metadata: run_metadata: 104 rows where devstage_curation = "Pharyngula" and tissue

104 rows where devstage_curation = "Pharyngula" 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.attributes	study.PMIDs	sample.title	sample.alias	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.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.r3_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
25091	25091	SRR25567703	SRX21296461	SRS18545739	SRP453968	PRJNA1003386	Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish	GSE240329	Transcriptome Analysis	To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.		pubmed:38742432	EC tie1 Homo replicate 2 RNAseq	GSM7696246	source name:homozygous tie1 mutant embryos\|tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed\|geo loc name:missing\|collection date:missing	EC tie1 Homo replicate 2 RNAseq	RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.	homozygous tie1 mutant embryos		Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760		tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed	GSM7696246	GSM7696246: EC tie1 Homo replicate 2 RNAseq; Danio rerio; RNA Seq	GSM7696246 r1	GSM7696246	1	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP453968		413-Tie1-KO2_S4_L001_R1_001.fastq.gz	fastq	445428400.0	5860900.0	GSM7696246 r1	0:76	A:143568074;C:79903177;G:79677344;T:142230186;N:49619	76			143568074	79903177	79677344	142230186	49619	SRX21296461	SRS18545739	SRA1688627	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.75644		0.67481		0.78062		0.49002		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	Japan	2023-08-08	Pharyngula	Embryo	Multi-tissue	Multi-system
25092	25092	SRR25567704	SRX21296461	SRS18545739	SRP453968	PRJNA1003386	Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish	GSE240329	Transcriptome Analysis	To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.		pubmed:38742432	EC tie1 Homo replicate 2 RNAseq	GSM7696246	source name:homozygous tie1 mutant embryos\|tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed\|geo loc name:missing\|collection date:missing	EC tie1 Homo replicate 2 RNAseq	RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.	homozygous tie1 mutant embryos		Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760		tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed	GSM7696246	GSM7696246: EC tie1 Homo replicate 2 RNAseq; Danio rerio; RNA Seq	GSM7696246 r1	GSM7696246	1	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP453968		413-Tie1-KO2_S4_L002_R1_001.fastq.gz	fastq	436280280.0	5740530.0	GSM7696246 r2	0:76	A:140668025;C:78248456;G:77919880;T:139381210;N:62709	76			140668025	78248456	77919880	139381210	62709	SRX21296461	SRS18545739	SRA1688627	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.75737		0.67543		0.77796		0.494		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	Japan	2023-08-08	Pharyngula	Embryo	Multi-tissue	Multi-system
25093	25093	SRR25567705	SRX21296461	SRS18545739	SRP453968	PRJNA1003386	Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish	GSE240329	Transcriptome Analysis	To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.		pubmed:38742432	EC tie1 Homo replicate 2 RNAseq	GSM7696246	source name:homozygous tie1 mutant embryos\|tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed\|geo loc name:missing\|collection date:missing	EC tie1 Homo replicate 2 RNAseq	RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.	homozygous tie1 mutant embryos		Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760		tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed	GSM7696246	GSM7696246: EC tie1 Homo replicate 2 RNAseq; Danio rerio; RNA Seq	GSM7696246 r1	GSM7696246	1	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP453968		413-Tie1-KO2_S4_L003_R1_001.fastq.gz	fastq	453115800.0	5962050.0	GSM7696246 r3	0:76	A:145977328;C:81331359;G:81042932;T:144726596;N:37585	76			145977328	81331359	81042932	144726596	37585	SRX21296461	SRS18545739	SRA1688627	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.75941		0.67812		0.78255		0.49198		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	Japan	2023-08-08	Pharyngula	Embryo	Multi-tissue	Multi-system
25094	25094	SRR25567706	SRX21296461	SRS18545739	SRP453968	PRJNA1003386	Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish	GSE240329	Transcriptome Analysis	To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.		pubmed:38742432	EC tie1 Homo replicate 2 RNAseq	GSM7696246	source name:homozygous tie1 mutant embryos\|tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed\|geo loc name:missing\|collection date:missing	EC tie1 Homo replicate 2 RNAseq	RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.	homozygous tie1 mutant embryos		Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760		tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed	GSM7696246	GSM7696246: EC tie1 Homo replicate 2 RNAseq; Danio rerio; RNA Seq	GSM7696246 r1	GSM7696246	1	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP453968		413-Tie1-KO2_S4_L004_R1_001.fastq.gz	fastq	451629316.0	5942491.0	GSM7696246 r4	0:76	A:145539227;C:81081378;G:80692220;T:144283694;N:32797	76			145539227	81081378	80692220	144283694	32797	SRX21296461	SRS18545739	SRA1688627	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.75907		0.67763		0.78074		0.49757		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	Japan	2023-08-08	Pharyngula	Embryo	Multi-tissue	Multi-system
25095	25095	SRR25567707	SRX21296460	SRS18545738	SRP453968	PRJNA1003386	Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish	GSE240329	Transcriptome Analysis	To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.		pubmed:38742432	EC tie1 Homo replicate 1 RNAseq	GSM7696245	source name:homozygous tie1 mutant embryos\|tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed\|geo loc name:missing\|collection date:missing	EC tie1 Homo replicate 1 RNAseq	RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.	homozygous tie1 mutant embryos		Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760		tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed	GSM7696245	GSM7696245: EC tie1 Homo replicate 1 RNAseq; Danio rerio; RNA Seq	GSM7696245 r1	GSM7696245	1	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP453968		412-Tie1-KO1_S3_L001_R1_001.fastq.gz	fastq	438903344.0	5775044.0	GSM7696245 r1	0:76	A:141636851;C:79318996;G:78779375;T:139120411;N:47711	76			141636851	79318996	78779375	139120411	47711	SRX21296460	SRS18545738	SRA1688627	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.76357		0.65866		0.76238		0.48958		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	Japan	2023-08-08	Pharyngula	Embryo	Multi-tissue	Multi-system
25096	25096	SRR25567708	SRX21296460	SRS18545738	SRP453968	PRJNA1003386	Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish	GSE240329	Transcriptome Analysis	To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.		pubmed:38742432	EC tie1 Homo replicate 1 RNAseq	GSM7696245	source name:homozygous tie1 mutant embryos\|tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed\|geo loc name:missing\|collection date:missing	EC tie1 Homo replicate 1 RNAseq	RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.	homozygous tie1 mutant embryos		Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760		tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed	GSM7696245	GSM7696245: EC tie1 Homo replicate 1 RNAseq; Danio rerio; RNA Seq	GSM7696245 r1	GSM7696245	1	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP453968		412-Tie1-KO1_S3_L002_R1_001.fastq.gz	fastq	429344216.0	5649266.0	GSM7696245 r2	0:76	A:138620131;C:77579442;G:76950101;T:136131396;N:63146	76			138620131	77579442	76950101	136131396	63146	SRX21296460	SRS18545738	SRA1688627	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.76216		0.65728		0.76132		0.4958		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	Japan	2023-08-08	Pharyngula	Embryo	Multi-tissue	Multi-system
25097	25097	SRR25567709	SRX21296460	SRS18545738	SRP453968	PRJNA1003386	Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish	GSE240329	Transcriptome Analysis	To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.		pubmed:38742432	EC tie1 Homo replicate 1 RNAseq	GSM7696245	source name:homozygous tie1 mutant embryos\|tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed\|geo loc name:missing\|collection date:missing	EC tie1 Homo replicate 1 RNAseq	RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.	homozygous tie1 mutant embryos		Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760		tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed	GSM7696245	GSM7696245: EC tie1 Homo replicate 1 RNAseq; Danio rerio; RNA Seq	GSM7696245 r1	GSM7696245	1	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP453968		412-Tie1-KO1_S3_L003_R1_001.fastq.gz	fastq	446301792.0	5872392.0	GSM7696245 r3	0:76	A:143941333;C:80689335;G:80111561;T:141523625;N:35938	76			143941333	80689335	80111561	141523625	35938	SRX21296460	SRS18545738	SRA1688627	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.76416		0.65858		0.76177		0.48634		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	Japan	2023-08-08	Pharyngula	Embryo	Multi-tissue	Multi-system
25098	25098	SRR25567710	SRX21296460	SRS18545738	SRP453968	PRJNA1003386	Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish	GSE240329	Transcriptome Analysis	To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.		pubmed:38742432	EC tie1 Homo replicate 1 RNAseq	GSM7696245	source name:homozygous tie1 mutant embryos\|tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed\|geo loc name:missing\|collection date:missing	EC tie1 Homo replicate 1 RNAseq	RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.	homozygous tie1 mutant embryos		Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760		tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed	GSM7696245	GSM7696245: EC tie1 Homo replicate 1 RNAseq; Danio rerio; RNA Seq	GSM7696245 r1	GSM7696245	1	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP453968		412-Tie1-KO1_S3_L004_R1_001.fastq.gz	fastq	443971252.0	5841727.0	GSM7696245 r4	0:76	A:143197029;C:80287228;G:79639533;T:140816381;N:31081	76			143197029	80287228	79639533	140816381	31081	SRX21296460	SRS18545738	SRA1688627	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.77093		0.66467		0.76081		0.49407		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	Japan	2023-08-08	Pharyngula	Embryo	Multi-tissue	Multi-system
25099	25099	SRR25567711	SRX21296459	SRS18545737	SRP453968	PRJNA1003386	Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish	GSE240329	Transcriptome Analysis	To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.		pubmed:38742432	EC tie1 WT/Het replicate 2 RNAseq	GSM7696244	source name:wild type and heterozygous siblings\|tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed\|geo loc name:missing\|collection date:missing	EC tie1 WT/Het replicate 2 RNAseq	RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.	wild type and heterozygous siblings		Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760		tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed	GSM7696244	GSM7696244: EC tie1 WT/Het replicate 2 RNAseq; Danio rerio; RNA Seq	GSM7696244 r1	GSM7696244	1	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP453968		411-Tie1-WT-HT2_S2_L001_R1_001.fastq.gz	fastq	392537796.0	5164971.0	GSM7696244 r1	0:76	A:124144181;C:72762157;G:72562894;T:123025322;N:43242	76			124144181	72762157	72562894	123025322	43242	SRX21296459	SRS18545737	SRA1688627	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.78106		0.59772		0.73553		0.48949		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	Japan	2023-08-08	Pharyngula	Embryo	Multi-tissue	Multi-system
25100	25100	SRR25567712	SRX21296459	SRS18545737	SRP453968	PRJNA1003386	Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish	GSE240329	Transcriptome Analysis	To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.		pubmed:38742432	EC tie1 WT/Het replicate 2 RNAseq	GSM7696244	source name:wild type and heterozygous siblings\|tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed\|geo loc name:missing\|collection date:missing	EC tie1 WT/Het replicate 2 RNAseq	RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.	wild type and heterozygous siblings		Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760		tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed	GSM7696244	GSM7696244: EC tie1 WT/Het replicate 2 RNAseq; Danio rerio; RNA Seq	GSM7696244 r1	GSM7696244	1	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP453968		411-Tie1-WT-HT2_S2_L002_R1_001.fastq.gz	fastq	384487572.0	5059047.0	GSM7696244 r2	0:76	A:121620414;C:71266999;G:70967086;T:120577709;N:55364	76			121620414	71266999	70967086	120577709	55364	SRX21296459	SRS18545737	SRA1688627	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.77986		0.59517		0.73547		0.48651		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	Japan	2023-08-08	Pharyngula	Embryo	Multi-tissue	Multi-system
25101	25101	SRR25567713	SRX21296459	SRS18545737	SRP453968	PRJNA1003386	Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish	GSE240329	Transcriptome Analysis	To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.		pubmed:38742432	EC tie1 WT/Het replicate 2 RNAseq	GSM7696244	source name:wild type and heterozygous siblings\|tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed\|geo loc name:missing\|collection date:missing	EC tie1 WT/Het replicate 2 RNAseq	RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.	wild type and heterozygous siblings		Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760		tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed	GSM7696244	GSM7696244: EC tie1 WT/Het replicate 2 RNAseq; Danio rerio; RNA Seq	GSM7696244 r1	GSM7696244	1	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP453968		411-Tie1-WT-HT2_S2_L003_R1_001.fastq.gz	fastq	399939360.0	5262360.0	GSM7696244 r3	0:76	A:126400057;C:74196301;G:73931308;T:125379595;N:32099	76			126400057	74196301	73931308	125379595	32099	SRX21296459	SRS18545737	SRA1688627	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.77917		0.59465		0.7359		0.48952		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	Japan	2023-08-08	Pharyngula	Embryo	Multi-tissue	Multi-system
25102	25102	SRR25567714	SRX21296459	SRS18545737	SRP453968	PRJNA1003386	Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish	GSE240329	Transcriptome Analysis	To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.		pubmed:38742432	EC tie1 WT/Het replicate 2 RNAseq	GSM7696244	source name:wild type and heterozygous siblings\|tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed\|geo loc name:missing\|collection date:missing	EC tie1 WT/Het replicate 2 RNAseq	RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.	wild type and heterozygous siblings		Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760		tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed	GSM7696244	GSM7696244: EC tie1 WT/Het replicate 2 RNAseq; Danio rerio; RNA Seq	GSM7696244 r1	GSM7696244	1	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP453968		411-Tie1-WT-HT2_S2_L004_R1_001.fastq.gz	fastq	398035712.0	5237312.0	GSM7696244 r4	0:76	A:125843687;C:73845902;G:73489490;T:124828195;N:28438	76			125843687	73845902	73489490	124828195	28438	SRX21296459	SRS18545737	SRA1688627	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.77934		0.59613		0.73608		0.48475		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	Japan	2023-08-08	Pharyngula	Embryo	Multi-tissue	Multi-system
25103	25103	SRR25567715	SRX21296458	SRS18545736	SRP453968	PRJNA1003386	Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish	GSE240329	Transcriptome Analysis	To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.		pubmed:38742432	EC tie1 WT/Het replicate 1 RNAseq	GSM7696243	source name:wild type and heterozygous siblings\|tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed\|geo loc name:missing\|collection date:missing	EC tie1 WT/Het replicate 1 RNAseq	RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.	wild type and heterozygous siblings		Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760		tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed	GSM7696243	GSM7696243: EC tie1 WT/Het replicate 1 RNAseq; Danio rerio; RNA Seq	GSM7696243 r1	GSM7696243	1	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP453968		410-Tie1-WT-HT1_S1_L001_R1_001.fastq.gz	fastq	412291944.0	5424894.0	GSM7696243 r1	0:76	A:129182868;C:77123147;G:77053023;T:128887593;N:45313	76			129182868	77123147	77053023	128887593	45313	SRX21296458	SRS18545736	SRA1688627	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.79085		0.52962		0.7349		0.48594		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	Japan	2023-08-08	Pharyngula	Embryo	Multi-tissue	Multi-system
25104	25104	SRR25567716	SRX21296458	SRS18545736	SRP453968	PRJNA1003386	Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish	GSE240329	Transcriptome Analysis	To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.		pubmed:38742432	EC tie1 WT/Het replicate 1 RNAseq	GSM7696243	source name:wild type and heterozygous siblings\|tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed\|geo loc name:missing\|collection date:missing	EC tie1 WT/Het replicate 1 RNAseq	RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.	wild type and heterozygous siblings		Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760		tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed	GSM7696243	GSM7696243: EC tie1 WT/Het replicate 1 RNAseq; Danio rerio; RNA Seq	GSM7696243 r1	GSM7696243	1	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP453968		410-Tie1-WT-HT1_S1_L002_R1_001.fastq.gz	fastq	404294768.0	5319668.0	GSM7696243 r2	0:76	A:126685179;C:75658897;G:75455501;T:126437486;N:57705	76			126685179	75658897	75455501	126437486	57705	SRX21296458	SRS18545736	SRA1688627	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.79163		0.52938		0.73304		0.48118		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	Japan	2023-08-08	Pharyngula	Embryo	Multi-tissue	Multi-system
25105	25105	SRR25567717	SRX21296458	SRS18545736	SRP453968	PRJNA1003386	Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish	GSE240329	Transcriptome Analysis	To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.		pubmed:38742432	EC tie1 WT/Het replicate 1 RNAseq	GSM7696243	source name:wild type and heterozygous siblings\|tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed\|geo loc name:missing\|collection date:missing	EC tie1 WT/Het replicate 1 RNAseq	RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.	wild type and heterozygous siblings		Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760		tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed	GSM7696243	GSM7696243: EC tie1 WT/Het replicate 1 RNAseq; Danio rerio; RNA Seq	GSM7696243 r1	GSM7696243	1	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP453968		410-Tie1-WT-HT1_S1_L003_R1_001.fastq.gz	fastq	419693128.0	5522278.0	GSM7696243 r3	0:76	A:131491219;C:78551884;G:78434940;T:131179828;N:35257	76			131491219	78551884	78434940	131179828	35257	SRX21296458	SRS18545736	SRA1688627	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.79077		0.52836		0.73419		0.48215		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	Japan	2023-08-08	Pharyngula	Embryo	Multi-tissue	Multi-system
25106	25106	SRR25567718	SRX21296458	SRS18545736	SRP453968	PRJNA1003386	Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish	GSE240329	Transcriptome Analysis	To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.		pubmed:38742432	EC tie1 WT/Het replicate 1 RNAseq	GSM7696243	source name:wild type and heterozygous siblings\|tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed\|geo loc name:missing\|collection date:missing	EC tie1 WT/Het replicate 1 RNAseq	RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.	wild type and heterozygous siblings		Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760		tissue:Trunk and Tail\|cell type:Endothelial cells\|genotype:Tgkdrl:EGFP;Tglyve1:DsRed	GSM7696243	GSM7696243: EC tie1 WT/Het replicate 1 RNAseq; Danio rerio; RNA Seq	GSM7696243 r1	GSM7696243	1	Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP453968		410-Tie1-WT-HT1_S1_L004_R1_001.fastq.gz	fastq	418155268.0	5502043.0	GSM7696243 r4	0:76	A:130978746;C:78285682;G:78062725;T:130798846;N:29269	76			130978746	78285682	78062725	130798846	29269	SRX21296458	SRS18545736	SRA1688627	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.78728		0.52541		0.73484		0.48813		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	Japan	2023-08-08	Pharyngula	Embryo	Multi-tissue	Multi-system
29808	29808	SRR27450807	SRX23122487	SRS20076037	SRP482328	PRJNA1061565	Akt is the main kinase mediating the embryonic specification of artery cells	GSE252648	Transcriptome Analysis	This study aimed at understanding the function of Akt signaling in vascular development in Zebrafish. Overall design: This study used Zebrafish endothelial cells sorted from WT and akt full mutant embryos at 24hpf. Endothelial cells were sorted via the use of transgenic line kdrl:mCherry+. Only mCherry+ were sequenced. So here you can find sample WT and sample akt mutant.		pubmed:39101673	Zebrafish EC 24hpf Aktmutant	GSM8004755	source name:FAC sorted cells\|tissue:FAC sorted cells\|cell line:kdrl:mCherry+\|cell type:Endothelial Cells\|genotype:Aktmutant\|geo loc name:missing\|collection date:missing	Zebrafish EC 24hpf Aktmutant	The barcoded processing gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Supplementary files format and content: Tab separated values files and matrix files Assembly: Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: 3 files of barcodes features and matrix	FAC sorted cells	No treatments	Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics	Normal zebrafish growth condition	tissue:FAC sorted cells\|cell line:kdrl:mCherry+\|cell type:Endothelial Cells\|genotype:Aktmutant	GSM8004755	GSM8004755: Zebrafish EC 24hpf Aktmutant; Danio rerio; RNA Seq	GSM8004755 r1	GSM8004755	1	Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP482328	loader:fastq load.py	mu1-23-19_DRT_S2_L001_I1_001.fastq.gz mu1-23-19_DRT_S2_L001_R1_001.fastq.gz mu1-23-19_DRT_S2_L001_R2_001.fastq.gz	fastq fastq fastq	23281472741.0	183318683.0	GSM8004755 r1	0:8 1:28 2:91	A:4703583066;C:3702175361;G:3998796644;T:4271932211;N:5512871	8	28	91	4703583066	3702175361	3998796644	4271932211	5512871	SRX23122487	SRS20076037	SRA1780571	Nicoli lab, School of Medicine, Yale University	Nicoli lab, School of Medicine, Yale University												B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-01-05	Pharyngula	Embryo	Multi-tissue	Multi-system
29809	29809	SRR27450808	SRX23122487	SRS20076037	SRP482328	PRJNA1061565	Akt is the main kinase mediating the embryonic specification of artery cells	GSE252648	Transcriptome Analysis	This study aimed at understanding the function of Akt signaling in vascular development in Zebrafish. Overall design: This study used Zebrafish endothelial cells sorted from WT and akt full mutant embryos at 24hpf. Endothelial cells were sorted via the use of transgenic line kdrl:mCherry+. Only mCherry+ were sequenced. So here you can find sample WT and sample akt mutant.		pubmed:39101673	Zebrafish EC 24hpf Aktmutant	GSM8004755	source name:FAC sorted cells\|tissue:FAC sorted cells\|cell line:kdrl:mCherry+\|cell type:Endothelial Cells\|genotype:Aktmutant\|geo loc name:missing\|collection date:missing	Zebrafish EC 24hpf Aktmutant	The barcoded processing gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Supplementary files format and content: Tab separated values files and matrix files Assembly: Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: 3 files of barcodes features and matrix	FAC sorted cells	No treatments	Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics	Normal zebrafish growth condition	tissue:FAC sorted cells\|cell line:kdrl:mCherry+\|cell type:Endothelial Cells\|genotype:Aktmutant	GSM8004755	GSM8004755: Zebrafish EC 24hpf Aktmutant; Danio rerio; RNA Seq	GSM8004755 r1	GSM8004755	1	Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP482328	loader:fastq load.py	mu1-23-19_DRT_S2_L002_I1_001.fastq.gz mu1-23-19_DRT_S2_L002_R1_001.fastq.gz mu1-23-19_DRT_S2_L002_R2_001.fastq.gz	fastq fastq fastq	21009317138.0	165427694.0	GSM8004755 r2	0:8 1:28 2:91	A:4231955850;C:3363548064;G:3603913589;T:3849411287;N:5091364	8	28	91	4231955850	3363548064	3603913589	3849411287	5091364	SRX23122487	SRS20076037	SRA1780571	Nicoli lab, School of Medicine, Yale University	Nicoli lab, School of Medicine, Yale University												B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-01-05	Pharyngula	Embryo	Multi-tissue	Multi-system
29810	29810	SRR27450809	SRX23122486	SRS20076036	SRP482328	PRJNA1061565	Akt is the main kinase mediating the embryonic specification of artery cells	GSE252648	Transcriptome Analysis	This study aimed at understanding the function of Akt signaling in vascular development in Zebrafish. Overall design: This study used Zebrafish endothelial cells sorted from WT and akt full mutant embryos at 24hpf. Endothelial cells were sorted via the use of transgenic line kdrl:mCherry+. Only mCherry+ were sequenced. So here you can find sample WT and sample akt mutant.		pubmed:39101673	Zebrafish EC 24hpf WT	GSM8004754	source name:FAC sorted cells\|tissue:FAC sorted cells\|cell line:kdrl:mCherry+\|cell type:Endothelial Cells\|genotype:WT\|geo loc name:missing\|collection date:missing	Zebrafish EC 24hpf WT	The barcoded processing gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Supplementary files format and content: Tab separated values files and matrix files Assembly: Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: 3 files of barcodes features and matrix	FAC sorted cells	No treatments	Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics	Normal zebrafish growth condition	tissue:FAC sorted cells\|cell line:kdrl:mCherry+\|cell type:Endothelial Cells\|genotype:WT	GSM8004754	GSM8004754: Zebrafish EC 24hpf WT; Danio rerio; RNA Seq	GSM8004754 r1	GSM8004754	1	Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP482328	loader:fastq load.py	wt1-23-19_DRT_S1_L001_I1_001.fastq.gz wt1-23-19_DRT_S1_L001_R1_001.fastq.gz wt1-23-19_DRT_S1_L001_R2_001.fastq.gz	fastq fastq fastq	22261273232.0	175285616.0	GSM8004754 r1	0:8 1:28 2:91	A:4475749188;C:3578353646;G:3836029871;T:4055646794;N:5211557	8	28	91	4475749188	3578353646	3836029871	4055646794	5211557	SRX23122486	SRS20076036	SRA1780571	Nicoli lab, School of Medicine, Yale University	Nicoli lab, School of Medicine, Yale University												B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-01-05	Pharyngula	Embryo	Multi-tissue	Multi-system
29811	29811	SRR27450810	SRX23122486	SRS20076036	SRP482328	PRJNA1061565	Akt is the main kinase mediating the embryonic specification of artery cells	GSE252648	Transcriptome Analysis	This study aimed at understanding the function of Akt signaling in vascular development in Zebrafish. Overall design: This study used Zebrafish endothelial cells sorted from WT and akt full mutant embryos at 24hpf. Endothelial cells were sorted via the use of transgenic line kdrl:mCherry+. Only mCherry+ were sequenced. So here you can find sample WT and sample akt mutant.		pubmed:39101673	Zebrafish EC 24hpf WT	GSM8004754	source name:FAC sorted cells\|tissue:FAC sorted cells\|cell line:kdrl:mCherry+\|cell type:Endothelial Cells\|genotype:WT\|geo loc name:missing\|collection date:missing	Zebrafish EC 24hpf WT	The barcoded processing gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Supplementary files format and content: Tab separated values files and matrix files Assembly: Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: 3 files of barcodes features and matrix	FAC sorted cells	No treatments	Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics	Normal zebrafish growth condition	tissue:FAC sorted cells\|cell line:kdrl:mCherry+\|cell type:Endothelial Cells\|genotype:WT	GSM8004754	GSM8004754: Zebrafish EC 24hpf WT; Danio rerio; RNA Seq	GSM8004754 r1	GSM8004754	1	Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP482328	loader:fastq load.py	wt1-23-19_DRT_S1_L002_I1_001.fastq.gz wt1-23-19_DRT_S1_L002_R1_001.fastq.gz wt1-23-19_DRT_S1_L002_R2_001.fastq.gz	fastq fastq fastq	20084395188.0	158144844.0	GSM8004754 r2	0:8 1:28 2:91	A:4028678970;C:3250176957;G:3455600305;T:3651884457;N:4840115	8	28	91	4028678970	3250176957	3455600305	3651884457	4840115	SRX23122486	SRS20076036	SRA1780571	Nicoli lab, School of Medicine, Yale University	Nicoli lab, School of Medicine, Yale University												B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-01-05	Pharyngula	Embryo	Multi-tissue	Multi-system
49611	49611	SRR7989641	SRX4820831	SRS3895222	SRP164769	PRJNA495391	Wnt/ß catenin signaling regulates VE cadherin mediated anastomosis of brain capillaries by counteracting S1pr1 signaling	GSE121041	Transcriptome Analysis	Canonical Wnt signaling is crucial for vascularization of the central nervous system and blood brain barrier BBB formation. BBB formation and modulation are not only important for development but also relevant for vascular and neurodegenerative diseases. However beyond the early requirement of Wnt signaling for brain capillary development there is little understanding of how Wnt signaling further contributes to brain angiogenesis and BBB formation. By combining high resolution in vivo imaging with temporally and spatially controlled manipulation of Wnt signaling we were able to dissect different requirements for Wnt signaling during brain angiogenesis and BBB formation. In the absence of Wnt signaling premature Sphingosine 1 phosphate receptor S1pr signaling leads to a reduction of VE cadherin and Esama at cell cell junctions. Wnt signaling most likely suppresses S1pr signaling during angiogenesis to enable the dynamic junction formation during anastomosis whereas later S1pr signaling regulates BBB maturation and VE cadherin stabilization. Our data provides a novel link between brain capillary angiogenesis and BBB formation and identifies Wnt signaling as coordinator of the timing and as regulator of anastomosis. Overall design: Isolation of the zebrafish CtA endothelial cells from 36hpf old Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos treated with IWR 1 or DMSO		pubmed:30451830;pubmed:38570687	IWR 1 rep3	GSM3424991	source name:brain endothelial cells\|lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos\|tissue:hindbrain endothelium\|age:36hpf	IWR 1 rep3	Raw reads were assessed for quality adapter content and duplication rates with FastQC available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “ outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Genome build: DanRer10 Supplementary files format and content: tab delimited text files include library size normlized counts per gene	brain endothelial cells		Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser 5 iterations 50s. post several washes in HBSS Hank’s Balanced Salt Solution Gibco without xxx+/Mg2+ zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged frozen by liquid nitrogen and stored at 80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.		lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos\|tissue:hindbrain endothelium\|age:36hpf	GSM3424991	GSM3424991: IWR 1 rep3; Danio rerio; RNA Seq	GSM3424991		1	Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser 5 iterations 50s. post several washes in HBSS Hank's Balanced Salt Solution Gibco without xxx+/Mg2+ zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged frozen by liquid nitrogen and stored at 80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.	GEO Accession:GSM3424991	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP164769		vanHollebeke_IWR_4_R1.fastq.gz	fastq	2256000713.0	30503539.0	GSM3424991 r1	0:73.96 1:0	A:657293471;C:471495202;G:469388740;T:657813037;N:10263	73	0		657293471	471495202	469388740	657813037	10263	SRX4820831	SRS3895222	SRA791232	GEO	MPI for heart and lung research	1	0.82891		0.22262		0.78894		0.52843		75		B		usable mapping rate	illumina	nextseq	full_length	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Germany	2018-10-09	Pharyngula	Embryo	Multi-tissue	Multi-system
49612	49612	SRR7989640	SRX4820830	SRS3895220	SRP164769	PRJNA495391	Wnt/ß catenin signaling regulates VE cadherin mediated anastomosis of brain capillaries by counteracting S1pr1 signaling	GSE121041	Transcriptome Analysis	Canonical Wnt signaling is crucial for vascularization of the central nervous system and blood brain barrier BBB formation. BBB formation and modulation are not only important for development but also relevant for vascular and neurodegenerative diseases. However beyond the early requirement of Wnt signaling for brain capillary development there is little understanding of how Wnt signaling further contributes to brain angiogenesis and BBB formation. By combining high resolution in vivo imaging with temporally and spatially controlled manipulation of Wnt signaling we were able to dissect different requirements for Wnt signaling during brain angiogenesis and BBB formation. In the absence of Wnt signaling premature Sphingosine 1 phosphate receptor S1pr signaling leads to a reduction of VE cadherin and Esama at cell cell junctions. Wnt signaling most likely suppresses S1pr signaling during angiogenesis to enable the dynamic junction formation during anastomosis whereas later S1pr signaling regulates BBB maturation and VE cadherin stabilization. Our data provides a novel link between brain capillary angiogenesis and BBB formation and identifies Wnt signaling as coordinator of the timing and as regulator of anastomosis. Overall design: Isolation of the zebrafish CtA endothelial cells from 36hpf old Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos treated with IWR 1 or DMSO		pubmed:30451830;pubmed:38570687	IWR 1 rep2	GSM3424990	source name:brain endothelial cells\|lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos\|tissue:hindbrain endothelium\|age:36hpf	IWR 1 rep2	Raw reads were assessed for quality adapter content and duplication rates with FastQC available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “ outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Genome build: DanRer10 Supplementary files format and content: tab delimited text files include library size normlized counts per gene	brain endothelial cells		Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser 5 iterations 50s. post several washes in HBSS Hank’s Balanced Salt Solution Gibco without xxx+/Mg2+ zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged frozen by liquid nitrogen and stored at 80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.		lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos\|tissue:hindbrain endothelium\|age:36hpf	GSM3424990	GSM3424990: IWR 1 rep2; Danio rerio; RNA Seq	GSM3424990		1	Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser 5 iterations 50s. post several washes in HBSS Hank's Balanced Salt Solution Gibco without xxx+/Mg2+ zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged frozen by liquid nitrogen and stored at 80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.	GEO Accession:GSM3424990	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP164769		vanHollebeke_IWR_3_R1.fastq.gz	fastq	2320219813.0	31532406.0	GSM3424990 r1	0:73.58 1:0	A:660022378;C:501448817;G:498586533;T:660148405;N:13680	73	0		660022378	501448817	498586533	660148405	13680	SRX4820830	SRS3895220	SRA791232	GEO	MPI for heart and lung research	1	0.76766		0.17893		0.78206		0.5236		74		B		usable mapping rate	illumina	nextseq	full_length	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Germany	2018-10-09	Pharyngula	Embryo	Multi-tissue	Multi-system
49613	49613	SRR7989639	SRX4820829	SRS3895221	SRP164769	PRJNA495391	Wnt/ß catenin signaling regulates VE cadherin mediated anastomosis of brain capillaries by counteracting S1pr1 signaling	GSE121041	Transcriptome Analysis	Canonical Wnt signaling is crucial for vascularization of the central nervous system and blood brain barrier BBB formation. BBB formation and modulation are not only important for development but also relevant for vascular and neurodegenerative diseases. However beyond the early requirement of Wnt signaling for brain capillary development there is little understanding of how Wnt signaling further contributes to brain angiogenesis and BBB formation. By combining high resolution in vivo imaging with temporally and spatially controlled manipulation of Wnt signaling we were able to dissect different requirements for Wnt signaling during brain angiogenesis and BBB formation. In the absence of Wnt signaling premature Sphingosine 1 phosphate receptor S1pr signaling leads to a reduction of VE cadherin and Esama at cell cell junctions. Wnt signaling most likely suppresses S1pr signaling during angiogenesis to enable the dynamic junction formation during anastomosis whereas later S1pr signaling regulates BBB maturation and VE cadherin stabilization. Our data provides a novel link between brain capillary angiogenesis and BBB formation and identifies Wnt signaling as coordinator of the timing and as regulator of anastomosis. Overall design: Isolation of the zebrafish CtA endothelial cells from 36hpf old Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos treated with IWR 1 or DMSO		pubmed:30451830;pubmed:38570687	IWR 1 rep1	GSM3424989	source name:brain endothelial cells\|lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos\|tissue:hindbrain endothelium\|age:36hpf	IWR 1 rep1	Raw reads were assessed for quality adapter content and duplication rates with FastQC available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “ outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Genome build: DanRer10 Supplementary files format and content: tab delimited text files include library size normlized counts per gene	brain endothelial cells		Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser 5 iterations 50s. post several washes in HBSS Hank’s Balanced Salt Solution Gibco without xxx+/Mg2+ zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged frozen by liquid nitrogen and stored at 80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.		lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos\|tissue:hindbrain endothelium\|age:36hpf	GSM3424989	GSM3424989: IWR 1 rep1; Danio rerio; RNA Seq	GSM3424989		1	Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser 5 iterations 50s. post several washes in HBSS Hank's Balanced Salt Solution Gibco without xxx+/Mg2+ zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged frozen by liquid nitrogen and stored at 80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.	GEO Accession:GSM3424989	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP164769		vanHollebeke_IWR_1_R1.fastq.gz	fastq	3130301804.0	42242865.0	GSM3424989 r1	0:74.10 1:0	A:906281071;C:658248293;G:654046147;T:911712569;N:13724	74	0		906281071	658248293	654046147	911712569	13724	SRX4820829	SRS3895221	SRA791232	GEO	MPI for heart and lung research	1	0.83335		0.2301		0.77703		0.51424		75		B		usable mapping rate	illumina	nextseq	full_length	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Germany	2018-10-09	Pharyngula	Embryo	Multi-tissue	Multi-system
49614	49614	SRR7989638	SRX4820828	SRS3895223	SRP164769	PRJNA495391	Wnt/ß catenin signaling regulates VE cadherin mediated anastomosis of brain capillaries by counteracting S1pr1 signaling	GSE121041	Transcriptome Analysis	Canonical Wnt signaling is crucial for vascularization of the central nervous system and blood brain barrier BBB formation. BBB formation and modulation are not only important for development but also relevant for vascular and neurodegenerative diseases. However beyond the early requirement of Wnt signaling for brain capillary development there is little understanding of how Wnt signaling further contributes to brain angiogenesis and BBB formation. By combining high resolution in vivo imaging with temporally and spatially controlled manipulation of Wnt signaling we were able to dissect different requirements for Wnt signaling during brain angiogenesis and BBB formation. In the absence of Wnt signaling premature Sphingosine 1 phosphate receptor S1pr signaling leads to a reduction of VE cadherin and Esama at cell cell junctions. Wnt signaling most likely suppresses S1pr signaling during angiogenesis to enable the dynamic junction formation during anastomosis whereas later S1pr signaling regulates BBB maturation and VE cadherin stabilization. Our data provides a novel link between brain capillary angiogenesis and BBB formation and identifies Wnt signaling as coordinator of the timing and as regulator of anastomosis. Overall design: Isolation of the zebrafish CtA endothelial cells from 36hpf old Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos treated with IWR 1 or DMSO		pubmed:30451830;pubmed:38570687	DMSO rep3	GSM3424988	source name:brain endothelial cells\|lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos\|tissue:hindbrain endothelium\|age:36hpf	DMSO rep3	Raw reads were assessed for quality adapter content and duplication rates with FastQC available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “ outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Genome build: DanRer10 Supplementary files format and content: tab delimited text files include library size normlized counts per gene	brain endothelial cells		Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser 5 iterations 50s. post several washes in HBSS Hank’s Balanced Salt Solution Gibco without xxx+/Mg2+ zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged frozen by liquid nitrogen and stored at 80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.		lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos\|tissue:hindbrain endothelium\|age:36hpf	GSM3424988	GSM3424988: DMSO rep3; Danio rerio; RNA Seq	GSM3424988		1	Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser 5 iterations 50s. post several washes in HBSS Hank's Balanced Salt Solution Gibco without xxx+/Mg2+ zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged frozen by liquid nitrogen and stored at 80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.	GEO Accession:GSM3424988	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP164769		vanHollebeke_WT_3_R1.fastq.gz	fastq	2942028868.0	39840018.0	GSM3424988 r1	0:73.85 1:0	A:849808636;C:623040120;G:619275913;T:849871928;N:32271	73	0		849808636	623040120	619275913	849871928	32271	SRX4820828	SRS3895223	SRA791232	GEO	MPI for heart and lung research	1	0.83348		0.20415		0.79147		0.51054		74		B		usable mapping rate	illumina	nextseq	full_length	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Germany	2018-10-09	Pharyngula	Embryo	Multi-tissue	Multi-system
49615	49615	SRR7989637	SRX4820827	SRS3895219	SRP164769	PRJNA495391	Wnt/ß catenin signaling regulates VE cadherin mediated anastomosis of brain capillaries by counteracting S1pr1 signaling	GSE121041	Transcriptome Analysis	Canonical Wnt signaling is crucial for vascularization of the central nervous system and blood brain barrier BBB formation. BBB formation and modulation are not only important for development but also relevant for vascular and neurodegenerative diseases. However beyond the early requirement of Wnt signaling for brain capillary development there is little understanding of how Wnt signaling further contributes to brain angiogenesis and BBB formation. By combining high resolution in vivo imaging with temporally and spatially controlled manipulation of Wnt signaling we were able to dissect different requirements for Wnt signaling during brain angiogenesis and BBB formation. In the absence of Wnt signaling premature Sphingosine 1 phosphate receptor S1pr signaling leads to a reduction of VE cadherin and Esama at cell cell junctions. Wnt signaling most likely suppresses S1pr signaling during angiogenesis to enable the dynamic junction formation during anastomosis whereas later S1pr signaling regulates BBB maturation and VE cadherin stabilization. Our data provides a novel link between brain capillary angiogenesis and BBB formation and identifies Wnt signaling as coordinator of the timing and as regulator of anastomosis. Overall design: Isolation of the zebrafish CtA endothelial cells from 36hpf old Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos treated with IWR 1 or DMSO		pubmed:30451830;pubmed:38570687	DMSO rep2	GSM3424987	source name:brain endothelial cells\|lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos\|tissue:hindbrain endothelium\|age:36hpf	DMSO rep2	Raw reads were assessed for quality adapter content and duplication rates with FastQC available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “ outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Genome build: DanRer10 Supplementary files format and content: tab delimited text files include library size normlized counts per gene	brain endothelial cells		Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser 5 iterations 50s. post several washes in HBSS Hank’s Balanced Salt Solution Gibco without xxx+/Mg2+ zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged frozen by liquid nitrogen and stored at 80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.		lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos\|tissue:hindbrain endothelium\|age:36hpf	GSM3424987	GSM3424987: DMSO rep2; Danio rerio; RNA Seq	GSM3424987		1	Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser 5 iterations 50s. post several washes in HBSS Hank's Balanced Salt Solution Gibco without xxx+/Mg2+ zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged frozen by liquid nitrogen and stored at 80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.	GEO Accession:GSM3424987	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP164769		vanHollebeke_WT_2_R1.fastq.gz	fastq	2807935583.0	38002656.0	GSM3424987 r1	0:73.89 1:0	A:815631502;C:589381721;G:586257915;T:816652021;N:12424	73	0		815631502	589381721	586257915	816652021	12424	SRX4820827	SRS3895219	SRA791232	GEO	MPI for heart and lung research	1	0.84347		0.20267		0.77419		0.51656		75		B		usable mapping rate	illumina	nextseq	full_length	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Germany	2018-10-09	Pharyngula	Embryo	Multi-tissue	Multi-system
49616	49616	SRR7989636	SRX4820826	SRS3895218	SRP164769	PRJNA495391	Wnt/ß catenin signaling regulates VE cadherin mediated anastomosis of brain capillaries by counteracting S1pr1 signaling	GSE121041	Transcriptome Analysis	Canonical Wnt signaling is crucial for vascularization of the central nervous system and blood brain barrier BBB formation. BBB formation and modulation are not only important for development but also relevant for vascular and neurodegenerative diseases. However beyond the early requirement of Wnt signaling for brain capillary development there is little understanding of how Wnt signaling further contributes to brain angiogenesis and BBB formation. By combining high resolution in vivo imaging with temporally and spatially controlled manipulation of Wnt signaling we were able to dissect different requirements for Wnt signaling during brain angiogenesis and BBB formation. In the absence of Wnt signaling premature Sphingosine 1 phosphate receptor S1pr signaling leads to a reduction of VE cadherin and Esama at cell cell junctions. Wnt signaling most likely suppresses S1pr signaling during angiogenesis to enable the dynamic junction formation during anastomosis whereas later S1pr signaling regulates BBB maturation and VE cadherin stabilization. Our data provides a novel link between brain capillary angiogenesis and BBB formation and identifies Wnt signaling as coordinator of the timing and as regulator of anastomosis. Overall design: Isolation of the zebrafish CtA endothelial cells from 36hpf old Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos treated with IWR 1 or DMSO		pubmed:30451830;pubmed:38570687	DMSO rep1	GSM3424986	source name:brain endothelial cells\|lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos\|tissue:hindbrain endothelium\|age:36hpf	DMSO rep1	Raw reads were assessed for quality adapter content and duplication rates with FastQC available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “ outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Genome build: DanRer10 Supplementary files format and content: tab delimited text files include library size normlized counts per gene	brain endothelial cells		Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser 5 iterations 50s. post several washes in HBSS Hank’s Balanced Salt Solution Gibco without xxx+/Mg2+ zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged frozen by liquid nitrogen and stored at 80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.		lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos\|tissue:hindbrain endothelium\|age:36hpf	GSM3424986	GSM3424986: DMSO rep1; Danio rerio; RNA Seq	GSM3424986		1	Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser 5 iterations 50s. post several washes in HBSS Hank's Balanced Salt Solution Gibco without xxx+/Mg2+ zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged frozen by liquid nitrogen and stored at 80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.	GEO Accession:GSM3424986	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP164769		vanHollebeke_WT_1_R1.fastq.gz	fastq	2675908817.0	36130876.0	GSM3424986 r1	0:74.06 1:0	A:789957205;C:549799082;G:546545868;T:789594811;N:11851	74	0		789957205	549799082	546545868	789594811	11851	SRX4820826	SRS3895218	SRA791232	GEO	MPI for heart and lung research	1	0.90594		0.2159		0.76765		0.50407		75		B		usable mapping rate	illumina	nextseq	full_length	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Germany	2018-10-09	Pharyngula	Embryo	Multi-tissue	Multi-system
53493	53493	SRR9881612	SRX6634133	SRS5205093	SRP217216	PRJNA558070	N Glycome regulation limits the transdifferentiation of endothelial cells into hematopoietic stem cells	GSE135246	Transcriptome Analysis	Hematopoietic stem and progenitor cells HSPCs are required to establish and maintain the adult blood system in vertebrates. During development HPSCs are generated from hemogenic endothelial cells that undergo an endothelial to hematopoietic transition EHT. Growth factors and epigenetic changes can promote EHT but these mechanisms do not explain its tight spatiotemporal regulation during development. Here we show that microRNA miR miR 223 mediated regulation of N glycan biosynthesis intrinsically restrains EHT representing a new pathway that prevents excessive HSPC production. We find that miR 223 is uniquely expressed in hemogenic endothelial cells undergoing EHT and in nascent HSPCs. Loss of miR 223 promotes the expansion of these cells in the zebrafish and mouse aorta gonad mesonephros AGM where EHT occurs. miR 223 targets alg2 alpha 1 3/ 1 6 mannosyltransferase in the AGM endothelium to restrict hemogenic and HSPC specification. This enzyme is involved in the attachment of the N glycans a common co translational modification9 12 that influences several pathophysiological processes but has not yet been implicated in EHT. Using an N glycosensor we demonstrate that abundant protein N glycan attachment occurs in vascular cells during EHT and this process is required for HSPC production. High throughput glycome analysis upon loss of miR 223 revealed that terminal alpha 1 3/6 mannose modifications are increased at the expense of alpha 2 3/6 sialic acid sugars. Importantly pharmacological manipulation targeting these N glycan types in wild type embryos phenocopies the loss of miR 223 and enhances EHT as well as HSPC production. Thus the N glycome plays a previously unappreciated role as an intrinsic regulator of EHT with specific mannose and sialic acid modifications serving as key endothelial determinants to restrict the hematopoietic fate. Overall design: Single cell RNA sequencing for zebrafish Tgkdrl:hras mCherrys896 endothelial cells at 27 hpf for wildtype and miR 223ya303 backgrounds		pubmed:33273096	223mut 27hpf EC1	GSM3996907	source name:endothelial cell\|tissue:trunk endothelium\|cell type:endothelial cell\|developmental stage:27 hpf 223:KalTA4ya363; Tg5xUAS:eGFPnkuasgfp1a; Tgkdrl:hras mCherrys896; miR 223ya303\|genotype:223mut	223mut 27hpf EC1	The reads were demultiplexed using bcl2fastq provided by the 10X genomics. The demultiplexed reads were aligned to the reference genome Grz11 modified to add mCherry GAL4 and eGFP to obtain digital gene expression matrix data using cellranger program The output of the cellranger was then processed using Seurat in R. All the cells with less than 200 unique transcripts were eliminared. All genes which are expressed in less than 3 cells were also eliminated. The data was normalized using sctransform and then clustered. The clusters were projected for viualization in R using the PHATE algorithm. Genome build: GRCz11 Supplementary files format and content: Average Gene expression matrix for average gene expression per cluster per condition. This is a tab separated values file where each row represents a gene and each column represents the cluster and the condition and each cell represents normalized expression values across all the cells in that cluster for that condition.	endothelial cell		Trunk tissue was dissected from 27 hpf zebrafish embryos under 0.1% tricaine anesthesia and then disassociated into a single cell suspension using 0.25 mg/ml liberase for 45 minutes. Tgkdrl:hras mCherrys896 endothelial cells were isolated from the single cell suspension via FACS into 0.04% BSA in PBS and applied to the 10X genomics single cell RNA sequencing platform. 10 X genomics Chromium Next GEM Single Cell 3’ Library Construction Kit v2.1	Zebrafish were raised and maintained at 28.5˚C using standard methods and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2017 11473.	tissue:trunk endothelium\|cell type:endothelial cell\|developmental stage:27 hpf 223:KalTA4ya363; Tg5xUAS:eGFPnkuasgfp1a; Tgkdrl:hras mCherrys896; miR 223ya303\|genotype:223mut	GSM3996907	GSM3996907: 223mut 27hpf EC1; Danio rerio; RNA Seq	GSM3996907		1	Trunk tissue was dissected from 27 hpf zebrafish embryos under 0.1% tricaine anesthesia and then disassociated into a single cell suspension using 0.25 mg/ml liberase for 45 minutes. Tgkdrl:hras mCherrys896 endothelial cells were isolated from the single cell suspension via FACS into 0.04% BSA in PBS and applied to the 10X genomics single cell RNA sequencing platform. 10 X genomics Chromium Next GEM Single Cell three prime Library Construction Kit v2.1	GEO Accession:GSM3996907	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP217216		Mut_pssorted_genome_bam.bam	10X Genomics bam file	31174899854.0	318111223.0	GSM3996907 r1	0:98	A:8464403532;C:7291172763;G:7282393533;T:8131647604;N:5282422	98			8464403532	7291172763	7282393533	8131647604	5282422	SRX6634133	SRS5205093	SRA930499	GEO	Internal Medicine, Yale University	1	0.92745		0.05306		0.84502		0.46383		98		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	sc	single_cell_droplet	10x	United States	2019-08-01	Pharyngula	Embryo	Multi-tissue	Multi-system
53494	53494	SRR9881611	SRX6634132	SRS5205092	SRP217216	PRJNA558070	N Glycome regulation limits the transdifferentiation of endothelial cells into hematopoietic stem cells	GSE135246	Transcriptome Analysis	Hematopoietic stem and progenitor cells HSPCs are required to establish and maintain the adult blood system in vertebrates. During development HPSCs are generated from hemogenic endothelial cells that undergo an endothelial to hematopoietic transition EHT. Growth factors and epigenetic changes can promote EHT but these mechanisms do not explain its tight spatiotemporal regulation during development. Here we show that microRNA miR miR 223 mediated regulation of N glycan biosynthesis intrinsically restrains EHT representing a new pathway that prevents excessive HSPC production. We find that miR 223 is uniquely expressed in hemogenic endothelial cells undergoing EHT and in nascent HSPCs. Loss of miR 223 promotes the expansion of these cells in the zebrafish and mouse aorta gonad mesonephros AGM where EHT occurs. miR 223 targets alg2 alpha 1 3/ 1 6 mannosyltransferase in the AGM endothelium to restrict hemogenic and HSPC specification. This enzyme is involved in the attachment of the N glycans a common co translational modification9 12 that influences several pathophysiological processes but has not yet been implicated in EHT. Using an N glycosensor we demonstrate that abundant protein N glycan attachment occurs in vascular cells during EHT and this process is required for HSPC production. High throughput glycome analysis upon loss of miR 223 revealed that terminal alpha 1 3/6 mannose modifications are increased at the expense of alpha 2 3/6 sialic acid sugars. Importantly pharmacological manipulation targeting these N glycan types in wild type embryos phenocopies the loss of miR 223 and enhances EHT as well as HSPC production. Thus the N glycome plays a previously unappreciated role as an intrinsic regulator of EHT with specific mannose and sialic acid modifications serving as key endothelial determinants to restrict the hematopoietic fate. Overall design: Single cell RNA sequencing for zebrafish Tgkdrl:hras mCherrys896 endothelial cells at 27 hpf for wildtype and miR 223ya303 backgrounds		pubmed:33273096	wildtype 27hpf EC1	GSM3996906	source name:endothelial cell\|tissue:trunk endothelium\|cell type:endothelial cell\|developmental stage:27 hpf 223:KalTA4ya362; Tg5xUAS:eGFPnkuasgfp1a; Tgkdrl:hras mCherrys896\|genotype:wildtype	wildtype 27hpf EC1	The reads were demultiplexed using bcl2fastq provided by the 10X genomics. The demultiplexed reads were aligned to the reference genome Grz11 modified to add mCherry GAL4 and eGFP to obtain digital gene expression matrix data using cellranger program The output of the cellranger was then processed using Seurat in R. All the cells with less than 200 unique transcripts were eliminared. All genes which are expressed in less than 3 cells were also eliminated. The data was normalized using sctransform and then clustered. The clusters were projected for viualization in R using the PHATE algorithm. Genome build: GRCz11 Supplementary files format and content: Average Gene expression matrix for average gene expression per cluster per condition. This is a tab separated values file where each row represents a gene and each column represents the cluster and the condition and each cell represents normalized expression values across all the cells in that cluster for that condition.	endothelial cell		Trunk tissue was dissected from 27 hpf zebrafish embryos under 0.1% tricaine anesthesia and then disassociated into a single cell suspension using 0.25 mg/ml liberase for 45 minutes. Tgkdrl:hras mCherrys896 endothelial cells were isolated from the single cell suspension via FACS into 0.04% BSA in PBS and applied to the 10X genomics single cell RNA sequencing platform. 10 X genomics Chromium Next GEM Single Cell 3’ Library Construction Kit v2.1	Zebrafish were raised and maintained at 28.5˚C using standard methods and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2017 11473.	tissue:trunk endothelium\|cell type:endothelial cell\|developmental stage:27 hpf 223:KalTA4ya362; Tg5xUAS:eGFPnkuasgfp1a; Tgkdrl:hras mCherrys896\|genotype:wildtype	GSM3996906	GSM3996906: wildtype 27hpf EC1; Danio rerio; RNA Seq	GSM3996906		1	Trunk tissue was dissected from 27 hpf zebrafish embryos under 0.1% tricaine anesthesia and then disassociated into a single cell suspension using 0.25 mg/ml liberase for 45 minutes. Tgkdrl:hras mCherrys896 endothelial cells were isolated from the single cell suspension via FACS into 0.04% BSA in PBS and applied to the 10X genomics single cell RNA sequencing platform. 10 X genomics Chromium Next GEM Single Cell three prime Library Construction Kit v2.1	GEO Accession:GSM3996906	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP217216		WT_pssorted_genome_bam.bam	10X Genomics bam file	26866951370.0	274152565.0	GSM3996906 r1	0:98	A:7373453026;C:6169004304;G:6196779570;T:7121490110;N:6224360	98			7373453026	6169004304	6196779570	7121490110	6224360	SRX6634132	SRS5205092	SRA930499	GEO	Internal Medicine, Yale University	1	0.93015		0.0602		0.83853		0.4683		98		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	sc	single_cell_droplet	10x	United States	2019-08-01	Pharyngula	Embryo	Multi-tissue	Multi-system
53504	53504	SRR9879915	SRX6632436	SRS5202043	SRP217196	PRJNA558085	Zebrafish Danio rerio neural crest cell RNA sequencing	GSE135237	Transcriptome Analysis	RNA sequencing of neural crest cells collected from Gtfoxd3:mCherry;Tgsox10:mEGFP embryos Overall design: foxd3+/sox10+ double positive neural crest cells NCC were collected from the trunk of Gtfoxd3:mCherry;Tgsox10:mEGFP embryos at 36 hpf and 72 hpf and sent for sequencing. 3 replicates for each condition.		pubmed:31495570	36hpfNCC rep3	GSM3996851	source name:Neural crest cells from larval trunk\|tissue:Neural crest cells from larval trunk\|transgene:Gtfoxd3:mCherry\|transgene:Tgsox10:mEGFP\|Stage:36 hpf	36hpfNCC rep3	For data quality control FASTQC was used to check the raw fastq data quality and Trimmomatic was used to remove adaptors and to trim quality bases. post adapter clipping we removed leading and trailing ambiguous or low quality bases below Phred quality scores of 3. Trimmomatic works with a user defined window spanning the read from 5′ to 3′ and removes bases only at the 3′ end; we set up a window length of 4 and a quality threshold Q of 20. When the average quality drops below 20 the 3′ end is clipped. The reads were then mapped to the latest UCSC danRer10 transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. Genome build: danRer10 Supplementary files format and content: normalized FPKM counts with annotations	Neural crest cells from larval trunk	36 hpf and 72 hpf Gtfoxd3:mCherry;Tgsox10:mEGFP embryos were chilled in egg water on ice and the anterior halves of the embryos were removed using a scalpel. Trunk pieces were placed in calcium free Ringer’s solution with 2.5mM EDTA and rocked for 15 minutes at 4 °C. The trunk pieces were washed three times with chilled Dulbecco’s PBS D PBS and then transferred to microcentrifuge tubes along with 100ul D PBS. A pellet pestle was used to break up the trunk pieces and then 30ul Liberase TM was added. The samples were incubated for 15 minutes at 28.5 °C 1ml 1x Trypsin with 5% EDTA solution was added and the samples were incubated for 15 more minutes at 28.5 °C. The samples were pipetted into 5ml D PBS with 1% BSA and then passed through a 40 μm cell strainer and a syringe plunger was used to gently mash the samples into a petri dish. The contents of the petri dish were passed through a new cell strainer and the samples were then transferred to a microcentrifuge tube and were washed 2x with D PBS+BSA. Three samples of cells 1750 ± 750 at each stage were used for RNA sequencing.	Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing	Gtfoxd3:mCherry;Tgsox10:mEGFP zebrafish embryos were raised in egg water at 28.5C to desired stages	tissue:Neural crest cells from larval trunk\|transgene:Gtfoxd3:mCherry\|transgene:Tgsox10:mEGFP\|Stage:36 hpf	GSM3996851	GSM3996851: 36hpfNCC rep3; Danio rerio; RNA Seq	GSM3996851		1	Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing	GEO Accession:GSM3996851	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP217196		Sample3_S3_R1_001.fastq.gz Sample3_S3_R2_001.fastq.gz	fastq fastq	5670363307.0	19001526.0	GSM3996851 r1	0:149.23 1:149.19	A:1557295113;C:1251445377;G:1252062318;T:1609175566;N:384933	149	149		1557295113	1251445377	1252062318	1609175566	384933	SRX6632436	SRS5202043	SRA930488	GEO	Kucenas Lab, Biology, University of Virginia	2	0.85581	0.858	0.14092	0.14122	0.78784	0.7935	0.55466	0.55065	150	149	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2019-08-01	Pharyngula	Embryo	Multi-tissue	Multi-system
53505	53505	SRR9879914	SRX6632435	SRS5202042	SRP217196	PRJNA558085	Zebrafish Danio rerio neural crest cell RNA sequencing	GSE135237	Transcriptome Analysis	RNA sequencing of neural crest cells collected from Gtfoxd3:mCherry;Tgsox10:mEGFP embryos Overall design: foxd3+/sox10+ double positive neural crest cells NCC were collected from the trunk of Gtfoxd3:mCherry;Tgsox10:mEGFP embryos at 36 hpf and 72 hpf and sent for sequencing. 3 replicates for each condition.		pubmed:31495570	36hpfNCC rep2	GSM3996850	source name:Neural crest cells from larval trunk\|tissue:Neural crest cells from larval trunk\|transgene:Gtfoxd3:mCherry\|transgene:Tgsox10:mEGFP\|Stage:36 hpf	36hpfNCC rep2	For data quality control FASTQC was used to check the raw fastq data quality and Trimmomatic was used to remove adaptors and to trim quality bases. post adapter clipping we removed leading and trailing ambiguous or low quality bases below Phred quality scores of 3. Trimmomatic works with a user defined window spanning the read from 5′ to 3′ and removes bases only at the 3′ end; we set up a window length of 4 and a quality threshold Q of 20. When the average quality drops below 20 the 3′ end is clipped. The reads were then mapped to the latest UCSC danRer10 transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. Genome build: danRer10 Supplementary files format and content: normalized FPKM counts with annotations	Neural crest cells from larval trunk	36 hpf and 72 hpf Gtfoxd3:mCherry;Tgsox10:mEGFP embryos were chilled in egg water on ice and the anterior halves of the embryos were removed using a scalpel. Trunk pieces were placed in calcium free Ringer’s solution with 2.5mM EDTA and rocked for 15 minutes at 4 °C. The trunk pieces were washed three times with chilled Dulbecco’s PBS D PBS and then transferred to microcentrifuge tubes along with 100ul D PBS. A pellet pestle was used to break up the trunk pieces and then 30ul Liberase TM was added. The samples were incubated for 15 minutes at 28.5 °C 1ml 1x Trypsin with 5% EDTA solution was added and the samples were incubated for 15 more minutes at 28.5 °C. The samples were pipetted into 5ml D PBS with 1% BSA and then passed through a 40 μm cell strainer and a syringe plunger was used to gently mash the samples into a petri dish. The contents of the petri dish were passed through a new cell strainer and the samples were then transferred to a microcentrifuge tube and were washed 2x with D PBS+BSA. Three samples of cells 1750 ± 750 at each stage were used for RNA sequencing.	Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing	Gtfoxd3:mCherry;Tgsox10:mEGFP zebrafish embryos were raised in egg water at 28.5C to desired stages	tissue:Neural crest cells from larval trunk\|transgene:Gtfoxd3:mCherry\|transgene:Tgsox10:mEGFP\|Stage:36 hpf	GSM3996850	GSM3996850: 36hpfNCC rep2; Danio rerio; RNA Seq	GSM3996850		1	Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing	GEO Accession:GSM3996850	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP217196		Sample2_S2_R2_001.fastq.gz Sample2_S2_R1_001.fastq.gz	fastq fastq	7936706863.0	26647099.0	GSM3996850 r1	0:148.93 1:148.91	A:2180170247;C:1758018091;G:1758076526;T:2239839139;N:602860	148	148		2180170247	1758018091	1758076526	2239839139	602860	SRX6632435	SRS5202042	SRA930488	GEO	Kucenas Lab, Biology, University of Virginia	2	0.85787	0.85726	0.14387	0.14335	0.7864	0.79123	0.55424	0.54305	150	149	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2019-08-01	Pharyngula	Embryo	Multi-tissue	Multi-system
53506	53506	SRR9879913	SRX6632434	SRS5202041	SRP217196	PRJNA558085	Zebrafish Danio rerio neural crest cell RNA sequencing	GSE135237	Transcriptome Analysis	RNA sequencing of neural crest cells collected from Gtfoxd3:mCherry;Tgsox10:mEGFP embryos Overall design: foxd3+/sox10+ double positive neural crest cells NCC were collected from the trunk of Gtfoxd3:mCherry;Tgsox10:mEGFP embryos at 36 hpf and 72 hpf and sent for sequencing. 3 replicates for each condition.		pubmed:31495570	36hpfNCC rep1	GSM3996849	source name:Neural crest cells from larval trunk\|tissue:Neural crest cells from larval trunk\|transgene:Gtfoxd3:mCherry\|transgene:Tgsox10:mEGFP\|Stage:36 hpf	36hpfNCC rep1	For data quality control FASTQC was used to check the raw fastq data quality and Trimmomatic was used to remove adaptors and to trim quality bases. post adapter clipping we removed leading and trailing ambiguous or low quality bases below Phred quality scores of 3. Trimmomatic works with a user defined window spanning the read from 5′ to 3′ and removes bases only at the 3′ end; we set up a window length of 4 and a quality threshold Q of 20. When the average quality drops below 20 the 3′ end is clipped. The reads were then mapped to the latest UCSC danRer10 transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. Genome build: danRer10 Supplementary files format and content: normalized FPKM counts with annotations	Neural crest cells from larval trunk	36 hpf and 72 hpf Gtfoxd3:mCherry;Tgsox10:mEGFP embryos were chilled in egg water on ice and the anterior halves of the embryos were removed using a scalpel. Trunk pieces were placed in calcium free Ringer’s solution with 2.5mM EDTA and rocked for 15 minutes at 4 °C. The trunk pieces were washed three times with chilled Dulbecco’s PBS D PBS and then transferred to microcentrifuge tubes along with 100ul D PBS. A pellet pestle was used to break up the trunk pieces and then 30ul Liberase TM was added. The samples were incubated for 15 minutes at 28.5 °C 1ml 1x Trypsin with 5% EDTA solution was added and the samples were incubated for 15 more minutes at 28.5 °C. The samples were pipetted into 5ml D PBS with 1% BSA and then passed through a 40 μm cell strainer and a syringe plunger was used to gently mash the samples into a petri dish. The contents of the petri dish were passed through a new cell strainer and the samples were then transferred to a microcentrifuge tube and were washed 2x with D PBS+BSA. Three samples of cells 1750 ± 750 at each stage were used for RNA sequencing.	Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing	Gtfoxd3:mCherry;Tgsox10:mEGFP zebrafish embryos were raised in egg water at 28.5C to desired stages	tissue:Neural crest cells from larval trunk\|transgene:Gtfoxd3:mCherry\|transgene:Tgsox10:mEGFP\|Stage:36 hpf	GSM3996849	GSM3996849: 36hpfNCC rep1; Danio rerio; RNA Seq	GSM3996849		1	Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing	GEO Accession:GSM3996849	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP217196		Sample1_S1_R1_001.fastq.gz Sample1_S1_R2_001.fastq.gz	fastq fastq	5567367667.0	18627261.0	GSM3996849 r1	0:149.46 1:149.42	A:1451891750;C:1299527629;G:1299734297;T:1515800229;N:413762	149	149		1451891750	1299527629	1299734297	1515800229	413762	SRX6632434	SRS5202041	SRA930488	GEO	Kucenas Lab, Biology, University of Virginia	2	0.70717	0.70612	0.10919	0.10754	0.83366	0.83875	0.55253	0.55519	149	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2019-08-01	Pharyngula	Embryo	Multi-tissue	Multi-system
59847	59847	SRR12045011	SRX8573981	SRS6865979	SRP267842	PRJNA640350	Bulk RNA seq data to assess an improved zebrafish transcriptome annotation	GSE152759	Transcriptome Analysis	oligo dT and random primed RNA seq libraries were used to test an improved annotation of the zebrafish transcriptome Overall design: RNA seq was performed on transgene positive cells isolated by FACS		pubmed:32831172	Y1 positive rep3	GSM4625932	tissue:non venous endothelial blood and arch mesenchyme\|Stage:38 hpf isolated cells	Y1 positive rep3	Raw HiSeq2000 data files were processed with CASAVA 1.8.2 Illumina to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples if index sequences were non redundant we allowed for 1 mismatch or N in the index. Paired end reads were mapped to the zebrafish genome GRCz11 using STAR Mapped reads were quantified using Ensembl v95 RefSeq GCF 000002035.6 or a custom annotation V4.3.gtf included as processed file using RSEM Differentially expressed genes were identified using DEseq2 RNAseq pipeline was run in the DolphinNext environment Genome build: GRz11 Supplementary files format and content: CSV formatted output from DEseq2 for differential gene expression and normalized expression values quantified with 3 different annotations; GTF file for customized V4.3 annotation	non venous endothelial blood and arch mesenchyme	embryos were dissociated into single cell suspensions immunostained with Nr2fantibody and secondary fluorescent tagged antibody; EGFP and Nr2f2 positive cells were isolated by fluorescence activated cell sorting.	total RNA was treated with Ribogone and libraries constructed using the SMARTer Stranded RNA Seq Kit Clontech		Stage:38 hpf isolated cells	GSM4625932	GSM4625932: Y1 positive rep3; Danio rerio; RNA Seq	GSM4625932		1	total RNA was treated with Ribogone and libraries constructed using the SMARTer Stranded RNA Seq Kit Clontech	GEO Accession:GSM4625932	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP267842		y1_WT3.R1.fastq y1_WT3.R2.fastq	fastq fastq	5234292300.0	52342923.0	GSM4625932 r1	0:50 1:50	A:1227937371;C:1289958798;G:1435480505;T:1278798354;N:2117272	50	50		1227937371	1289958798	1435480505	1278798354	2117272	SRX8573981	SRS6865979	SRA1088645	GEO	Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School	2	0.82522	0.83953	0.3086	0.32178	0.76656	0.76719	0.70833	0.52608	50	50	B	B	biological fallback assumption	illumina	hiseq_era	full_length	poly_a	smarter	bulk	bulk	bulk	United States	2020-06-18	Pharyngula	Embryo	Multi-tissue	Multi-system
59848	59848	SRR12045010	SRX8573980	SRS6865978	SRP267842	PRJNA640350	Bulk RNA seq data to assess an improved zebrafish transcriptome annotation	GSE152759	Transcriptome Analysis	oligo dT and random primed RNA seq libraries were used to test an improved annotation of the zebrafish transcriptome Overall design: RNA seq was performed on transgene positive cells isolated by FACS		pubmed:32831172	Y1 positive rep2	GSM4625931	tissue:non venous endothelial blood and arch mesenchyme\|Stage:38 hpf isolated cells	Y1 positive rep2	Raw HiSeq2000 data files were processed with CASAVA 1.8.2 Illumina to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples if index sequences were non redundant we allowed for 1 mismatch or N in the index. Paired end reads were mapped to the zebrafish genome GRCz11 using STAR Mapped reads were quantified using Ensembl v95 RefSeq GCF 000002035.6 or a custom annotation V4.3.gtf included as processed file using RSEM Differentially expressed genes were identified using DEseq2 RNAseq pipeline was run in the DolphinNext environment Genome build: GRz11 Supplementary files format and content: CSV formatted output from DEseq2 for differential gene expression and normalized expression values quantified with 3 different annotations; GTF file for customized V4.3 annotation	non venous endothelial blood and arch mesenchyme	embryos were dissociated into single cell suspensions immunostained with Nr2fantibody and secondary fluorescent tagged antibody; EGFP and Nr2f2 positive cells were isolated by fluorescence activated cell sorting.	total RNA was treated with Ribogone and libraries constructed using the SMARTer Stranded RNA Seq Kit Clontech		Stage:38 hpf isolated cells	GSM4625931	GSM4625931: Y1 positive rep2; Danio rerio; RNA Seq	GSM4625931		1	total RNA was treated with Ribogone and libraries constructed using the SMARTer Stranded RNA Seq Kit Clontech	GEO Accession:GSM4625931	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP267842		y1_WT2.R1.fastq y1_WT2.R2.fastq	fastq fastq	4819929000.0	48199290.0	GSM4625931 r1	0:50 1:50	A:1127729164;C:1190781602;G:1322881210;T:1176579941;N:1957083	50	50		1127729164	1190781602	1322881210	1176579941	1957083	SRX8573980	SRS6865978	SRA1088645	GEO	Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School	2	0.82508	0.83939	0.30667	0.31875	0.76607	0.76601	0.71058	0.50542	50	50	B	B	biological fallback assumption	illumina	hiseq_era	full_length	poly_a	smarter	bulk	bulk	bulk	United States	2020-06-18	Pharyngula	Embryo	Multi-tissue	Multi-system
59849	59849	SRR12045009	SRX8573979	SRS6865976	SRP267842	PRJNA640350	Bulk RNA seq data to assess an improved zebrafish transcriptome annotation	GSE152759	Transcriptome Analysis	oligo dT and random primed RNA seq libraries were used to test an improved annotation of the zebrafish transcriptome Overall design: RNA seq was performed on transgene positive cells isolated by FACS		pubmed:32831172	Y1 positive rep1	GSM4625930	tissue:non venous endothelial blood and arch mesenchyme\|Stage:38 hpf isolated cells	Y1 positive rep1	Raw HiSeq2000 data files were processed with CASAVA 1.8.2 Illumina to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples if index sequences were non redundant we allowed for 1 mismatch or N in the index. Paired end reads were mapped to the zebrafish genome GRCz11 using STAR Mapped reads were quantified using Ensembl v95 RefSeq GCF 000002035.6 or a custom annotation V4.3.gtf included as processed file using RSEM Differentially expressed genes were identified using DEseq2 RNAseq pipeline was run in the DolphinNext environment Genome build: GRz11 Supplementary files format and content: CSV formatted output from DEseq2 for differential gene expression and normalized expression values quantified with 3 different annotations; GTF file for customized V4.3 annotation	non venous endothelial blood and arch mesenchyme	embryos were dissociated into single cell suspensions immunostained with Nr2fantibody and secondary fluorescent tagged antibody; EGFP and Nr2f2 positive cells were isolated by fluorescence activated cell sorting.	total RNA was treated with Ribogone and libraries constructed using the SMARTer Stranded RNA Seq Kit Clontech		Stage:38 hpf isolated cells	GSM4625930	GSM4625930: Y1 positive rep1; Danio rerio; RNA Seq	GSM4625930		1	total RNA was treated with Ribogone and libraries constructed using the SMARTer Stranded RNA Seq Kit Clontech	GEO Accession:GSM4625930	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP267842		y1_WT1.R1.fastq y1_WT1.R2.fastq	fastq fastq	5013318600.0	50133186.0	GSM4625930 r1	0:50 1:50	A:1107366794;C:1303452559;G:1450795494;T:1149648426;N:2055327	50	50		1107366794	1303452559	1450795494	1149648426	2055327	SRX8573979	SRS6865976	SRA1088645	GEO	Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School	2	0.84299	0.85327	0.23393	0.24314	0.76396	0.76572	0.71204	0.56072	50	50	B	B	biological fallback assumption	illumina	hiseq_era	full_length	poly_a	smarter	bulk	bulk	bulk	United States	2020-06-18	Pharyngula	Embryo	Multi-tissue	Multi-system
62679	62679	SRR13311744	SRX9739651	SRS7936985	SRP299375	PRJNA688157	Single cell RNA analysis of trunk neural crest cells in zebrafish	GSE163907	Other	Single cell RNA seq data of tgsox10:GFP cells from 20 hpf 24 hpf zebrafish. Sequenced with 10x genomics. Overall design: tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing		pubmed:34397384	tgsox10:GFP	GSM4990514	source name:zebrafish trunk tgsox10:GFP positive cells\|genotype:tgsox10:GFP ba2\|tissue:trunk neural crest cells\|developmental stage:24 hpf	tgsox10:GFP	cellranger v3.2 seurat v3.2.2 Genome build: GRCz11 Supplementary files format and content: features barcodes counts matrix for scRNAseq Supplementary files format and content: Cluster assignments	zebrafish trunk tgsox10:GFP positive cells		tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing		genotype:tgsox10:GFP ba2\|tissue:trunk neural crest cells\|developmental stage:24 hpf	GSM4990514	GSM4990514: tgsox10:GFP; Danio rerio; RNA Seq	GSM4990514		1	tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing	GEO Accession:GSM4990514	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP299375		Cut_Sox10_GFP_24hpf_12142018_1_S21_L001_R1_001.fastq.gz Cut_Sox10_GFP_24hpf_12142018_1_S21_L001_R2_001.fastq.gz	fastq fastq	23474658448.0	77935654.0	GSM4990514 r1	0:150.58 1:150.62	A:5315661572;C:4260464374;G:7908155075;T:5989858000;N:519427	150	150		5315661572	4260464374	7908155075	5989858000	519427	SRX9739651	SRS7936985	SRA1178122	GEO	Artinger Laboratory, Craniofacial Biology, University of Colorado Denver \| Anschutz	2	0.0	0.90618	0.0	0.11433	1.0	0.80178		0.51559	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-12-28	Pharyngula	Embryo	Multi-tissue	Multi-system
62680	62680	SRR13311745	SRX9739651	SRS7936985	SRP299375	PRJNA688157	Single cell RNA analysis of trunk neural crest cells in zebrafish	GSE163907	Other	Single cell RNA seq data of tgsox10:GFP cells from 20 hpf 24 hpf zebrafish. Sequenced with 10x genomics. Overall design: tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing		pubmed:34397384	tgsox10:GFP	GSM4990514	source name:zebrafish trunk tgsox10:GFP positive cells\|genotype:tgsox10:GFP ba2\|tissue:trunk neural crest cells\|developmental stage:24 hpf	tgsox10:GFP	cellranger v3.2 seurat v3.2.2 Genome build: GRCz11 Supplementary files format and content: features barcodes counts matrix for scRNAseq Supplementary files format and content: Cluster assignments	zebrafish trunk tgsox10:GFP positive cells		tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing		genotype:tgsox10:GFP ba2\|tissue:trunk neural crest cells\|developmental stage:24 hpf	GSM4990514	GSM4990514: tgsox10:GFP; Danio rerio; RNA Seq	GSM4990514		1	tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing	GEO Accession:GSM4990514	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP299375		Cut_Sox10_GFP_24hpf_12142018_1_S21_L002_R1_001.fastq.gz Cut_Sox10_GFP_24hpf_12142018_1_S21_L002_R2_001.fastq.gz	fastq fastq	23453047207.0	77864343.0	GSM4990514 r2	0:150.58 1:150.62	A:5353428042;C:4272250712;G:7801502473;T:6025426926;N:439054	150	150		5353428042	4272250712	7801502473	6025426926	439054	SRX9739651	SRS7936985	SRA1178122	GEO	Artinger Laboratory, Craniofacial Biology, University of Colorado Denver \| Anschutz	2	0.0	0.90571	0.0	0.11445	1.0	0.80326		0.51014	149	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-12-28	Pharyngula	Embryo	Multi-tissue	Multi-system
62681	62681	SRR13311746	SRX9739651	SRS7936985	SRP299375	PRJNA688157	Single cell RNA analysis of trunk neural crest cells in zebrafish	GSE163907	Other	Single cell RNA seq data of tgsox10:GFP cells from 20 hpf 24 hpf zebrafish. Sequenced with 10x genomics. Overall design: tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing		pubmed:34397384	tgsox10:GFP	GSM4990514	source name:zebrafish trunk tgsox10:GFP positive cells\|genotype:tgsox10:GFP ba2\|tissue:trunk neural crest cells\|developmental stage:24 hpf	tgsox10:GFP	cellranger v3.2 seurat v3.2.2 Genome build: GRCz11 Supplementary files format and content: features barcodes counts matrix for scRNAseq Supplementary files format and content: Cluster assignments	zebrafish trunk tgsox10:GFP positive cells		tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing		genotype:tgsox10:GFP ba2\|tissue:trunk neural crest cells\|developmental stage:24 hpf	GSM4990514	GSM4990514: tgsox10:GFP; Danio rerio; RNA Seq	GSM4990514		1	tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing	GEO Accession:GSM4990514	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP299375		Cut_Sox10_GFP_24hpf_12142018_2_S22_L001_R1_001.fastq.gz Cut_Sox10_GFP_24hpf_12142018_2_S22_L001_R2_001.fastq.gz	fastq fastq	18693961077.0	62064026.0	GSM4990514 r3	0:150.58 1:150.62	A:4223627306;C:3394276969;G:6298948837;T:4776692177;N:415788	150	150		4223627306	3394276969	6298948837	4776692177	415788	SRX9739651	SRS7936985	SRA1178122	GEO	Artinger Laboratory, Craniofacial Biology, University of Colorado Denver \| Anschutz	2	0.0	0.90754	0.0	0.11555	1.0	0.8018		0.50793	150	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-12-28	Pharyngula	Embryo	Multi-tissue	Multi-system
62682	62682	SRR13311747	SRX9739651	SRS7936985	SRP299375	PRJNA688157	Single cell RNA analysis of trunk neural crest cells in zebrafish	GSE163907	Other	Single cell RNA seq data of tgsox10:GFP cells from 20 hpf 24 hpf zebrafish. Sequenced with 10x genomics. Overall design: tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing		pubmed:34397384	tgsox10:GFP	GSM4990514	source name:zebrafish trunk tgsox10:GFP positive cells\|genotype:tgsox10:GFP ba2\|tissue:trunk neural crest cells\|developmental stage:24 hpf	tgsox10:GFP	cellranger v3.2 seurat v3.2.2 Genome build: GRCz11 Supplementary files format and content: features barcodes counts matrix for scRNAseq Supplementary files format and content: Cluster assignments	zebrafish trunk tgsox10:GFP positive cells		tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing		genotype:tgsox10:GFP ba2\|tissue:trunk neural crest cells\|developmental stage:24 hpf	GSM4990514	GSM4990514: tgsox10:GFP; Danio rerio; RNA Seq	GSM4990514		1	tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing	GEO Accession:GSM4990514	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP299375		Cut_Sox10_GFP_24hpf_12142018_2_S22_L002_R1_001.fastq.gz Cut_Sox10_GFP_24hpf_12142018_2_S22_L002_R2_001.fastq.gz	fastq fastq	18650610191.0	61920476.0	GSM4990514 r4	0:150.58 1:150.62	A:4248232322;C:3398942457;G:6205002760;T:4798080435;N:352217	150	150		4248232322	3398942457	6205002760	4798080435	352217	SRX9739651	SRS7936985	SRA1178122	GEO	Artinger Laboratory, Craniofacial Biology, University of Colorado Denver \| Anschutz	2	0.0	0.90621	0.0	0.11451	1.0	0.80223		0.51751	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-12-28	Pharyngula	Embryo	Multi-tissue	Multi-system
62683	62683	SRR13311748	SRX9739651	SRS7936985	SRP299375	PRJNA688157	Single cell RNA analysis of trunk neural crest cells in zebrafish	GSE163907	Other	Single cell RNA seq data of tgsox10:GFP cells from 20 hpf 24 hpf zebrafish. Sequenced with 10x genomics. Overall design: tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing		pubmed:34397384	tgsox10:GFP	GSM4990514	source name:zebrafish trunk tgsox10:GFP positive cells\|genotype:tgsox10:GFP ba2\|tissue:trunk neural crest cells\|developmental stage:24 hpf	tgsox10:GFP	cellranger v3.2 seurat v3.2.2 Genome build: GRCz11 Supplementary files format and content: features barcodes counts matrix for scRNAseq Supplementary files format and content: Cluster assignments	zebrafish trunk tgsox10:GFP positive cells		tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing		genotype:tgsox10:GFP ba2\|tissue:trunk neural crest cells\|developmental stage:24 hpf	GSM4990514	GSM4990514: tgsox10:GFP; Danio rerio; RNA Seq	GSM4990514		1	tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing	GEO Accession:GSM4990514	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP299375		Cut_Sox10_GFP_24hpf_12142018_3_S23_L001_R1_001.fastq.gz Cut_Sox10_GFP_24hpf_12142018_3_S23_L001_R2_001.fastq.gz	fastq fastq	21139583045.0	70183976.0	GSM4990514 r5	0:150.58 1:150.62	A:4766130433;C:3847270802;G:7123755600;T:5401957528;N:468682	150	150		4766130433	3847270802	7123755600	5401957528	468682	SRX9739651	SRS7936985	SRA1178122	GEO	Artinger Laboratory, Craniofacial Biology, University of Colorado Denver \| Anschutz	2	0.0	0.90939	0.0	0.11373	1.0	0.80044		0.51922	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-12-28	Pharyngula	Embryo	Multi-tissue	Multi-system
62684	62684	SRR13311749	SRX9739651	SRS7936985	SRP299375	PRJNA688157	Single cell RNA analysis of trunk neural crest cells in zebrafish	GSE163907	Other	Single cell RNA seq data of tgsox10:GFP cells from 20 hpf 24 hpf zebrafish. Sequenced with 10x genomics. Overall design: tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing		pubmed:34397384	tgsox10:GFP	GSM4990514	source name:zebrafish trunk tgsox10:GFP positive cells\|genotype:tgsox10:GFP ba2\|tissue:trunk neural crest cells\|developmental stage:24 hpf	tgsox10:GFP	cellranger v3.2 seurat v3.2.2 Genome build: GRCz11 Supplementary files format and content: features barcodes counts matrix for scRNAseq Supplementary files format and content: Cluster assignments	zebrafish trunk tgsox10:GFP positive cells		tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing		genotype:tgsox10:GFP ba2\|tissue:trunk neural crest cells\|developmental stage:24 hpf	GSM4990514	GSM4990514: tgsox10:GFP; Danio rerio; RNA Seq	GSM4990514		1	tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing	GEO Accession:GSM4990514	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP299375		Cut_Sox10_GFP_24hpf_12142018_3_S23_L002_R1_001.fastq.gz Cut_Sox10_GFP_24hpf_12142018_3_S23_L002_R2_001.fastq.gz	fastq fastq	21127496209.0	70144256.0	GSM4990514 r6	0:150.58 1:150.62	A:4801779342;C:3857990471;G:7030522815;T:5436808841;N:394740	150	150		4801779342	3857990471	7030522815	5436808841	394740	SRX9739651	SRS7936985	SRA1178122	GEO	Artinger Laboratory, Craniofacial Biology, University of Colorado Denver \| Anschutz	2	0.0	0.90941	0.0	0.11435	1.0	0.80087		0.51663	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-12-28	Pharyngula	Embryo	Multi-tissue	Multi-system
62685	62685	SRR13311750	SRX9739651	SRS7936985	SRP299375	PRJNA688157	Single cell RNA analysis of trunk neural crest cells in zebrafish	GSE163907	Other	Single cell RNA seq data of tgsox10:GFP cells from 20 hpf 24 hpf zebrafish. Sequenced with 10x genomics. Overall design: tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing		pubmed:34397384	tgsox10:GFP	GSM4990514	source name:zebrafish trunk tgsox10:GFP positive cells\|genotype:tgsox10:GFP ba2\|tissue:trunk neural crest cells\|developmental stage:24 hpf	tgsox10:GFP	cellranger v3.2 seurat v3.2.2 Genome build: GRCz11 Supplementary files format and content: features barcodes counts matrix for scRNAseq Supplementary files format and content: Cluster assignments	zebrafish trunk tgsox10:GFP positive cells		tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing		genotype:tgsox10:GFP ba2\|tissue:trunk neural crest cells\|developmental stage:24 hpf	GSM4990514	GSM4990514: tgsox10:GFP; Danio rerio; RNA Seq	GSM4990514		1	tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing	GEO Accession:GSM4990514	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP299375		Cut_Sox10_GFP_24hpf_12142018_4_S24_L001_R1_001.fastq.gz Cut_Sox10_GFP_24hpf_12142018_4_S24_L001_R2_001.fastq.gz	fastq fastq	19213599440.0	63789538.0	GSM4990514 r7	0:150.58 1:150.62	A:4332795032;C:3494053982;G:6477323231;T:4908999176;N:428019	150	150		4332795032	3494053982	6477323231	4908999176	428019	SRX9739651	SRS7936985	SRA1178122	GEO	Artinger Laboratory, Craniofacial Biology, University of Colorado Denver \| Anschutz	2	0.0	0.9086	0.0	0.11426	1.0	0.80257		0.51017	151	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-12-28	Pharyngula	Embryo	Multi-tissue	Multi-system
62686	62686	SRR13311751	SRX9739651	SRS7936985	SRP299375	PRJNA688157	Single cell RNA analysis of trunk neural crest cells in zebrafish	GSE163907	Other	Single cell RNA seq data of tgsox10:GFP cells from 20 hpf 24 hpf zebrafish. Sequenced with 10x genomics. Overall design: tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing		pubmed:34397384	tgsox10:GFP	GSM4990514	source name:zebrafish trunk tgsox10:GFP positive cells\|genotype:tgsox10:GFP ba2\|tissue:trunk neural crest cells\|developmental stage:24 hpf	tgsox10:GFP	cellranger v3.2 seurat v3.2.2 Genome build: GRCz11 Supplementary files format and content: features barcodes counts matrix for scRNAseq Supplementary files format and content: Cluster assignments	zebrafish trunk tgsox10:GFP positive cells		tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing		genotype:tgsox10:GFP ba2\|tissue:trunk neural crest cells\|developmental stage:24 hpf	GSM4990514	GSM4990514: tgsox10:GFP; Danio rerio; RNA Seq	GSM4990514		1	tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing	GEO Accession:GSM4990514	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP299375		Cut_Sox10_GFP_24hpf_12142018_4_S24_L002_R1_001.fastq.gz Cut_Sox10_GFP_24hpf_12142018_4_S24_L002_R2_001.fastq.gz	fastq fastq	19195135075.0	63728553.0	GSM4990514 r8	0:150.58 1:150.62	A:4363501238;C:3503247240;G:6390188740;T:4937837783;N:360074	150	150		4363501238	3503247240	6390188740	4937837783	360074	SRX9739651	SRS7936985	SRA1178122	GEO	Artinger Laboratory, Craniofacial Biology, University of Colorado Denver \| Anschutz	2	0.0	0.90626	0.0	0.11537	1.0	0.8032		0.50845	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-12-28	Pharyngula	Embryo	Multi-tissue	Multi-system
63260	63260	SRR13724987	SRX10113011	SRS8268907	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 26	GSM5087790	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 26	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:11\|genotype or treatment see plate layout:LY294002 treated	GSM5087790	GSM5087790: SBF 26; Danio rerio; RNA Seq	GSM5087790		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087790	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		HUB-SF-026_HNN3JBGXC_S4_L001_R1_001.fastq.gz HUB-SF-026_HNN3JBGXC_S4_L001_R2_001.fastq.gz	fastq fastq	724015252.0	8418782.0	GSM5087790 r1	0:26 1:60	A:181448033;C:140181369;G:139987828;T:262155531;N:242491	26	60		181448033	140181369	139987828	262155531	242491	SRX10113011	SRS8268907	SRA1196923	GEO	Hubrecht Institute	2	0.10352	0.78777	0.09808	0.22696	0.99078	0.81389	0.60135	0.52625	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63261	63261	SRR13724988	SRX10113011	SRS8268907	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 26	GSM5087790	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 26	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:11\|genotype or treatment see plate layout:LY294002 treated	GSM5087790	GSM5087790: SBF 26; Danio rerio; RNA Seq	GSM5087790		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087790	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		HUB-SF-026_HNN3JBGXC_S4_L002_R1_001.fastq.gz HUB-SF-026_HNN3JBGXC_S4_L002_R2_001.fastq.gz	fastq fastq	710763770.0	8264695.0	GSM5087790 r2	0:26 1:60	A:177328072;C:137060064;G:139543912;T:256619367;N:212355	26	60		177328072	137060064	139543912	256619367	212355	SRX10113011	SRS8268907	SRA1196923	GEO	Hubrecht Institute	2	0.10309	0.78735	0.09769	0.22712	0.9907	0.81434	0.59399	0.51403	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63262	63262	SRR13724989	SRX10113011	SRS8268907	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 26	GSM5087790	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 26	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:11\|genotype or treatment see plate layout:LY294002 treated	GSM5087790	GSM5087790: SBF 26; Danio rerio; RNA Seq	GSM5087790		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087790	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		HUB-SF-026_HNN3JBGXC_S4_L003_R1_001.fastq.gz HUB-SF-026_HNN3JBGXC_S4_L003_R2_001.fastq.gz	fastq fastq	733552222.0	8529677.0	GSM5087790 r3	0:26 1:60	A:183770046;C:141936571;G:141851405;T:265713964;N:280236	26	60		183770046	141936571	141851405	265713964	280236	SRX10113011	SRS8268907	SRA1196923	GEO	Hubrecht Institute	2	0.10305	0.78993	0.0974	0.22773	0.99058	0.81477	0.59145	0.52341	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63263	63263	SRR13724990	SRX10113011	SRS8268907	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 26	GSM5087790	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 26	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:11\|genotype or treatment see plate layout:LY294002 treated	GSM5087790	GSM5087790: SBF 26; Danio rerio; RNA Seq	GSM5087790		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087790	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		HUB-SF-026_HNN3JBGXC_S4_L004_R1_001.fastq.gz HUB-SF-026_HNN3JBGXC_S4_L004_R2_001.fastq.gz	fastq fastq	721320614.0	8387449.0	GSM5087790 r4	0:26 1:60	A:179946156;C:139058546;G:141752407;T:260320288;N:243217	26	60		179946156	139058546	141752407	260320288	243217	SRX10113011	SRS8268907	SRA1196923	GEO	Hubrecht Institute	2	0.10209	0.7864	0.09672	0.22655	0.99088	0.81688	0.56585	0.52923	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63264	63264	SRR13724983	SRX10113010	SRS8268906	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 25	GSM5087789	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 25	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:11 and 12\|genotype or treatment see plate layout:LY294002 treated	GSM5087789	GSM5087789: SBF 25; Danio rerio; RNA Seq	GSM5087789		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087789	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		HUB-SF-025_HNN3JBGXC_S3_L001_R1_001.fastq.gz HUB-SF-025_HNN3JBGXC_S3_L001_R2_001.fastq.gz	fastq fastq	563057824.0	6547184.0	GSM5087789 r1	0:26 1:60	A:133647343;C:107580359;G:102130933;T:219507850;N:191339	26	60		133647343	107580359	102130933	219507850	191339	SRX10113010	SRS8268906	SRA1196923	GEO	Hubrecht Institute	2	0.09959	0.88637	0.09191	0.22223	0.98841	0.7893	0.60149	0.5034	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63265	63265	SRR13724984	SRX10113010	SRS8268906	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 25	GSM5087789	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 25	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:11 and 12\|genotype or treatment see plate layout:LY294002 treated	GSM5087789	GSM5087789: SBF 25; Danio rerio; RNA Seq	GSM5087789		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087789	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		HUB-SF-025_HNN3JBGXC_S3_L002_R1_001.fastq.gz HUB-SF-025_HNN3JBGXC_S3_L002_R2_001.fastq.gz	fastq fastq	554827796.0	6451486.0	GSM5087789 r2	0:26 1:60	A:131279108;C:105552087;G:102233068;T:215597875;N:165658	26	60		131279108	105552087	102233068	215597875	165658	SRX10113010	SRS8268906	SRA1196923	GEO	Hubrecht Institute	2	0.09895	0.88574	0.09115	0.22146	0.98849	0.79048	0.60201	0.50402	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63266	63266	SRR13724985	SRX10113010	SRS8268906	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 25	GSM5087789	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 25	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:11 and 12\|genotype or treatment see plate layout:LY294002 treated	GSM5087789	GSM5087789: SBF 25; Danio rerio; RNA Seq	GSM5087789		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087789	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		HUB-SF-025_HNN3JBGXC_S3_L003_R1_001.fastq.gz HUB-SF-025_HNN3JBGXC_S3_L003_R2_001.fastq.gz	fastq fastq	572299814.0	6654649.0	GSM5087789 r3	0:26 1:60	A:135756854;C:109312452;G:103917320;T:223090484;N:222704	26	60		135756854	109312452	103917320	223090484	222704	SRX10113010	SRS8268906	SRA1196923	GEO	Hubrecht Institute	2	0.09998	0.88647	0.09216	0.22088	0.98841	0.7881	0.56617	0.49783	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63267	63267	SRR13724986	SRX10113010	SRS8268906	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 25	GSM5087789	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 25	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:11 and 12\|genotype or treatment see plate layout:LY294002 treated	GSM5087789	GSM5087789: SBF 25; Danio rerio; RNA Seq	GSM5087789		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087789	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		HUB-SF-025_HNN3JBGXC_S3_L004_R1_001.fastq.gz HUB-SF-025_HNN3JBGXC_S3_L004_R2_001.fastq.gz	fastq fastq	561898716.0	6533706.0	GSM5087789 r4	0:26 1:60	A:132858077;C:106892850;G:103648903;T:218299356;N:199530	26	60		132858077	106892850	103648903	218299356	199530	SRX10113010	SRS8268906	SRA1196923	GEO	Hubrecht Institute	2	0.09901	0.88605	0.09109	0.22144	0.98965	0.79074	0.51912	0.50131	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63268	63268	SRR13724979	SRX10113009	SRS8268905	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 24	GSM5087788	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 24	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:11\|genotype or treatment see plate layout:LY294002 treated	GSM5087788	GSM5087788: SBF 24; Danio rerio; RNA Seq	GSM5087788		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087788	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		HUB-SF-024_HNN3JBGXC_S2_L001_R1_001.fastq.gz HUB-SF-024_HNN3JBGXC_S2_L001_R2_001.fastq.gz	fastq fastq	453515324.0	5273434.0	GSM5087788 r1	0:26 1:60	A:109074977;C:85225133;G:81350727;T:177710223;N:154264	26	60		109074977	85225133	81350727	177710223	154264	SRX10113009	SRS8268905	SRA1196923	GEO	Hubrecht Institute	2	0.10905	0.86212	0.10222	0.18864	0.9919	0.79261	0.6034	0.53442	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63269	63269	SRR13724980	SRX10113009	SRS8268905	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 24	GSM5087788	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 24	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:11\|genotype or treatment see plate layout:LY294002 treated	GSM5087788	GSM5087788: SBF 24; Danio rerio; RNA Seq	GSM5087788		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087788	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		HUB-SF-024_HNN3JBGXC_S2_L002_R1_001.fastq.gz HUB-SF-024_HNN3JBGXC_S2_L002_R2_001.fastq.gz	fastq fastq	446302418.0	5189563.0	GSM5087788 r2	0:26 1:60	A:106865192;C:83450626;G:81614410;T:174238330;N:133860	26	60		106865192	83450626	81614410	174238330	133860	SRX10113009	SRS8268905	SRA1196923	GEO	Hubrecht Institute	2	0.10841	0.8604	0.10133	0.1894	0.99153	0.79448	0.5982	0.54405	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63270	63270	SRR13724981	SRX10113009	SRS8268905	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 24	GSM5087788	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 24	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:11\|genotype or treatment see plate layout:LY294002 treated	GSM5087788	GSM5087788: SBF 24; Danio rerio; RNA Seq	GSM5087788		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087788	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		HUB-SF-024_HNN3JBGXC_S2_L003_R1_001.fastq.gz HUB-SF-024_HNN3JBGXC_S2_L003_R2_001.fastq.gz	fastq fastq	460232096.0	5351536.0	GSM5087788 r3	0:26 1:60	A:110609261;C:86416065;G:82666816;T:180361735;N:178219	26	60		110609261	86416065	82666816	180361735	178219	SRX10113009	SRS8268905	SRA1196923	GEO	Hubrecht Institute	2	0.10769	0.86203	0.1007	0.18972	0.99127	0.79147	0.61515	0.51848	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63271	63271	SRR13724982	SRX10113009	SRS8268905	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 24	GSM5087788	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 24	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:11\|genotype or treatment see plate layout:LY294002 treated	GSM5087788	GSM5087788: SBF 24; Danio rerio; RNA Seq	GSM5087788		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087788	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		HUB-SF-024_HNN3JBGXC_S2_L004_R1_001.fastq.gz HUB-SF-024_HNN3JBGXC_S2_L004_R2_001.fastq.gz	fastq fastq	452332050.0	5259675.0	GSM5087788 r4	0:26 1:60	A:108267618;C:84551070;G:82750927;T:176603395;N:159040	26	60		108267618	84551070	82750927	176603395	159040	SRX10113009	SRS8268905	SRA1196923	GEO	Hubrecht Institute	2	0.10794	0.85996	0.10109	0.18768	0.99186	0.79155	0.60436	0.53563	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63288	63288	SRR13724959	SRX10113004	SRS8268900	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 19	GSM5087783	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 19	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:11 and 12\|genotype or treatment see plate layout:wildtype and LY294002 treated	GSM5087783	GSM5087783: SBF 19; Danio rerio; RNA Seq	GSM5087783		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087783	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		HUB-SF-019_HNN3JBGXC_S1_L001_R1_001.fastq.gz HUB-SF-019_HNN3JBGXC_S1_L001_R2_001.fastq.gz	fastq fastq	512895658.0	5963903.0	GSM5087783 r1	0:26 1:60	A:120657922;C:97018481;G:93066359;T:201974967;N:177929	26	60		120657922	97018481	93066359	201974967	177929	SRX10113004	SRS8268900	SRA1196923	GEO	Hubrecht Institute	2	0.10618	0.89183	0.09932	0.15723	0.99289	0.79697	0.64665	0.51501	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63289	63289	SRR13724960	SRX10113004	SRS8268900	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 19	GSM5087783	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 19	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:11 and 12\|genotype or treatment see plate layout:wildtype and LY294002 treated	GSM5087783	GSM5087783: SBF 19; Danio rerio; RNA Seq	GSM5087783		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087783	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		HUB-SF-019_HNN3JBGXC_S1_L002_R1_001.fastq.gz HUB-SF-019_HNN3JBGXC_S1_L002_R2_001.fastq.gz	fastq fastq	505286894.0	5875429.0	GSM5087783 r2	0:26 1:60	A:118287675;C:95129666;G:93501877;T:198218457;N:149219	26	60		118287675	95129666	93501877	198218457	149219	SRX10113004	SRS8268900	SRA1196923	GEO	Hubrecht Institute	2	0.10457	0.88947	0.0982	0.15596	0.99245	0.79717	0.6419	0.51385	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63290	63290	SRR13724961	SRX10113004	SRS8268900	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 19	GSM5087783	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 19	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:11 and 12\|genotype or treatment see plate layout:wildtype and LY294002 treated	GSM5087783	GSM5087783: SBF 19; Danio rerio; RNA Seq	GSM5087783		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087783	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		HUB-SF-019_HNN3JBGXC_S1_L003_R1_001.fastq.gz HUB-SF-019_HNN3JBGXC_S1_L003_R2_001.fastq.gz	fastq fastq	520563590.0	6053065.0	GSM5087783 r3	0:26 1:60	A:122370650;C:98437640;G:94573308;T:204982625;N:199367	26	60		122370650	98437640	94573308	204982625	199367	SRX10113004	SRS8268900	SRA1196923	GEO	Hubrecht Institute	2	0.10455	0.89316	0.09799	0.15826	0.99352	0.79602	0.64228	0.51728	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63291	63291	SRR13724962	SRX10113004	SRS8268900	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 19	GSM5087783	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 19	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:11 and 12\|genotype or treatment see plate layout:wildtype and LY294002 treated	GSM5087783	GSM5087783: SBF 19; Danio rerio; RNA Seq	GSM5087783		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087783	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		HUB-SF-019_HNN3JBGXC_S1_L004_R1_001.fastq.gz HUB-SF-019_HNN3JBGXC_S1_L004_R2_001.fastq.gz	fastq fastq	511418178.0	5946723.0	GSM5087783 r4	0:26 1:60	A:119653614;C:96220209;G:94759226;T:200596303;N:188826	26	60		119653614	96220209	94759226	200596303	188826	SRX10113004	SRS8268900	SRA1196923	GEO	Hubrecht Institute	2	0.10519	0.88809	0.09876	0.15771	0.9932	0.7976	0.64098	0.51551	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63292	63292	SRR13724955	SRX10113003	SRS8268899	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 18	GSM5087782	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 18	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:10 and 11\|genotype or treatment see plate layout:wildtype	GSM5087782	GSM5087782: SBF 18; Danio rerio; RNA Seq	GSM5087782		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087782	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		HUB-SF-018_HNMNYBGXC_S4_L001_R1_001.fastq.gz HUB-SF-018_HNMNYBGXC_S4_L001_R2_001.fastq.gz	fastq fastq	607020680.0	7058380.0	GSM5087782 r1	0:26 1:60	A:140183095;C:115207153;G:112295533;T:239312982;N:21917	26	60		140183095	115207153	112295533	239312982	21917	SRX10113003	SRS8268899	SRA1196923	GEO	Hubrecht Institute	2	0.1065	0.90122	0.09986	0.12875	0.99409	0.79886	0.54213	0.49434	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63293	63293	SRR13724956	SRX10113003	SRS8268899	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 18	GSM5087782	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 18	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:10 and 11\|genotype or treatment see plate layout:wildtype	GSM5087782	GSM5087782: SBF 18; Danio rerio; RNA Seq	GSM5087782		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087782	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		HUB-SF-018_HNMNYBGXC_S4_L002_R1_001.fastq.gz HUB-SF-018_HNMNYBGXC_S4_L002_R2_001.fastq.gz	fastq fastq	601756276.0	6997166.0	GSM5087782 r2	0:26 1:60	A:138291767;C:113586795;G:113460316;T:236406500;N:10898	26	60		138291767	113586795	113460316	236406500	10898	SRX10113003	SRS8268899	SRA1196923	GEO	Hubrecht Institute	2	0.10623	0.89793	0.1	0.12868	0.99373	0.79736	0.56624	0.48875	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63294	63294	SRR13724957	SRX10113003	SRS8268899	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 18	GSM5087782	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 18	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:10 and 11\|genotype or treatment see plate layout:wildtype	GSM5087782	GSM5087782: SBF 18; Danio rerio; RNA Seq	GSM5087782		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087782	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		HUB-SF-018_HNMNYBGXC_S4_L003_R1_001.fastq.gz HUB-SF-018_HNMNYBGXC_S4_L003_R2_001.fastq.gz	fastq fastq	609228472.0	7084052.0	GSM5087782 r3	0:26 1:60	A:140535790;C:115667471;G:112769371;T:240222708;N:33132	26	60		140535790	115667471	112769371	240222708	33132	SRX10113003	SRS8268899	SRA1196923	GEO	Hubrecht Institute	2	0.10644	0.90117	0.10007	0.12821	0.99373	0.79555	0.57799	0.49876	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63295	63295	SRR13724958	SRX10113003	SRS8268899	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 18	GSM5087782	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 18	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:10 and 11\|genotype or treatment see plate layout:wildtype	GSM5087782	GSM5087782: SBF 18; Danio rerio; RNA Seq	GSM5087782		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087782	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		HUB-SF-018_HNMNYBGXC_S4_L004_R1_001.fastq.gz HUB-SF-018_HNMNYBGXC_S4_L004_R2_001.fastq.gz	fastq fastq	611656080.0	7112280.0	GSM5087782 r4	0:26 1:60	A:140638258;C:115528635;G:114971815;T:240469585;N:47787	26	60		140638258	115528635	114971815	240469585	47787	SRX10113003	SRS8268899	SRA1196923	GEO	Hubrecht Institute	2	0.10488	0.89678	0.09883	0.12836	0.99401	0.79874	0.53879	0.50271	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63296	63296	SRR13724951	SRX10113002	SRS8268898	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 17	GSM5087781	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 17	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:10\|genotype or treatment see plate layout:wildtype	GSM5087781	GSM5087781: SBF 17; Danio rerio; RNA Seq	GSM5087781		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087781	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		HUB-SF-017_HNMNYBGXC_S3_L001_R1_001.fastq.gz HUB-SF-017_HNMNYBGXC_S3_L001_R2_001.fastq.gz	fastq fastq	550210542.0	6397797.0	GSM5087781 r1	0:26 1:60	A:129629378;C:105408321;G:101310529;T:213842712;N:19602	26	60		129629378	105408321	101310529	213842712	19602	SRX10113002	SRS8268898	SRA1196923	GEO	Hubrecht Institute	2	0.10176	0.85145	0.09561	0.12666	0.99228	0.79715	0.65986	0.49363	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63297	63297	SRR13724952	SRX10113002	SRS8268898	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 17	GSM5087781	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 17	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:10\|genotype or treatment see plate layout:wildtype	GSM5087781	GSM5087781: SBF 17; Danio rerio; RNA Seq	GSM5087781		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087781	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		HUB-SF-017_HNMNYBGXC_S3_L002_R1_001.fastq.gz HUB-SF-017_HNMNYBGXC_S3_L002_R2_001.fastq.gz	fastq fastq	544852140.0	6335490.0	GSM5087781 r2	0:26 1:60	A:127605846;C:103730258;G:102606915;T:210899244;N:9877	26	60		127605846	103730258	102606915	210899244	9877	SRX10113002	SRS8268898	SRA1196923	GEO	Hubrecht Institute	2	0.10057	0.84909	0.09431	0.12623	0.99285	0.79809	0.66527	0.49628	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63298	63298	SRR13724953	SRX10113002	SRS8268898	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 17	GSM5087781	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 17	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:10\|genotype or treatment see plate layout:wildtype	GSM5087781	GSM5087781: SBF 17; Danio rerio; RNA Seq	GSM5087781		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087781	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		HUB-SF-017_HNMNYBGXC_S3_L003_R1_001.fastq.gz HUB-SF-017_HNMNYBGXC_S3_L003_R2_001.fastq.gz	fastq fastq	552000976.0	6418616.0	GSM5087781 r3	0:26 1:60	A:129943041;C:105738992;G:101687286;T:214600933;N:30724	26	60		129943041	105738992	101687286	214600933	30724	SRX10113002	SRS8268898	SRA1196923	GEO	Hubrecht Institute	2	0.10203	0.85152	0.09564	0.12515	0.99212	0.79693	0.66008	0.49617	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63299	63299	SRR13724954	SRX10113002	SRS8268898	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 17	GSM5087781	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 17	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:10\|genotype or treatment see plate layout:wildtype	GSM5087781	GSM5087781: SBF 17; Danio rerio; RNA Seq	GSM5087781		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087781	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		HUB-SF-017_HNMNYBGXC_S3_L004_R1_001.fastq.gz HUB-SF-017_HNMNYBGXC_S3_L004_R2_001.fastq.gz	fastq fastq	554433572.0	6446902.0	GSM5087781 r4	0:26 1:60	A:129958370;C:105617900;G:104105493;T:214710300;N:41509	26	60		129958370	105617900	104105493	214710300	41509	SRX10113002	SRS8268898	SRA1196923	GEO	Hubrecht Institute	2	0.101	0.84666	0.09491	0.12434	0.99271	0.80052	0.65868	0.50218	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63316	63316	SRR13724931	SRX10112997	SRS8268893	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 6	GSM5087776	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 6	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:4\|genotype or treatment see plate layout:LY294002 treated	GSM5087776	GSM5087776: SBF 6; Danio rerio; RNA Seq	GSM5087776		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087776	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		SBF6_AH333MBGX9_S2_L001_R1_001.fastq.gz SBF6_AH333MBGX9_S2_L001_R2_001.fastq.gz	fastq fastq	1277423615.0	8461048.0	GSM5087776 r1	0:75.53 1:75.45	A:355718095;C:180588233;G:186496300;T:554167681;N:453306	75	75		355718095	180588233	186496300	554167681	453306	SRX10112997	SRS8268893	SRA1196923	GEO	Hubrecht Institute	2	0.1772	0.84028	0.11265	0.22285	0.98946	0.89936	0.50938	0.51879	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63317	63317	SRR13724932	SRX10112997	SRS8268893	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 6	GSM5087776	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 6	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:4\|genotype or treatment see plate layout:LY294002 treated	GSM5087776	GSM5087776: SBF 6; Danio rerio; RNA Seq	GSM5087776		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087776	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		SBF6_AH333MBGX9_S2_L002_R1_001.fastq.gz SBF6_AH333MBGX9_S2_L002_R2_001.fastq.gz	fastq fastq	1428463292.0	9460235.0	GSM5087776 r2	0:75.53 1:75.47	A:393204544;C:206178548;G:226631642;T:601950555;N:498003	75	75		393204544	206178548	226631642	601950555	498003	SRX10112997	SRS8268893	SRA1196923	GEO	Hubrecht Institute	2	0.19986	0.8458	0.12219	0.22132	0.97822	0.8616	0.48286	0.50011	75	74	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63318	63318	SRR13724933	SRX10112997	SRS8268893	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 6	GSM5087776	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 6	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:4\|genotype or treatment see plate layout:LY294002 treated	GSM5087776	GSM5087776: SBF 6; Danio rerio; RNA Seq	GSM5087776		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087776	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		SBF6_AH333MBGX9_S2_L003_R1_001.fastq.gz SBF6_AH333MBGX9_S2_L003_R2_001.fastq.gz	fastq fastq	1197534302.0	7935963.0	GSM5087776 r3	0:75.45 1:75.45	A:343317356;C:167744193;G:179840173;T:506420153;N:212427	75	75		343317356	167744193	179840173	506420153	212427	SRX10112997	SRS8268893	SRA1196923	GEO	Hubrecht Institute	2	0.16914	0.83932	0.11169	0.22325	0.99036	0.88745	0.45846	0.51895	75	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63319	63319	SRR13724934	SRX10112997	SRS8268893	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 6	GSM5087776	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 6	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:4\|genotype or treatment see plate layout:LY294002 treated	GSM5087776	GSM5087776: SBF 6; Danio rerio; RNA Seq	GSM5087776		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087776	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		SBF6_AH333MBGX9_S2_L004_R1_001.fastq.gz SBF6_AH333MBGX9_S2_L004_R2_001.fastq.gz	fastq fastq	1154537853.0	7651049.0	GSM5087776 r4	0:75.44 1:75.46	A:330092661;C:161606869;G:181064371;T:481566601;N:207351	75	75		330092661	161606869	181064371	481566601	207351	SRX10112997	SRS8268893	SRA1196923	GEO	Hubrecht Institute	2	0.18689	0.83323	0.11629	0.22137	0.98524	0.87677	0.50562	0.52611	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63320	63320	SRR13724927	SRX10112996	SRS8268892	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 5	GSM5087775	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 5	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:4\|genotype or treatment see plate layout:LY294002 treated	GSM5087775	GSM5087775: SBF 5; Danio rerio; RNA Seq	GSM5087775		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087775	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		SBF5_AH333MBGX9_S1_L001_R1_001.fastq.gz SBF5_AH333MBGX9_S1_L001_R2_001.fastq.gz	fastq fastq	1088370818.0	7206853.0	GSM5087775 r1	0:75.54 1:75.48	A:295469865;C:163970733;G:170086472;T:458445260;N:398488	75	75		295469865	163970733	170086472	458445260	398488	SRX10112996	SRS8268892	SRA1196923	GEO	Hubrecht Institute	2	0.26005	0.85502	0.19687	0.28684	0.9847	0.89161	0.48864	0.54017	74	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63321	63321	SRR13724928	SRX10112996	SRS8268892	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 5	GSM5087775	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 5	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:4\|genotype or treatment see plate layout:LY294002 treated	GSM5087775	GSM5087775: SBF 5; Danio rerio; RNA Seq	GSM5087775		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087775	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		SBF5_AH333MBGX9_S1_L002_R1_001.fastq.gz SBF5_AH333MBGX9_S1_L002_R2_001.fastq.gz	fastq fastq	1295570350.0	8577614.0	GSM5087775 r2	0:75.55 1:75.49	A:348091187;C:198053540;G:214980570;T:533988605;N:456448	75	75		348091187	198053540	214980570	533988605	456448	SRX10112996	SRS8268892	SRA1196923	GEO	Hubrecht Institute	2	0.28518	0.83096	0.21289	0.27752	0.97021	0.85729	0.48622	0.52931	75	74	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63322	63322	SRR13724929	SRX10112996	SRS8268892	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 5	GSM5087775	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 5	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:4\|genotype or treatment see plate layout:LY294002 treated	GSM5087775	GSM5087775: SBF 5; Danio rerio; RNA Seq	GSM5087775		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087775	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		SBF5_AH333MBGX9_S1_L003_R1_001.fastq.gz SBF5_AH333MBGX9_S1_L003_R2_001.fastq.gz	fastq fastq	1101611186.0	7297680.0	GSM5087775 r3	0:75.48 1:75.48	A:305906619;C:164420793;G:175650639;T:455425822;N:207313	75	75		305906619	164420793	175650639	455425822	207313	SRX10112996	SRS8268892	SRA1196923	GEO	Hubrecht Institute	2	0.25329	0.85303	0.19276	0.28474	0.98636	0.88055	0.50839	0.55071	76	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63323	63323	SRR13724930	SRX10112996	SRS8268892	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 5	GSM5087775	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 5	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:4\|genotype or treatment see plate layout:LY294002 treated	GSM5087775	GSM5087775: SBF 5; Danio rerio; RNA Seq	GSM5087775		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087775	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		SBF5_AH333MBGX9_S1_L004_R1_001.fastq.gz SBF5_AH333MBGX9_S1_L004_R2_001.fastq.gz	fastq fastq	1032362340.0	6839045.0	GSM5087775 r4	0:75.47 1:75.49	A:286580573;C:153625198;G:170370416;T:421602918;N:183235	75	75		286580573	153625198	170370416	421602918	183235	SRX10112996	SRS8268892	SRA1196923	GEO	Hubrecht Institute	2	0.26925	0.84457	0.2052	0.28507	0.98048	0.86815	0.49424	0.54795	75	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63324	63324	SRR13724923	SRX10112995	SRS8268891	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 4	GSM5087774	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 4	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:3\|genotype or treatment see plate layout:wildtype and LY294002 treated	GSM5087774	GSM5087774: SBF 4; Danio rerio; RNA Seq	GSM5087774		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087774	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		SBF-4_AH5WKHBGX3_S5_L001_R1_001.fastq.gz SBF-4_AH5WKHBGX3_S5_L001_R2_001.fastq.gz	fastq fastq	2411223196.0	15966823.0	GSM5087774 r1	0:75.52 1:75.49	A:644674430;C:333992035;G:384770311;T:1047444511;N:341909	75	75		644674430	333992035	384770311	1047444511	341909	SRX10112995	SRS8268891	SRA1196923	GEO	Hubrecht Institute	2	0.33554	0.83519	0.19659	0.21757	0.97402	0.80062	0.49709	0.50299	74	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63325	63325	SRR13724924	SRX10112995	SRS8268891	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 4	GSM5087774	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 4	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:3\|genotype or treatment see plate layout:wildtype and LY294002 treated	GSM5087774	GSM5087774: SBF 4; Danio rerio; RNA Seq	GSM5087774		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087774	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		SBF-4_AH5WKHBGX3_S5_L002_R1_001.fastq.gz SBF-4_AH5WKHBGX3_S5_L002_R2_001.fastq.gz	fastq fastq	2451975555.0	16238043.0	GSM5087774 r2	0:75.51 1:75.49	A:657663872;C:335089008;G:401426684;T:1057502726;N:293265	75	75		657663872	335089008	401426684	1057502726	293265	SRX10112995	SRS8268891	SRA1196923	GEO	Hubrecht Institute	2	0.34808	0.82817	0.20122	0.21406	0.96952	0.80624	0.5081	0.51204	75	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63326	63326	SRR13724925	SRX10112995	SRS8268891	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 4	GSM5087774	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 4	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:3\|genotype or treatment see plate layout:wildtype and LY294002 treated	GSM5087774	GSM5087774: SBF 4; Danio rerio; RNA Seq	GSM5087774		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087774	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		SBF-4_AH5WKHBGX3_S5_L003_R1_001.fastq.gz SBF-4_AH5WKHBGX3_S5_L003_R2_001.fastq.gz	fastq fastq	2433467285.0	16115065.0	GSM5087774 r3	0:75.51 1:75.49	A:649651175;C:332209980;G:393925739;T:1057547874;N:132517	75	75		649651175	332209980	393925739	1057547874	132517	SRX10112995	SRS8268891	SRA1196923	GEO	Hubrecht Institute	2	0.35242	0.83424	0.20776	0.2186	0.97561	0.80255	0.505	0.51812	76	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63327	63327	SRR13724926	SRX10112995	SRS8268891	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 4	GSM5087774	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 4	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:3\|genotype or treatment see plate layout:wildtype and LY294002 treated	GSM5087774	GSM5087774: SBF 4; Danio rerio; RNA Seq	GSM5087774		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087774	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		SBF-4_AH5WKHBGX3_S5_L004_R1_001.fastq.gz SBF-4_AH5WKHBGX3_S5_L004_R2_001.fastq.gz	fastq fastq	2398267715.0	15883759.0	GSM5087774 r4	0:75.50 1:75.49	A:643613425;C:328877849;G:388880564;T:1036811141;N:84736	75	75		643613425	328877849	388880564	1036811141	84736	SRX10112995	SRS8268891	SRA1196923	GEO	Hubrecht Institute	2	0.33562	0.83085	0.20341	0.21767	0.97735	0.80184	0.50029	0.51498	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63328	63328	SRR13724919	SRX10112994	SRS8268890	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 3	GSM5087773	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 3	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:3\|genotype or treatment see plate layout:wildtype and LY294002 treated	GSM5087773	GSM5087773: SBF 3; Danio rerio; RNA Seq	GSM5087773		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087773	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		SBF-3_AH5WKHBGX3_S4_L001_R1_001.fastq.gz SBF-3_AH5WKHBGX3_S4_L001_R2_001.fastq.gz	fastq fastq	3195541787.0	21161310.0	GSM5087773 r1	0:75.54 1:75.47	A:903731324;C:453063501;G:545122790;T:1293158952;N:465220	75	75		903731324	453063501	545122790	1293158952	465220	SRX10112994	SRS8268890	SRA1196923	GEO	Hubrecht Institute	2	0.31678	0.74007	0.23751	0.27632	0.97344	0.82548	0.46646	0.46858	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63329	63329	SRR13724920	SRX10112994	SRS8268890	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 3	GSM5087773	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 3	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:3\|genotype or treatment see plate layout:wildtype and LY294002 treated	GSM5087773	GSM5087773: SBF 3; Danio rerio; RNA Seq	GSM5087773		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087773	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		SBF-3_AH5WKHBGX3_S4_L002_R1_001.fastq.gz SBF-3_AH5WKHBGX3_S4_L002_R2_001.fastq.gz	fastq fastq	3222130047.0	21338414.0	GSM5087773 r2	0:75.53 1:75.47	A:911955596;C:450527126;G:564151778;T:1295111718;N:383829	75	75		911955596	450527126	564151778	1295111718	383829	SRX10112994	SRS8268890	SRA1196923	GEO	Hubrecht Institute	2	0.31155	0.73818	0.23573	0.27589	0.96968	0.83114	0.46101	0.52203	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63330	63330	SRR13724921	SRX10112994	SRS8268890	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 3	GSM5087773	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 3	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:3\|genotype or treatment see plate layout:wildtype and LY294002 treated	GSM5087773	GSM5087773: SBF 3; Danio rerio; RNA Seq	GSM5087773		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087773	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		SBF-3_AH5WKHBGX3_S4_L003_R1_001.fastq.gz SBF-3_AH5WKHBGX3_S4_L003_R2_001.fastq.gz	fastq fastq	3222462119.0	21339984.0	GSM5087773 r3	0:75.53 1:75.47	A:909869219;C:451636784;G:557091828;T:1303683831;N:180457	75	75		909869219	451636784	557091828	1303683831	180457	SRX10112994	SRS8268890	SRA1196923	GEO	Hubrecht Institute	2	0.29341	0.74071	0.22113	0.27868	0.97546	0.82869	0.47864	0.53241	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63331	63331	SRR13724922	SRX10112994	SRS8268890	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF 3	GSM5087773	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 3	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:3\|genotype or treatment see plate layout:wildtype and LY294002 treated	GSM5087773	GSM5087773: SBF 3; Danio rerio; RNA Seq	GSM5087773		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087773	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		SBF-3_AH5WKHBGX3_S4_L004_R1_001.fastq.gz SBF-3_AH5WKHBGX3_S4_L004_R2_001.fastq.gz	fastq fastq	3198542940.0	21184892.0	GSM5087773 r4	0:75.51 1:75.47	A:908150005;C:449327559;G:554336886;T:1286617646;N:110844	75	75		908150005	449327559	554336886	1286617646	110844	SRX10112994	SRS8268890	SRA1196923	GEO	Hubrecht Institute	2	0.31174	0.73875	0.2333	0.27833	0.97587	0.82735	0.44495	0.52152	75	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63332	63332	SRR13724915	SRX10112993	SRS8268889	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF b	GSM5087772	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF b	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:1\|genotype or treatment see plate layout:wildtype	GSM5087772	GSM5087772: SBF b; Danio rerio; RNA Seq	GSM5087772		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087772	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		SBFb_AHMK3CBGXY_S6_L001_R1_001.fastq.gz SBFb_AHMK3CBGXY_S6_L001_R2_001.fastq.gz	fastq fastq	1371717182.0	9096160.0	GSM5087772 r1	0:75.32 1:75.49	A:431208814;C:182975788;G:191474217;T:565708541;N:349822	75	75		431208814	182975788	191474217	565708541	349822	SRX10112993	SRS8268889	SRA1196923	GEO	Hubrecht Institute	2	0.20858	0.86563	0.09681	0.16003	0.97417	0.80977	0.4986	0.5051	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63333	63333	SRR13724916	SRX10112993	SRS8268889	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF b	GSM5087772	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF b	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:1\|genotype or treatment see plate layout:wildtype	GSM5087772	GSM5087772: SBF b; Danio rerio; RNA Seq	GSM5087772		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087772	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		SBFb_AHMK3CBGXY_S6_L002_R1_001.fastq.gz SBFb_AHMK3CBGXY_S6_L002_R2_001.fastq.gz	fastq fastq	1389974740.0	9216925.0	GSM5087772 r2	0:75.32 1:75.49	A:432611387;C:185298654;G:195582180;T:576097261;N:385258	75	75		432611387	185298654	195582180	576097261	385258	SRX10112993	SRS8268889	SRA1196923	GEO	Hubrecht Institute	2	0.19445	0.86622	0.08995	0.16164	0.97486	0.81107	0.49507	0.51217	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63334	63334	SRR13724917	SRX10112993	SRS8268889	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF b	GSM5087772	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF b	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:1\|genotype or treatment see plate layout:wildtype	GSM5087772	GSM5087772: SBF b; Danio rerio; RNA Seq	GSM5087772		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087772	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		SBFb_AHMK3CBGXY_S6_L003_R1_001.fastq.gz SBFb_AHMK3CBGXY_S6_L003_R2_001.fastq.gz	fastq fastq	1344249576.0	8912874.0	GSM5087772 r3	0:75.34 1:75.49	A:417103394;C:179153160;G:189101644;T:558793788;N:97590	75	75		417103394	179153160	189101644	558793788	97590	SRX10112993	SRS8268889	SRA1196923	GEO	Hubrecht Institute	2	0.20291	0.86448	0.09728	0.16345	0.97589	0.81331	0.51276	0.48907	75	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63335	63335	SRR13724918	SRX10112993	SRS8268889	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF b	GSM5087772	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF b	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:1\|genotype or treatment see plate layout:wildtype	GSM5087772	GSM5087772: SBF b; Danio rerio; RNA Seq	GSM5087772		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087772	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		SBFb_AHMK3CBGXY_S6_L004_R1_001.fastq.gz SBFb_AHMK3CBGXY_S6_L004_R2_001.fastq.gz	fastq fastq	1406958228.0	9327733.0	GSM5087772 r4	0:75.34 1:75.49	A:425247477;C:188248952;G:203730376;T:589616502;N:114921	75	75		425247477	188248952	203730376	589616502	114921	SRX10112993	SRS8268889	SRA1196923	GEO	Hubrecht Institute	2	0.20529	0.86237	0.09578	0.15898	0.97364	0.80533	0.5159	0.51177	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63336	63336	SRR13724911	SRX10112992	SRS8268888	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF a	GSM5087771	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF a	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:1\|genotype or treatment see plate layout:wildtype	GSM5087771	GSM5087771: SBF a; Danio rerio; RNA Seq	GSM5087771		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087771	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		SBFa_AHMK3CBGXY_S5_L001_R1_001.fastq.gz SBFa_AHMK3CBGXY_S5_L001_R2_001.fastq.gz	fastq fastq	1795957614.0	11906763.0	GSM5087771 r1	0:75.36 1:75.48	A:556557758;C:271831603;G:276684005;T:690436759;N:447489	75	75		556557758	271831603	276684005	690436759	447489	SRX10112992	SRS8268888	SRA1196923	GEO	Hubrecht Institute	2	0.27373	0.79114	0.20032	0.33403	0.96207	0.81639	0.50247	0.51409	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63337	63337	SRR13724912	SRX10112992	SRS8268888	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF a	GSM5087771	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF a	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:1\|genotype or treatment see plate layout:wildtype	GSM5087771	GSM5087771: SBF a; Danio rerio; RNA Seq	GSM5087771		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087771	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		SBFa_AHMK3CBGXY_S5_L002_R1_001.fastq.gz SBFa_AHMK3CBGXY_S5_L002_R2_001.fastq.gz	fastq fastq	1834336394.0	12160842.0	GSM5087771 r2	0:75.36 1:75.48	A:564737521;C:276699534;G:284366491;T:708014403;N:518445	75	75		564737521	276699534	284366491	708014403	518445	SRX10112992	SRS8268888	SRA1196923	GEO	Hubrecht Institute	2	0.26884	0.78787	0.19458	0.33465	0.96004	0.82079	0.50759	0.51672	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63338	63338	SRR13724913	SRX10112992	SRS8268888	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF a	GSM5087771	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF a	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:1\|genotype or treatment see plate layout:wildtype	GSM5087771	GSM5087771: SBF a; Danio rerio; RNA Seq	GSM5087771		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087771	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		SBFa_AHMK3CBGXY_S5_L003_R1_001.fastq.gz SBFa_AHMK3CBGXY_S5_L003_R2_001.fastq.gz	fastq fastq	1756417626.0	11643382.0	GSM5087771 r3	0:75.37 1:75.48	A:538991548;C:264988843;G:272348964;T:679970786;N:117485	75	75		538991548	264988843	272348964	679970786	117485	SRX10112992	SRS8268888	SRA1196923	GEO	Hubrecht Institute	2	0.27143	0.79064	0.19748	0.33283	0.96266	0.823	0.50907	0.50684	75	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
63339	63339	SRR13724914	SRX10112992	SRS8268888	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985	SBF a	GSM5087771	tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF a	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:1\|genotype or treatment see plate layout:wildtype	GSM5087771	GSM5087771: SBF a; Danio rerio; RNA Seq	GSM5087771		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087771	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306756		SBFa_AHMK3CBGXY_S5_L004_R1_001.fastq.gz SBFa_AHMK3CBGXY_S5_L004_R2_001.fastq.gz	fastq fastq	1939499436.0	12856118.0	GSM5087771 r4	0:75.38 1:75.48	A:582243992;C:292051417;G:306410955;T:758635889;N:157183	75	75		582243992	292051417	306410955	758635889	157183	SRX10112992	SRS8268888	SRA1196923	GEO	Hubrecht Institute	2	0.26584	0.79482	0.19411	0.33124	0.96173	0.81225	0.52607	0.515	75	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system
66749	66749	SRR23717086	SRX19578256	SRS16961238	SRP342742	PRJNA773777	Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.scRNA seq]	GSE186423	Transcriptome Analysis	Using a combination of single cell multi omics lineage tracing and functional assays we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population but where and how HSPC heterogeneity occurs remain unclear. Here we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1 kdrl+runx1+ and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency we performed scRNA seq with the sorted ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf.	parent bioproject:PRJNA773771	pubmed:37016019	36 hpf Zebrafish VDA scRNA seq spi2 morphant	GSM7083029	source name:Zebrafish VDA\|tissue:Zebrafish VDA 36hpf\|cells:VDA derived kdrl+runx1 kdrl+runx1+ and kdrl runx1+ cells\|Stage:36 hpf	36 hpf Zebrafish VDA scRNA seq spi2 morphant	For scRNA seq and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters using the GRCz11 reference genome. For STRT seq raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates MACS2 was used for the peak calling. Assembly: GRCz11	Zebrafish VDA		For 10x Genomics based scRNA seq and scATAC seq in zebrafish 40 000 mCherry+ GFP cells 40 000 mCherry+ GFP+ cells and 30 000 mCherry GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG libraries were prepared according to Hyp…		tissue:Zebrafish VDA 36hpf\|cells:VDA derived kdrl+runx1 kdrl+runx1+ and kdrl runx1+ cells\|Stage:36 hpf	GSM7083029	GSM7083029: 36 hpf Zebrafish VDA scRNA seq spi2 morphant; Danio rerio; RNA Seq	GSM7083029 r1	GSM7083029	1	For 10x Genomics based scRNA seq and scATAC seq in zebrafish 40 000 mCherry+ GFP cells 40 000 mCherry+ GFP+ cells and 30 000 mCherry GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG libraries were prepare…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP342742		210954C_spi2_MO_S1_L001_R1_001.fastq.gz 210954C_spi2_MO_S1_L001_R2_001.fastq.gz	fastq fastq	38657555700.0	128858519.0	GSM7083029 r1	0:150 1:150	A:16254027461;C:6972577611;G:6733828903;T:8696771854;N:349871	150	150		16254027461	6972577611	6733828903	8696771854	349871	SRX19578256	SRS16961238	SRA1601408	Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES	Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES	2	0.0	0.92157	0.0	0.12849	1.0	0.7811		0.5613	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	China	2023-03-06	Pharyngula	Embryo	Multi-tissue	Multi-system
66750	66750	SRR23717087	SRX19578256	SRS16961238	SRP342742	PRJNA773777	Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.scRNA seq]	GSE186423	Transcriptome Analysis	Using a combination of single cell multi omics lineage tracing and functional assays we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population but where and how HSPC heterogeneity occurs remain unclear. Here we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1 kdrl+runx1+ and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency we performed scRNA seq with the sorted ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf.	parent bioproject:PRJNA773771	pubmed:37016019	36 hpf Zebrafish VDA scRNA seq spi2 morphant	GSM7083029	source name:Zebrafish VDA\|tissue:Zebrafish VDA 36hpf\|cells:VDA derived kdrl+runx1 kdrl+runx1+ and kdrl runx1+ cells\|Stage:36 hpf	36 hpf Zebrafish VDA scRNA seq spi2 morphant	For scRNA seq and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters using the GRCz11 reference genome. For STRT seq raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates MACS2 was used for the peak calling. Assembly: GRCz11	Zebrafish VDA		For 10x Genomics based scRNA seq and scATAC seq in zebrafish 40 000 mCherry+ GFP cells 40 000 mCherry+ GFP+ cells and 30 000 mCherry GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG libraries were prepared according to Hyp…		tissue:Zebrafish VDA 36hpf\|cells:VDA derived kdrl+runx1 kdrl+runx1+ and kdrl runx1+ cells\|Stage:36 hpf	GSM7083029	GSM7083029: 36 hpf Zebrafish VDA scRNA seq spi2 morphant; Danio rerio; RNA Seq	GSM7083029 r1	GSM7083029	1	For 10x Genomics based scRNA seq and scATAC seq in zebrafish 40 000 mCherry+ GFP cells 40 000 mCherry+ GFP+ cells and 30 000 mCherry GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG libraries were prepare…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP342742		210954C_spi2_MO_S1_L002_R1_001.fastq.gz 210954C_spi2_MO_S1_L002_R2_001.fastq.gz	fastq fastq	39767723700.0	132559079.0	GSM7083029 r2	0:150 1:150	A:16740739613;C:7166687108;G:6926997738;T:8932937589;N:361652	150	150		16740739613	7166687108	6926997738	8932937589	361652	SRX19578256	SRS16961238	SRA1601408	Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES	Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES	2	0.0	0.92006	0.0	0.12624	1.0	0.7808		0.56645	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	China	2023-03-06	Pharyngula	Embryo	Multi-tissue	Multi-system
66751	66751	SRR23717088	SRX19578256	SRS16961238	SRP342742	PRJNA773777	Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.scRNA seq]	GSE186423	Transcriptome Analysis	Using a combination of single cell multi omics lineage tracing and functional assays we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population but where and how HSPC heterogeneity occurs remain unclear. Here we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1 kdrl+runx1+ and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency we performed scRNA seq with the sorted ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf.	parent bioproject:PRJNA773771	pubmed:37016019	36 hpf Zebrafish VDA scRNA seq spi2 morphant	GSM7083029	source name:Zebrafish VDA\|tissue:Zebrafish VDA 36hpf\|cells:VDA derived kdrl+runx1 kdrl+runx1+ and kdrl runx1+ cells\|Stage:36 hpf	36 hpf Zebrafish VDA scRNA seq spi2 morphant	For scRNA seq and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters using the GRCz11 reference genome. For STRT seq raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates MACS2 was used for the peak calling. Assembly: GRCz11	Zebrafish VDA		For 10x Genomics based scRNA seq and scATAC seq in zebrafish 40 000 mCherry+ GFP cells 40 000 mCherry+ GFP+ cells and 30 000 mCherry GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG libraries were prepared according to Hyp…		tissue:Zebrafish VDA 36hpf\|cells:VDA derived kdrl+runx1 kdrl+runx1+ and kdrl runx1+ cells\|Stage:36 hpf	GSM7083029	GSM7083029: 36 hpf Zebrafish VDA scRNA seq spi2 morphant; Danio rerio; RNA Seq	GSM7083029 r1	GSM7083029	1	For 10x Genomics based scRNA seq and scATAC seq in zebrafish 40 000 mCherry+ GFP cells 40 000 mCherry+ GFP+ cells and 30 000 mCherry GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG libraries were prepare…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP342742		210954C_spi2_MO_S1_L003_R1_001.fastq.gz 210954C_spi2_MO_S1_L003_R2_001.fastq.gz	fastq fastq	33826342500.0	112754475.0	GSM7083029 r3	0:150 1:150	A:14247560719;C:6101219095;G:5882384356;T:7594866748;N:311582	150	150		14247560719	6101219095	5882384356	7594866748	311582	SRX19578256	SRS16961238	SRA1601408	Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES	Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES	2	0.0	0.91535	0.0	0.12519	1.0	0.7833		0.56425	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	China	2023-03-06	Pharyngula	Embryo	Multi-tissue	Multi-system
66752	66752	SRR23717089	SRX19578256	SRS16961238	SRP342742	PRJNA773777	Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.scRNA seq]	GSE186423	Transcriptome Analysis	Using a combination of single cell multi omics lineage tracing and functional assays we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population but where and how HSPC heterogeneity occurs remain unclear. Here we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1 kdrl+runx1+ and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency we performed scRNA seq with the sorted ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf.	parent bioproject:PRJNA773771	pubmed:37016019	36 hpf Zebrafish VDA scRNA seq spi2 morphant	GSM7083029	source name:Zebrafish VDA\|tissue:Zebrafish VDA 36hpf\|cells:VDA derived kdrl+runx1 kdrl+runx1+ and kdrl runx1+ cells\|Stage:36 hpf	36 hpf Zebrafish VDA scRNA seq spi2 morphant	For scRNA seq and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters using the GRCz11 reference genome. For STRT seq raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates MACS2 was used for the peak calling. Assembly: GRCz11	Zebrafish VDA		For 10x Genomics based scRNA seq and scATAC seq in zebrafish 40 000 mCherry+ GFP cells 40 000 mCherry+ GFP+ cells and 30 000 mCherry GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG libraries were prepared according to Hyp…		tissue:Zebrafish VDA 36hpf\|cells:VDA derived kdrl+runx1 kdrl+runx1+ and kdrl runx1+ cells\|Stage:36 hpf	GSM7083029	GSM7083029: 36 hpf Zebrafish VDA scRNA seq spi2 morphant; Danio rerio; RNA Seq	GSM7083029 r1	GSM7083029	1	For 10x Genomics based scRNA seq and scATAC seq in zebrafish 40 000 mCherry+ GFP cells 40 000 mCherry+ GFP+ cells and 30 000 mCherry GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG libraries were prepare…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP342742		210954C_spi2_MO_S1_L004_R1_001.fastq.gz 210954C_spi2_MO_S1_L004_R2_001.fastq.gz	fastq fastq	42436674900.0	141455583.0	GSM7083029 r4	0:150 1:150	A:17850346993;C:7641162936;G:7380219938;T:9564565232;N:379801	150	150		17850346993	7641162936	7380219938	9564565232	379801	SRX19578256	SRS16961238	SRA1601408	Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES	Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES	2	0.0	0.91972	0.0	0.12638	1.0	0.78131		0.56385	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	China	2023-03-06	Pharyngula	Embryo	Multi-tissue	Multi-system
66753	66753	SRR16539848	SRX12742420	SRS10690646	SRP342742	PRJNA773777	Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.scRNA seq]	GSE186423	Transcriptome Analysis	Using a combination of single cell multi omics lineage tracing and functional assays we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population but where and how HSPC heterogeneity occurs remain unclear. Here we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1 kdrl+runx1+ and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency we performed scRNA seq with the sorted ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf.	parent bioproject:PRJNA773771	pubmed:37016019	36 hpf Zebrafish VDA scRNA seq	GSM5651458	source name:Zebrafish VDA\|tissue:Zebrafish VDA 36hpf\|cells:VDA derived kdrl+runx1 kdrl+runx1+ and kdrl runx1+ cells\|Stage:36 hpf	36 hpf Zebrafish VDA scRNA seq	For scRNA seq and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters using the GRCz11 reference genome. For STRT seq raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates MACS2 was used for the peak calling. Assembly: GRCz11	Zebrafish VDA		For 10x Genomics based scRNA seq and scATAC seq in zebrafish 40 000 mCherry+ GFP cells 40 000 mCherry+ GFP+ cells and 30 000 mCherry GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG libraries were prepared according to Hyp…		tissue:Zebrafish VDA 36hpf\|cells:VDA derived kdrl+runx1 kdrl+runx1+ and kdrl runx1+ cells\|Stage:36 hpf	GSM5651458	GSM5651458: 36 hpf Zebrafish VDA scRNA seq; Danio rerio; RNA Seq	GSM5651458 r1	GSM5651458	1	For 10x Genomics based scRNA seq and scATAC seq in zebrafish 40 000 mCherry+ GFP cells 40 000 mCherry+ GFP+ cells and 30 000 mCherry GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG libraries were prepare…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP342742		190718O_ECHEHSC_R_1_1_R1.fq.gz 190718O_ECHEHSC_R_1_1_R2.fq.gz	fastq fastq	42862683000.0	142875610.0	GSM5651458 r1	0:150 1:150	A:19056076938;C:7513613524;G:7148399243;T:9144249423;N:343872	150	150		19056076938	7513613524	7148399243	9144249423	343872	SRX12742420	SRS10690646	SRA1600571	Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES	Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES	2	0.0	0.92848	0.0	0.09872	1.0	0.81797		0.52595	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	China	2021-10-22	Pharyngula	Embryo	Multi-tissue	Multi-system
66754	66754	SRR16539849	SRX12742420	SRS10690646	SRP342742	PRJNA773777	Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.scRNA seq]	GSE186423	Transcriptome Analysis	Using a combination of single cell multi omics lineage tracing and functional assays we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population but where and how HSPC heterogeneity occurs remain unclear. Here we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1 kdrl+runx1+ and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency we performed scRNA seq with the sorted ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf.	parent bioproject:PRJNA773771	pubmed:37016019	36 hpf Zebrafish VDA scRNA seq	GSM5651458	source name:Zebrafish VDA\|tissue:Zebrafish VDA 36hpf\|cells:VDA derived kdrl+runx1 kdrl+runx1+ and kdrl runx1+ cells\|Stage:36 hpf	36 hpf Zebrafish VDA scRNA seq	For scRNA seq and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters using the GRCz11 reference genome. For STRT seq raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates MACS2 was used for the peak calling. Assembly: GRCz11	Zebrafish VDA		For 10x Genomics based scRNA seq and scATAC seq in zebrafish 40 000 mCherry+ GFP cells 40 000 mCherry+ GFP+ cells and 30 000 mCherry GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG libraries were prepared according to Hyp…		tissue:Zebrafish VDA 36hpf\|cells:VDA derived kdrl+runx1 kdrl+runx1+ and kdrl runx1+ cells\|Stage:36 hpf	GSM5651458	GSM5651458: 36 hpf Zebrafish VDA scRNA seq; Danio rerio; RNA Seq	GSM5651458 r1	GSM5651458	1	For 10x Genomics based scRNA seq and scATAC seq in zebrafish 40 000 mCherry+ GFP cells 40 000 mCherry+ GFP+ cells and 30 000 mCherry GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG libraries were prepare…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP342742		190718O_ECHEHSC_R_2_1_R1.fq.gz 190718O_ECHEHSC_R_2_1_R2.fq.gz	fastq fastq	45613780500.0	152045935.0	GSM5651458 r2	0:150 1:150	A:20279847027;C:7989810705;G:7602659881;T:9741099780;N:363107	150	150		20279847027	7989810705	7602659881	9741099780	363107	SRX12742420	SRS10690646	SRA1600571	Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES	Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES	2	0.0	0.92821	0.0	0.09747	1.0	0.81706		0.52451	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	China	2021-10-22	Pharyngula	Embryo	Multi-tissue	Multi-system
66755	66755	SRR16539850	SRX12742420	SRS10690646	SRP342742	PRJNA773777	Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.scRNA seq]	GSE186423	Transcriptome Analysis	Using a combination of single cell multi omics lineage tracing and functional assays we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population but where and how HSPC heterogeneity occurs remain unclear. Here we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1 kdrl+runx1+ and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency we performed scRNA seq with the sorted ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf.	parent bioproject:PRJNA773771	pubmed:37016019	36 hpf Zebrafish VDA scRNA seq	GSM5651458	source name:Zebrafish VDA\|tissue:Zebrafish VDA 36hpf\|cells:VDA derived kdrl+runx1 kdrl+runx1+ and kdrl runx1+ cells\|Stage:36 hpf	36 hpf Zebrafish VDA scRNA seq	For scRNA seq and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters using the GRCz11 reference genome. For STRT seq raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates MACS2 was used for the peak calling. Assembly: GRCz11	Zebrafish VDA		For 10x Genomics based scRNA seq and scATAC seq in zebrafish 40 000 mCherry+ GFP cells 40 000 mCherry+ GFP+ cells and 30 000 mCherry GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG libraries were prepared according to Hyp…		tissue:Zebrafish VDA 36hpf\|cells:VDA derived kdrl+runx1 kdrl+runx1+ and kdrl runx1+ cells\|Stage:36 hpf	GSM5651458	GSM5651458: 36 hpf Zebrafish VDA scRNA seq; Danio rerio; RNA Seq	GSM5651458 r1	GSM5651458	1	For 10x Genomics based scRNA seq and scATAC seq in zebrafish 40 000 mCherry+ GFP cells 40 000 mCherry+ GFP+ cells and 30 000 mCherry GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG libraries were prepare…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP342742		190718O_ECHEHSC_R_3_1_R1.fq.gz 190718O_ECHEHSC_R_3_1_R2.fq.gz	fastq fastq	57137293500.0	190457645.0	GSM5651458 r3	0:150 1:150	A:25401821096;C:10031650741;G:9533037288;T:12170324099;N:460276	150	150		25401821096	10031650741	9533037288	12170324099	460276	SRX12742420	SRS10690646	SRA1600571	Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES	Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES	2	0.0	0.92958	0.0	0.09774	1.0	0.81773		0.52455	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	China	2021-10-22	Pharyngula	Embryo	Multi-tissue	Multi-system
66756	66756	SRR16539851	SRX12742420	SRS10690646	SRP342742	PRJNA773777	Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.scRNA seq]	GSE186423	Transcriptome Analysis	Using a combination of single cell multi omics lineage tracing and functional assays we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population but where and how HSPC heterogeneity occurs remain unclear. Here we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1 kdrl+runx1+ and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency we performed scRNA seq with the sorted ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf.	parent bioproject:PRJNA773771	pubmed:37016019	36 hpf Zebrafish VDA scRNA seq	GSM5651458	source name:Zebrafish VDA\|tissue:Zebrafish VDA 36hpf\|cells:VDA derived kdrl+runx1 kdrl+runx1+ and kdrl runx1+ cells\|Stage:36 hpf	36 hpf Zebrafish VDA scRNA seq	For scRNA seq and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters using the GRCz11 reference genome. For STRT seq raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates MACS2 was used for the peak calling. Assembly: GRCz11	Zebrafish VDA		For 10x Genomics based scRNA seq and scATAC seq in zebrafish 40 000 mCherry+ GFP cells 40 000 mCherry+ GFP+ cells and 30 000 mCherry GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG libraries were prepared according to Hyp…		tissue:Zebrafish VDA 36hpf\|cells:VDA derived kdrl+runx1 kdrl+runx1+ and kdrl runx1+ cells\|Stage:36 hpf	GSM5651458	GSM5651458: 36 hpf Zebrafish VDA scRNA seq; Danio rerio; RNA Seq	GSM5651458 r1	GSM5651458	1	For 10x Genomics based scRNA seq and scATAC seq in zebrafish 40 000 mCherry+ GFP cells 40 000 mCherry+ GFP+ cells and 30 000 mCherry GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG libraries were prepare…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP342742		190718O_ECHEHSC_R_4_1_R1.fq.gz 190718O_ECHEHSC_R_4_1_R2.fq.gz	fastq fastq	29835023100.0	99450077.0	GSM5651458 r4	0:150 1:150	A:13290644326;C:5233486555;G:4966979633;T:6343677510;N:235076	150	150		13290644326	5233486555	4966979633	6343677510	235076	SRX12742420	SRS10690646	SRA1600571	Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES	Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES	2	0.0	0.92872	0.0	0.098	1.0	0.8185		0.52198	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	China	2021-10-22	Pharyngula	Embryo	Multi-tissue	Multi-system
71549	71549	SRR21700247	SRX17697774	SRS15228561	SRP399479	PRJNA884084	RNA Seq data of gmfg morphants and their control siblings	PRJNA884084	Other	To more specifically explore the underlying mechanism by which gmfg regulates HSPC initiation we performed RNA sequencing RNA Seq with the dissected trunk and tail from 26 hpf gmfg morphants and their control siblings.			biological replicate 3	gmfg atgMO 3	strain:not applicable\|isolate:not applicable\|dev stage:26 hpf\|sex:not applicable\|tissue:the dissected trunk and tail\|collection date:2021 02 26\|geo loc name:China:Shenzhen Guangdong\|sample type:mo3\|BioSampleModel:Model organism or animal									RNA seq of Danio rerio	MO3 20210214	MO3 20210214	RNA seq of Danio rerio in different conditions			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	SINGLE	BGISEQ	BGISEQ-500	SRP399479		MO_3_1.fq.gz	fastq	1194263900.0	23885278.0	MO 3 1.fq.gz	0:50 1:0	A:315714579;C:274130504;G:282488713;T:321930104;N:0	50	0		315714579	274130504	282488713	321930104	0	SRX17697774	SRS15228561	SRA1506658	the First Affiliated Hospital, School of Medicine, Zhejiang University\|BoneMarrow Transplantation Center	the First Affiliated Hospital, School of Medicine, Zhejiang University	1	0.9415		0.07261		0.70701		0.47029		50		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2022-09-25	Pharyngula	Embryo	Multi-tissue	Multi-system
71550	71550	SRR21700248	SRX17697773	SRS15228560	SRP399479	PRJNA884084	RNA Seq data of gmfg morphants and their control siblings	PRJNA884084	Other	To more specifically explore the underlying mechanism by which gmfg regulates HSPC initiation we performed RNA sequencing RNA Seq with the dissected trunk and tail from 26 hpf gmfg morphants and their control siblings.			biological replicate 2	gmfg atgMO 2	strain:not applicable\|isolate:not applicable\|dev stage:26 hpf\|sex:not applicable\|tissue:the dissected trunk and tail\|collection date:2021 02 26\|geo loc name:China:Shenzhen Guangdong\|sample type:mo2\|BioSampleModel:Model organism or animal									RNA seq of Danio rerio	MO2 20210213	MO2 20210213	RNA seq of Danio rerio in different conditions			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	SINGLE	BGISEQ	BGISEQ-500	SRP399479		MO_2_1.fq.gz	fastq	1193697300.0	23873946.0	MO 2 1.fq.gz	0:50 1:0	A:316188077;C:272941933;G:282559962;T:322007328;N:0	50	0		316188077	272941933	282559962	322007328	0	SRX17697773	SRS15228560	SRA1506658	the First Affiliated Hospital, School of Medicine, Zhejiang University\|BoneMarrow Transplantation Center	the First Affiliated Hospital, School of Medicine, Zhejiang University	1	0.94144		0.07426		0.70715		0.47856		50		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2022-09-25	Pharyngula	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");;