092	SRS7055739	SRP273008	PRJNA647599	Transcriptome of nkx2.2a+ olig2+ dbx1b+ cells from 14hpf zebrafish embryo	GSE154885	Transcriptome Analysis	cDNA extracted from FACS sorted GFP positive cells taken from trunk region of 14hpf zebrafish embryo with transgenic reporter TgBACnkx2.2a:memGFP TgBAColig2:GFP or TgBACdbx1b:GFP Overall design: transcriptome of nkx2.2a+ olig2+ dbx1b+ cells from 14hpf zebrafish embryo	pubmed:33004519	TgBACnkx2.2a:memGFP positive cells 1	GSM4681841	tissue:FACS sorted nkx2.2a + neural progenitors\|age:14hpf\|genotype:WT	TgBACnkx2.2a:memGFP positive cells 1	Sequenced reads were filtered by fastqc 0.11.3 then mapped to GRCz10 whole genome using bowtie 1.1.1 with parameters q n 2 l 28 e 1000 I 0 X 1000 k 1 m 200 Reads Per Kilobase of exon per Megabase of library size RPKM were calculated. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include gene names gene length mapped count unmapped count Supplementary files format and content: excel spreadsheet with gene names and transcript count in each sample	FACS sorted nkx2.2a + neural progenitors	14hpf zebrafish embryos were dissected to remove the brain and tail region. The trunk region is dissociated by mechanical pipetting in FACSMax solution. The dissociated cells are resuspended in PBS FACS sorted for GFP positive cells. The sorted cells are spun down and the pellet was flash frozen in Trizol for RNA extraction. RNA libraries were prepared for sequencing using standard Illumina protocols	age:14hpf\|genotype:WT	GSM4681841	GSM4681841: TgBACnkx2.2a:memGFP positive cells 1; Danio rerio; RNA Seq	GSM4681841		1	14hpf zebrafish embryos were dissected to remove the brain and tail region. The trunk region is dissociated by mechanical pipetting in FACSMax solution. The dissociated cells are resuspended in PBS FACS sorted for GFP positive cells. The sorted cells are spun down and the pellet was flash frozen in Trizol for RNA extraction. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4681841	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP273008	LIB018768_TRA00046533_S10_L002_R1.fastq LIB018768_TRA00046533_S10_L002_R2.fastq	fastq fastq	2075770200.0	20757702.0	GSM4681841 r1	0:50 1:50	A:595497281;C:427137535;G:443303257;T:609571756;N:260371	50	50	595497281	427137535	443303257	609571756	260371	SRX8787092	SRS7055739	SRA1102160	GEO	Sean Megason, Systems Biology, Harvard Medical School	2	0.8636	0.84947	0.24936	0.2423	0.7568	0.76031	0.67066	0.6717	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2020-07-22	Segmentation	Embryo	Multi-tissue	Multi-system
63226	63226	SRR13660516	SRX10052201	SRS8215327	SRP305389	PRJNA700672	Endothelial progenitor migration and differentiation is regulated by distinct transcriptional effectors of Cloche/Npas4l	GSE166396	Transcriptome Analysis	Embryonic cells including endothelial progenitors undergo extensive migration and differentiation events; however whether and how these processes are interrelated remains unclear. The transcription factor Npas4l is necessary for endothelial specification in zebrafish by inducing the expression of the transcription factor genes etsrp tal1 and lmo2. We generated a knock in reporter in the npas4l locus to visualize endothelial progenitors and their derivatives in wild type and mutant embryos. We find that in npas4l mutants npas4l reporter expressing cells do not migrate to the midline and instead contribute to skeletal muscle and pronephric tubules. Investigating the Npas4l transcriptional effectors we find that npas4l reporter expressing cells in tal1 mutants fail to migrate while those in etsrp mutants migrate but fail to differentiate. In lmo2 mutants npas4l reporter expressing cells migrate and differentiate but many express pronephric tubule markers. Altogether these data reveal the complex regulation of endothelial progenitor migration differentiation and fate restriction. Overall design: Comparison of npas4l reporter positive cells from heterozygous and homozygous npas4l mutant embryos using single cell RNAseq on sorted cells.		npas4l mut	GSM5070576	tissue:npas4l reporter positive cells\|cell type:sorted npas4l reporter positive cells\|Stage:20 hpf	npas4l mut	Reads were aligned against the zebrafish genome DanRer11 and counted by StarSolo followed by secondary analysis in Annotated Data Format. Preprocessed counts were further analysed using Scanpy. Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed only 16 cells in total that did not express between 1000 and 7000 genes or had an mitochondrial content less than 6%. Further we filtered genes if they were detected in less than 30 cells <0.3%. Raw counts per cell were normalised to the median count over all cells and transformed into log space to stabilise variance. We initially reduced dimensionality of the dataset using PCA retaining 50 principal components. Subsequent steps like low dimensional UMAP embedding and cell clustering via community detection were based on the initial PCA. Final data visualization was done by scVelo and cellxgene packages. Genome build: DanRer11 Supplementary files format and content: Mattonet adata obs.csv: basic anndata observations Sample n genes by counts log1p total counts pct counts is mito n genes detected leiden clustering Supplementary files format and content: Mattonet udata obs.csv: velocity anmdata observations initial size unspliced initial size spliced initial size n counts velocity self transition root cells end points velocity pseudotime	npas4l reporter positive cells	Tails from 150 npas4l heterozygous npas4lbns423/+ and trans heterozygous npas4lbns423/bns297 mutant embryos were cut at the anterior end of the yolk extension at 20 hpf in DMEM/F10+5%FBS+0.01% tricaine on agarose coated plates. The cells were dissociated using the Pierce Cardiomyocyte dissociation kit according to manufacturer instructions and FACS sorted for GFP fluorescence using an AriaIII sorter and DAPI as indicator for dead cells. The cell suspensions were counted with Moxi cell counter and diluted according to manufacturer’s protocol to obtain 5000 single cell data points per sample. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 10xGenomics. Single cell RNAseq library preparation was done using standard protocol.	cell type:sorted npas4l reporter positive cells\|Stage:20 hpf	GSM5070576	GSM5070576: npas4l mut; Danio rerio; RNA Seq	GSM5070576		1	Tails from 150 npas4l heterozygous npas4lbns423/+ and trans heterozygous npas4lbns423/bns297 mutant embryos were cut at the anterior end of the yolk extension at 20 hpf in DMEM/F10+5%FBS+0.01% tricaine on agarose coated plates. The cells were dissociated using the Pierce Cardiomyocyte dissociation kit according to manufacturer instructions and FACS sorted for GFP fluorescence using an AriaIII sorter and DAPI as indicator for dead cells. The cell suspensions were counted with Moxi cell counter and diluted according to manufacturer's protocol to obtain 5000 single cell data points per sample. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 10xGenomics. Single cell RNAseq library preparation was done using standard protocol.	GEO Accession:GSM5070576	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP305389	Kenny_scRNA_Mut_BC.fastq.gz Kenny_scRNA_Mut_cDNA.fastq.gz	fastq fastq	15859812024.0	188807286.0	GSM5070576 r1	0:28 1:56	A:4422689365;C:3447909764;G:3545664942;T:4438912669;N:4635284	28	56	4422689365	3447909764	3545664942	4438912669	4635284	SRX10052201	SRS8215327	SRA1193720	GEO	MPI for heart and lung research	2	0.00208	0.92256	0.00079	0.14522	0.99602	0.81554	0.38888	0.49915	28	56	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Germany	2021-02-08	Segmentation	Embryo	Multi-tissue	Multi-system
63227	63227	SRR13660515	SRX10052200	SRS8215328	SRP305389	PRJNA700672	Endothelial progenitor migration and differentiation is regulated by distinct transcriptional effectors of Cloche/Npas4l	GSE166396	Transcriptome Analysis	Embryonic cells including endothelial progenitors undergo extensive migration and differentiation events; however whether and how these processes are interrelated remains unclear. The transcription factor Npas4l is necessary for endothelial specification in zebrafish by inducing the expression of the transcription factor genes etsrp tal1 and lmo2. We generated a knock in reporter in the npas4l locus to visualize endothelial progenitors and their derivatives in wild type and mutant embryos. We find that in npas4l mutants npas4l reporter expressing cells do not migrate to the midline and instead contribute to skeletal muscle and pronephric tubules. Investigating the Npas4l transcriptional effectors we find that npas4l reporter expressing cells in tal1 mutants fail to migrate while those in etsrp mutants migrate but fail to differentiate. In lmo2 mutants npas4l reporter expressing cells migrate and differentiate but many express pronephric tubule markers. Altogether these data reveal the complex regulation of endothelial progenitor migration differentiation and fate restriction. Overall design: Comparison of npas4l reporter positive cells from heterozygous and homozygous npas4l mutant embryos using single cell RNAseq on sorted cells.		npas4l het	GSM5070575	tissue:npas4l reporter positive cells\|cell type:sorted npas4l reporter positive cells\|Stage:20 hpf	npas4l het	Reads were aligned against the zebrafish genome DanRer11 and counted by StarSolo followed by secondary analysis in Annotated Data Format. Preprocessed counts were further analysed using Scanpy. Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed only 16 cells in total that did not express between 1000 and 7000 genes or had an mitochondrial content less than 6%. Further we filtered genes if they were detected in less than 30 cells <0.3%. Raw counts per cell were normalised to the median count over all cells and transformed into log space to stabilise variance. We initially reduced dimensionality of the dataset using PCA retaining 50 principal components. Subsequent steps like low dimensional UMAP embedding and cell clustering via community detection were based on the initial PCA. Final data visualization was done by scVelo and cellxgene packages. Genome build: DanRer11 Supplementary files format and content: Mattonet adata obs.csv: basic anndata observations Sample n genes by counts log1p total counts pct counts is mito n genes detected leiden clustering Supplementary files format and content: Mattonet udata obs.csv: velocity anmdata observations initial size unspliced initial size spliced initial size n counts velocity self transition root cells end points velocity pseudotime	npas4l reporter positive cells	Tails from 150 npas4l heterozygous npas4lbns423/+ and trans heterozygous npas4lbns423/bns297 mutant embryos were cut at the anterior end of the yolk extension at 20 hpf in DMEM/F10+5%FBS+0.01% tricaine on agarose coated plates. The cells were dissociated using the Pierce Cardiomyocyte dissociation kit according to manufacturer instructions and FACS sorted for GFP fluorescence using an AriaIII sorter and DAPI as indicator for dead cells. The cell suspensions were counted with Moxi cell counter and diluted according to manufacturer’s protocol to obtain 5000 single cell data points per sample. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 10xGenomics. Single cell RNAseq library preparation was done using standard protocol.	cell type:sorted npas4l reporter positive cells\|Stage:20 hpf	GSM5070575	GSM5070575: npas4l het; Danio rerio; RNA Seq	GSM5070575		1	Tails from 150 npas4l heterozygous npas4lbns423/+ and trans heterozygous npas4lbns423/bns297 mutant embryos were cut at the anterior end of the yolk extension at 20 hpf in DMEM/F10+5%FBS+0.01% tricaine on agarose coated plates. The cells were dissociated using the Pierce Cardiomyocyte dissociation kit according to manufacturer instructions and FACS sorted for GFP fluorescence using an AriaIII sorter and DAPI as indicator for dead cells. The cell suspensions were counted with Moxi cell counter and diluted according to manufacturer's protocol to obtain 5000 single cell data points per sample. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 10xGenomics. Single cell RNAseq library preparation was done using standard protocol.	GEO Accession:GSM5070575	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP305389	Kenny_scRNA_Het_BC.fastq.gz Kenny_scRNA_Het_cDNA.fastq.gz	fastq fastq	21384880020.0	254581905.0	GSM5070575 r1	0:28 1:56	A:5828925615;C:4816199698;G:4885826464;T:5847660976;N:6267267	28	56	5828925615	4816199698	4885826464	5847660976	6267267	SRX10052200	SRS8215328	SRA1193720	GEO	MPI for heart and lung research	2	0.00213	0.9288	0.00071	0.11864	0.99559	0.8312	0.43162	0.47914	28	56	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Germany	2021-02-08	Segmentation	Embryo	Multi-tissue	Multi-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");;