metadata: run_metadata: 156 rows where devstage_curation = "Pharyngula" and tissue_curation

156 rows where devstage_curation = "Pharyngula" and tissue_curation_coarse = "Multi-system"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.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.r4_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	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
25133	25133	SRR25634296	SRX21361065	SRS18605555	SRP454944	PRJNA1005241	Nkx2.7 is a Conserved Regulator of Craniofacial Development	GSE240780	Transcriptome Analysis	Pharyngeal arch cells are comprised of endoderm mesoderm and neural crest layers. We used single cell RNA sequencing scRNA seq to analyze the genetic differences in pharyngeal arch cell types between wild type and nkx2.7 / samples. Overall design: Pharyngeal arch cells were obtained through manual dissection of wild type and nkx2.7 / embryos at 26 hpf. All embryos were positive for TgBACtcf21:mcherry NTR which was used as a visual guide for dissection. Cells were FACS sorted to eliminate dead cells from sequencing. 2 wild type embryos and 2 nkx2.7 / samples were pooled for submission.	pubmed:40268889	KC002 scRNAseq	GSM7709162	source name:Pharyngeal arches\|genotype:nkx2.7 / \|tissue:Pharyngeal arches\|strain:AB\|developmental stage:26 hpf\|geo loc name:missing\|collection date:missing	KC002 scRNAseq	The read alignment and gene counting were made using the Cell Ranger software v6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 version 105 Supplementary files format and content: Tab separated values files and matrix files	Pharyngeal arches		From the offspring of an intercross of nkx2.7+/ ;Tgtcf21:NTRO mCherrypd108 two wild type and two nkx2.7 / embryos were identified by genotyping. The pharyngeal arches and surrounding tissue were dissected dissociated and submitted for flow cytometry. Cellular dissociation was performed with liberase solution in PBS at 28°C with pipetting every five minutes until adequately homogenized in solution. Fetal Bovine Serum FBS 5% of volume was then added to each sample to arrest the dissociation and each sample was centrifuged at 4°C. The excess supernatant was removed and the pellet was resuspended in PBS/1% FBS and filtered through a 40 m cell strainer. Finally DAPI and DRAQ5 were added and cells were sorted using a SORP FACSAriaTM Cell Sorter BD Biosciences under gentle conditions with the 130 μm nozzle at 12 PSI. NERL Diluent 2 Thermo Fisher DIL5522 solution was used for sheath fluid. The FACSAria was calibrated per the standard protocol in the CSCI Flow Cytometry Core Facility using Cytometer Setup and Tracking Beads BD Biosciences 655051 SPHERO Rainbow Calibration Particles 8 Peaks 3.0 m 5 mL Spherotech RCP 30 5A followed by optimization of the drop charge delay using BD FACS Accudrop Beads BD Biosciences 345249. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.		genotype:nkx2.7 / \|tissue:Pharyngeal arches\|strain:AB\|developmental stage:26 hpf	GSM7709162	GSM7709162: KC002 scRNAseq; Danio rerio; RNA Seq	GSM7709162 r1	GSM7709162	1	From the offspring of an intercross of nkx2.7+/ ;Tgtcf21:NTRO mCherrypd108 two wild type and two nkx2.7 / embryos were identified by genotyping. The pharyngeal arches and surrounding tissue were dissected dissociated and submitted for flow cytometry. Cellular dissociation was performed with liberase solution in PBS at 28°C with pipetting every five minutes until adequately homogenized in solution. Fetal Bovine Serum FBS 5% of volume was then added to each sample to arrest the dissociation and each sample was centrifuged at 4°C. The excess supernatant was removed and the pellet was resuspended in PBS/1% FBS and filtered through a 40 m cell strainer. Finally DAPI and DRAQ5 were added and cells were sorted using a SORP FACSAriaTM Cell Sorter BD Biosciences under gentle conditions with the 130 μm nozzle at 12 PSI. NERL Diluent 2 Thermo Fisher DIL5522 solution was used for sheath fluid. The FACSAria was calibrated per the standard protocol in the CSCI Flow Cytometry Core Facility using Cytometer Setup and Tracking Beads BD Biosciences 655051 SPHERO Rainbow Calibration Particles 8 Peaks 3.0 m 5 mL Spherotech RCP 30 5A followed by optimization of the drop charge delay using BD FACS Accudrop Beads BD Biosciences 345249. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index we…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP454944	loader:fastq load.py\|options: readTypes=TTBB read1PairFiles=KC002 S1 L004 I1 001.fastq.gz read2PairFiles=KC002 S1 L004 I2 001.fastq.gz read3PairFiles=KC002 S1 L004 R1 001.fastq.gz read4PairFiles=KC002 S1 L004 R2 001.fastq.gz	KC002_S1_L004_I1_001.fastq.gz KC002_S1_L004_I2_001.fastq.gz KC002_S1_L004_R1_001.fastq.gz KC002_S1_L004_R2_001.fastq.gz	fastq fastq fastq fastq	65825988564.0	296513462.0	GSM7709162 r1	0:10 1:10 2:101 3:101	A:14990994149;C:11485312838;G:11921291570;T:21497933732;N:187035	10	10	101	101	14990994149	11485312838	11921291570	21497933732	187035	SRX21361065	SRS18605555	SRA1692494	SangesLab Computational Genomics, NEUROSCIENCE, SISSA	SangesLab Computational Genomics, NEUROSCIENCE, SISSA	2	0.00059	0.93473	2e-05	0.14487	0.99949	0.78364	0.5	0.52799	101	101	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Italy	2023-08-14	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
25134	25134	SRR25634297	SRX21361064	SRS18605556	SRP454944	PRJNA1005241	Nkx2.7 is a Conserved Regulator of Craniofacial Development	GSE240780	Transcriptome Analysis	Pharyngeal arch cells are comprised of endoderm mesoderm and neural crest layers. We used single cell RNA sequencing scRNA seq to analyze the genetic differences in pharyngeal arch cell types between wild type and nkx2.7 / samples. Overall design: Pharyngeal arch cells were obtained through manual dissection of wild type and nkx2.7 / embryos at 26 hpf. All embryos were positive for TgBACtcf21:mcherry NTR which was used as a visual guide for dissection. Cells were FACS sorted to eliminate dead cells from sequencing. 2 wild type embryos and 2 nkx2.7 / samples were pooled for submission.	pubmed:40268889	KC001 scRNAseq	GSM7709161	source name:Pharyngeal arches\|genotype:wild type\|tissue:Pharyngeal arches\|strain:AB\|developmental stage:26 hpf\|geo loc name:missing\|collection date:missing	KC001 scRNAseq	The read alignment and gene counting were made using the Cell Ranger software v6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 version 105 Supplementary files format and content: Tab separated values files and matrix files	Pharyngeal arches		From the offspring of an intercross of nkx2.7+/ ;Tgtcf21:NTRO mCherrypd108 two wild type and two nkx2.7 / embryos were identified by genotyping. The pharyngeal arches and surrounding tissue were dissected dissociated and submitted for flow cytometry. Cellular dissociation was performed with liberase solution in PBS at 28°C with pipetting every five minutes until adequately homogenized in solution. Fetal Bovine Serum FBS 5% of volume was then added to each sample to arrest the dissociation and each sample was centrifuged at 4°C. The excess supernatant was removed and the pellet was resuspended in PBS/1% FBS and filtered through a 40 m cell strainer. Finally DAPI and DRAQ5 were added and cells were sorted using a SORP FACSAriaTM Cell Sorter BD Biosciences under gentle conditions with the 130 μm nozzle at 12 PSI. NERL Diluent 2 Thermo Fisher DIL5522 solution was used for sheath fluid. The FACSAria was calibrated per the standard protocol in the CSCI Flow Cytometry Core Facility using Cytometer Setup and Tracking Beads BD Biosciences 655051 SPHERO Rainbow Calibration Particles 8 Peaks 3.0 m 5 mL Spherotech RCP 30 5A followed by optimization of the drop charge delay using BD FACS Accudrop Beads BD Biosciences 345249. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.		genotype:wild type\|tissue:Pharyngeal arches\|strain:AB\|developmental stage:26 hpf	GSM7709161	GSM7709161: KC001 scRNAseq; Danio rerio; RNA Seq	GSM7709161 r1	GSM7709161	1	From the offspring of an intercross of nkx2.7+/ ;Tgtcf21:NTRO mCherrypd108 two wild type and two nkx2.7 / embryos were identified by genotyping. The pharyngeal arches and surrounding tissue were dissected dissociated and submitted for flow cytometry. Cellular dissociation was performed with liberase solution in PBS at 28°C with pipetting every five minutes until adequately homogenized in solution. Fetal Bovine Serum FBS 5% of volume was then added to each sample to arrest the dissociation and each sample was centrifuged at 4°C. The excess supernatant was removed and the pellet was resuspended in PBS/1% FBS and filtered through a 40 m cell strainer. Finally DAPI and DRAQ5 were added and cells were sorted using a SORP FACSAriaTM Cell Sorter BD Biosciences under gentle conditions with the 130 μm nozzle at 12 PSI. NERL Diluent 2 Thermo Fisher DIL5522 solution was used for sheath fluid. The FACSAria was calibrated per the standard protocol in the CSCI Flow Cytometry Core Facility using Cytometer Setup and Tracking Beads BD Biosciences 655051 SPHERO Rainbow Calibration Particles 8 Peaks 3.0 m 5 mL Spherotech RCP 30 5A followed by optimization of the drop charge delay using BD FACS Accudrop Beads BD Biosciences 345249. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index we…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP454944	loader:fastq load.py\|options: readTypes=TTBB read1PairFiles=KC001 S1 L004 I1 001.fastq.gz read2PairFiles=KC001 S1 L004 I2 001.fastq.gz read3PairFiles=KC001 S1 L004 R1 001.fastq.gz read4PairFiles=KC001 S1 L004 R2 001.fastq.gz	KC001_S1_L004_I1_001.fastq.gz KC001_S1_L004_I2_001.fastq.gz KC001_S1_L004_R1_001.fastq.gz KC001_S1_L004_R2_001.fastq.gz	fastq fastq fastq fastq	69380677872.0	312525576.0	GSM7709161 r1	0:10 1:10 2:101 3:101	A:16018222868;C:11704492905;G:12161620273;T:23245625739;N:204567	10	10	101	101	16018222868	11704492905	12161620273	23245625739	204567	SRX21361064	SRS18605556	SRA1692494	SangesLab Computational Genomics, NEUROSCIENCE, SISSA	SangesLab Computational Genomics, NEUROSCIENCE, SISSA	2	0.00071	0.93976	0.0001	0.12725	0.99945	0.78457	0.75	0.50121	101	101	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Italy	2023-08-14	Pharyngula	Embryo	Pharyngeal Arch	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
38049	38049	SRR1519899	SRX657112	SRS662299	SRP044634	PRJNA255636	mRNA sequencing of embryonic tails of sih mutants at 28 hpf	GSE59563	Transcriptome Analysis	We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf		sih3	GSM1439473	tissue:tail derived cells\|genotype/variation:sih\|embryonic stage:28 hpf	sih3	Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id Gene name and one column for each sample containing the normalized read counts	tail derived cells	sih embryos lack heart contraction	RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C 30 sec at 60°C 30 sec at 72°C] x 13 cycles; 5 min at 72°C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.	Embryos were grown in normal conditions	genotype/variation:sih\|embryonic stage:28 hpf	GSM1439473	GSM1439473: sih3; Danio rerio; RNA Seq	GSM1439473		1	RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C 30 sec at 60°C 30 sec at 72°C] x 13 cycles; 5 min at 72°C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.	GEO Accession:GSM1439473	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	SRP044634		JGZ-06.fastq.gz	fastq	1416036978.0	26222907.0	GSM1439473 r1	0:54	A:342287675;C:370618836;G:361870457;T:341179934;N:80076	54				342287675	370618836	361870457	341179934	80076	SRX657112	SRS662299	SRA175990	GEO	IGBMC	1	0.96217		0.03055		0.76869		0.44925		54		B		usable mapping rate	illumina	early_illumina	unknown	poly_a	unknown	bulk	unknown	unknown	France	2014-07-18	Pharyngula	Embryo	Tail	Multi-system
38050	38050	SRR1519898	SRX657111	SRS662291	SRP044634	PRJNA255636	mRNA sequencing of embryonic tails of sih mutants at 28 hpf	GSE59563	Transcriptome Analysis	We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf		WT3	GSM1439472	tissue:tail derived cells\|genotype/variation:WT\|embryonic stage:28 hpf	WT3	Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id Gene name and one column for each sample containing the normalized read counts	tail derived cells	sih embryos lack heart contraction	RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C 30 sec at 60°C 30 sec at 72°C] x 13 cycles; 5 min at 72°C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.	Embryos were grown in normal conditions	genotype/variation:WT\|embryonic stage:28 hpf	GSM1439472	GSM1439472: WT3; Danio rerio; RNA Seq	GSM1439472		1	RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C 30 sec at 60°C 30 sec at 72°C] x 13 cycles; 5 min at 72°C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.	GEO Accession:GSM1439472	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	SRP044634		JGZ-05.fastq.gz	fastq	1787680692.0	33105198.0	GSM1439472 r1	0:54	A:442553431;C:457003567;G:446438405;T:441598672;N:86617	54				442553431	457003567	446438405	441598672	86617	SRX657111	SRS662291	SRA175990	GEO	IGBMC	1	0.96318		0.03918		0.75371		0.4423		54		B		usable mapping rate	illumina	early_illumina	unknown	poly_a	unknown	bulk	unknown	unknown	France	2014-07-18	Pharyngula	Embryo	Tail	Multi-system
38051	38051	SRR1519897	SRX657110	SRS662290	SRP044634	PRJNA255636	mRNA sequencing of embryonic tails of sih mutants at 28 hpf	GSE59563	Transcriptome Analysis	We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf		sih2	GSM1439471	tissue:tail derived cells\|genotype/variation:sih\|embryonic stage:28 hpf	sih2	Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id Gene name and one column for each sample containing the normalized read counts	tail derived cells	sih embryos lack heart contraction	RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C 30 sec at 60°C 30 sec at 72°C] x 13 cycles; 5 min at 72°C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.	Embryos were grown in normal conditions	genotype/variation:sih\|embryonic stage:28 hpf	GSM1439471	GSM1439471: sih2; Danio rerio; RNA Seq	GSM1439471		1	RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C 30 sec at 60°C 30 sec at 72°C] x 13 cycles; 5 min at 72°C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.	GEO Accession:GSM1439471	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	SRP044634		JGZ-04.fastq.gz	fastq	1813069386.0	33575359.0	GSM1439471 r1	0:54	A:462594376;C:449896725;G:440482879;T:460019095;N:76311	54				462594376	449896725	440482879	460019095	76311	SRX657110	SRS662290	SRA175990	GEO	IGBMC	1	0.95859		0.05282		0.74199		0.47244		54		B		usable mapping rate	illumina	early_illumina	unknown	poly_a	unknown	bulk	unknown	unknown	France	2014-07-18	Pharyngula	Embryo	Tail	Multi-system
38052	38052	SRR1519896	SRX657109	SRS662289	SRP044634	PRJNA255636	mRNA sequencing of embryonic tails of sih mutants at 28 hpf	GSE59563	Transcriptome Analysis	We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf		WT2	GSM1439470	tissue:tail derived cells\|genotype/variation:WT\|embryonic stage:28 hpf	WT2	Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id Gene name and one column for each sample containing the normalized read counts	tail derived cells	sih embryos lack heart contraction	RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C 30 sec at 60°C 30 sec at 72°C] x 13 cycles; 5 min at 72°C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.	Embryos were grown in normal conditions	genotype/variation:WT\|embryonic stage:28 hpf	GSM1439470	GSM1439470: WT2; Danio rerio; RNA Seq	GSM1439470		1	RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C 30 sec at 60°C 30 sec at 72°C] x 13 cycles; 5 min at 72°C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.	GEO Accession:GSM1439470	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	SRP044634		JGZ-03.fastq.gz	fastq	1866194316.0	34559154.0	GSM1439470 r1	0:54	A:483946414;C:453986455;G:443561481;T:484623941;N:76025	54				483946414	453986455	443561481	484623941	76025	SRX657109	SRS662289	SRA175990	GEO	IGBMC	1	0.95615		0.06195		0.73594		0.47144		54		B		usable mapping rate	illumina	early_illumina	unknown	poly_a	unknown	bulk	unknown	unknown	France	2014-07-18	Pharyngula	Embryo	Tail	Multi-system
38053	38053	SRR1519895	SRX657108	SRS662288	SRP044634	PRJNA255636	mRNA sequencing of embryonic tails of sih mutants at 28 hpf	GSE59563	Transcriptome Analysis	We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf		sih1	GSM1439469	tissue:tail derived cells\|genotype/variation:sih\|embryonic stage:28 hpf	sih1	Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id Gene name and one column for each sample containing the normalized read counts	tail derived cells	sih embryos lack heart contraction	RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C 30 sec at 60°C 30 sec at 72°C] x 13 cycles; 5 min at 72°C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.	Embryos were grown in normal conditions	genotype/variation:sih\|embryonic stage:28 hpf	GSM1439469	GSM1439469: sih1; Danio rerio; RNA Seq	GSM1439469		1	RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C 30 sec at 60°C 30 sec at 72°C] x 13 cycles; 5 min at 72°C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.	GEO Accession:GSM1439469	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	SRP044634		JGZ-02.fastq.gz	fastq	1451212470.0	26874305.0	GSM1439469 r1	0:54	A:368354355;C:360129390;G:353350795;T:369317437;N:60493	54				368354355	360129390	353350795	369317437	60493	SRX657108	SRS662288	SRA175990	GEO	IGBMC	1	0.94911		0.04509		0.74604		0.46107		54		B		usable mapping rate	illumina	early_illumina	unknown	poly_a	unknown	bulk	unknown	unknown	France	2014-07-18	Pharyngula	Embryo	Tail	Multi-system
38054	38054	SRR1519894	SRX657107	SRS662287	SRP044634	PRJNA255636	mRNA sequencing of embryonic tails of sih mutants at 28 hpf	GSE59563	Transcriptome Analysis	We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf		WT1	GSM1439468	tissue:tail derived cells\|genotype/variation:WT\|embryonic stage:28 hpf	WT1	Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id Gene name and one column for each sample containing the normalized read counts	tail derived cells	sih embryos lack heart contraction	RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C 30 sec at 60°C 30 sec at 72°C] x 13 cycles; 5 min at 72°C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.	Embryos were grown in normal conditions	genotype/variation:WT\|embryonic stage:28 hpf	GSM1439468	GSM1439468: WT1; Danio rerio; RNA Seq	GSM1439468		1	RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C 30 sec at 60°C 30 sec at 72°C] x 13 cycles; 5 min at 72°C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.	GEO Accession:GSM1439468	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	SRP044634		JGZ-01.fastq.gz	fastq	1583485146.0	29323799.0	GSM1439468 r1	0:54	A:405051413;C:391145102;G:382645289;T:404569188;N:74154	54				405051413	391145102	382645289	404569188	74154	SRX657107	SRS662287	SRA175990	GEO	IGBMC	1	0.94743		0.05464		0.73156		0.46572		54		B		usable mapping rate	illumina	early_illumina	unknown	poly_a	unknown	bulk	unknown	unknown	France	2014-07-18	Pharyngula	Embryo	Tail	Multi-system
39921	39921	SRR2392494	SRX1240723	SRS1067356	SRP063659	PRJNA295533	Accelerated cartilage differentiation distinguishes the lower from the upper vertebrate face	GSE72985	Transcriptome Analysis	Distinct shaping of the upper versus lower facial skeleton is essential for function of the vertebrate jaw and middle ear yet the cellular mechanisms by which this occurs have remained unclear. Here we show that Endothelin1 Edn1 signaling accelerates mesenchymal condensation and subsequent cartilage formation in the lower face through antagonism of Jagged Notch signaling and Prrx1 transcription factors. A genomic analysis of facial skeletal precursors in mutants and overexpression embryos reveals that Jagged Notch signaling represses genes that are strongly induced as pharyngeal arch neural crest derived cells begin skeletal differentiation. In wild types initial Jagged Notch repression dorsally ensures that barx1+ condensations and cartilage differentiation occur first in ventral intermediate zones of the pharyngeal arches. Reduced Jagged Notch signaling results in an expansion of pre cartilage condensations in the upper face with loss of barx1 partially restoring dorsal cartilage shapes in jag1b mutants. Further by studying new mutants for zebrafish prrx1a and prrx1b we find that Prrx1 genes function in parallel to Jagged Notch signaling to restrict the formation of dorsal barx1+ pre cartilage condensations. Consistently combined losses of jag1b and prrx1a/b robustly rescue ventral barx1+ condensations and lower facial cartilage development in edn1 mutants. Together our work suggests that Edn1 works through parallel inhibition of Jagged Notch and Prrx1 pathways to promote an earlier and more extensive establishment of cartilage condensations in the lower face. Overall design: We performed RNAseq on FACS sorted neural crest derived pharyngeal arch cells fli1a:GFP; sox10:DsRed double positive from wild type embryos at 3 different stages 20 28 and 36 hpf and embryos with altered levels of Edn1 and Notch signaling edn1 mutants and hsp70I:Gal4; UAS:Edn1 transgenics; jag1b mutants dibenzazepine treated embryos and hsp70I:Gal4; UAS:NICD transgenics. We also sequenced RNA from heat shocked UAS:Edn1+ and hsp…	pubmed:27058748	UASEdn1 36hpf DP	GSM1876262	source name:Pharyngeal arches\|tissue:Pharyngeal arches\|developmental stage:embryo\|age:36 hpf\|genotype:UASEdn1\|treatment:Heat shocked	UASEdn1 36hpf DP	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the RPKM values. Genome build: GRCz10 Supplementary files format and content: csv text files include RPKM values for each gene in each sample	Pharyngeal arches		GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		tissue:Pharyngeal arches\|developmental stage:embryo\|age:36 hpf\|genotype:UASEdn1\|treatment:Heat shocked	GSM1876262	GSM1876262: UASEdn1 36hpf DP; Danio rerio; RNA Seq	GSM1876262		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM1876262	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP063659		GC-68_L000_R1_001.fastq.gz GC-68_L000_R2_001.fastq.gz	fastq fastq	7552509120.0	49687560.0	GSM1876262 r1	0:76 1:76	A:2200651776;C:1439090377;G:1524077665;T:2388535092;N:154210	76	76			2200651776	1439090377	1524077665	2388535092	154210	SRX1240723	SRS1067356	SRA297650	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.87955	0.93035	0.13705	0.14804	0.76274	0.77796	0.48221	0.47595	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2015-09-14	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
39922	39922	SRR2392493	SRX1240722	SRS1067357	SRP063659	PRJNA295533	Accelerated cartilage differentiation distinguishes the lower from the upper vertebrate face	GSE72985	Transcriptome Analysis	Distinct shaping of the upper versus lower facial skeleton is essential for function of the vertebrate jaw and middle ear yet the cellular mechanisms by which this occurs have remained unclear. Here we show that Endothelin1 Edn1 signaling accelerates mesenchymal condensation and subsequent cartilage formation in the lower face through antagonism of Jagged Notch signaling and Prrx1 transcription factors. A genomic analysis of facial skeletal precursors in mutants and overexpression embryos reveals that Jagged Notch signaling represses genes that are strongly induced as pharyngeal arch neural crest derived cells begin skeletal differentiation. In wild types initial Jagged Notch repression dorsally ensures that barx1+ condensations and cartilage differentiation occur first in ventral intermediate zones of the pharyngeal arches. Reduced Jagged Notch signaling results in an expansion of pre cartilage condensations in the upper face with loss of barx1 partially restoring dorsal cartilage shapes in jag1b mutants. Further by studying new mutants for zebrafish prrx1a and prrx1b we find that Prrx1 genes function in parallel to Jagged Notch signaling to restrict the formation of dorsal barx1+ pre cartilage condensations. Consistently combined losses of jag1b and prrx1a/b robustly rescue ventral barx1+ condensations and lower facial cartilage development in edn1 mutants. Together our work suggests that Edn1 works through parallel inhibition of Jagged Notch and Prrx1 pathways to promote an earlier and more extensive establishment of cartilage condensations in the lower face. Overall design: We performed RNAseq on FACS sorted neural crest derived pharyngeal arch cells fli1a:GFP; sox10:DsRed double positive from wild type embryos at 3 different stages 20 28 and 36 hpf and embryos with altered levels of Edn1 and Notch signaling edn1 mutants and hsp70I:Gal4; UAS:Edn1 transgenics; jag1b mutants dibenzazepine treated embryos and hsp70I:Gal4; UAS:NICD transgenics. We also sequenced RNA from heat shocked UAS:Edn1+ and hsp…	pubmed:27058748	hspGal4 36hpf DP	GSM1876261	source name:Pharyngeal arches\|tissue:Pharyngeal arches\|developmental stage:embryo\|age:36 hpf\|genotype:hspGal4\|treatment:Heat shocked	hspGal4 36hpf DP	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the RPKM values. Genome build: GRCz10 Supplementary files format and content: csv text files include RPKM values for each gene in each sample	Pharyngeal arches		GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		tissue:Pharyngeal arches\|developmental stage:embryo\|age:36 hpf\|genotype:hspGal4\|treatment:Heat shocked	GSM1876261	GSM1876261: hspGal4 36hpf DP; Danio rerio; RNA Seq	GSM1876261		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM1876261	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP063659		GC-67_L000_R1_001.fastq.gz GC-67_L000_R2_001.fastq.gz	fastq fastq	12101492616.0	79615083.0	GSM1876261 r1	0:76 1:76	A:3579849331;C:2226140960;G:2397001824;T:3898240336;N:260165	76	76			3579849331	2226140960	2397001824	3898240336	260165	SRX1240722	SRS1067357	SRA297650	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.85987	0.92528	0.14437	0.15795	0.7624	0.7781	0.50831	0.50375	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2015-09-14	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
39923	39923	SRR2392492	SRX1240721	SRS1067358	SRP063659	PRJNA295533	Accelerated cartilage differentiation distinguishes the lower from the upper vertebrate face	GSE72985	Transcriptome Analysis	Distinct shaping of the upper versus lower facial skeleton is essential for function of the vertebrate jaw and middle ear yet the cellular mechanisms by which this occurs have remained unclear. Here we show that Endothelin1 Edn1 signaling accelerates mesenchymal condensation and subsequent cartilage formation in the lower face through antagonism of Jagged Notch signaling and Prrx1 transcription factors. A genomic analysis of facial skeletal precursors in mutants and overexpression embryos reveals that Jagged Notch signaling represses genes that are strongly induced as pharyngeal arch neural crest derived cells begin skeletal differentiation. In wild types initial Jagged Notch repression dorsally ensures that barx1+ condensations and cartilage differentiation occur first in ventral intermediate zones of the pharyngeal arches. Reduced Jagged Notch signaling results in an expansion of pre cartilage condensations in the upper face with loss of barx1 partially restoring dorsal cartilage shapes in jag1b mutants. Further by studying new mutants for zebrafish prrx1a and prrx1b we find that Prrx1 genes function in parallel to Jagged Notch signaling to restrict the formation of dorsal barx1+ pre cartilage condensations. Consistently combined losses of jag1b and prrx1a/b robustly rescue ventral barx1+ condensations and lower facial cartilage development in edn1 mutants. Together our work suggests that Edn1 works through parallel inhibition of Jagged Notch and Prrx1 pathways to promote an earlier and more extensive establishment of cartilage condensations in the lower face. Overall design: We performed RNAseq on FACS sorted neural crest derived pharyngeal arch cells fli1a:GFP; sox10:DsRed double positive from wild type embryos at 3 different stages 20 28 and 36 hpf and embryos with altered levels of Edn1 and Notch signaling edn1 mutants and hsp70I:Gal4; UAS:Edn1 transgenics; jag1b mutants dibenzazepine treated embryos and hsp70I:Gal4; UAS:NICD transgenics. We also sequenced RNA from heat shocked UAS:Edn1+ and hsp…	pubmed:27058748	jag1b++ 36hpf DP	GSM1876260	source name:Pharyngeal arches\|tissue:Pharyngeal arches\|developmental stage:embryo\|age:36 hpf\|genotype:WT\|treatment:Genotyped	jag1b++ 36hpf DP	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the RPKM values. Genome build: GRCz10 Supplementary files format and content: csv text files include RPKM values for each gene in each sample	Pharyngeal arches		GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		tissue:Pharyngeal arches\|developmental stage:embryo\|age:36 hpf\|genotype:WT\|treatment:Genotyped	GSM1876260	GSM1876260: jag1b++ 36hpf DP; Danio rerio; RNA Seq	GSM1876260		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM1876260	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP063659		GC-62_L000_R1_001.fastq.gz GC-62_L000_R2_001.fastq.gz	fastq fastq	9196789944.0	60505197.0	GSM1876260 r1	0:76 1:76	A:2617231956;C:1761629764;G:1849570227;T:2965452565;N:2905432	76	76			2617231956	1761629764	1849570227	2965452565	2905432	SRX1240721	SRS1067358	SRA297650	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.87575	0.84626	0.14246	0.13869	0.76426	0.78595	0.49695	0.49462	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2015-09-14	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
39924	39924	SRR2392491	SRX1240720	SRS1067359	SRP063659	PRJNA295533	Accelerated cartilage differentiation distinguishes the lower from the upper vertebrate face	GSE72985	Transcriptome Analysis	Distinct shaping of the upper versus lower facial skeleton is essential for function of the vertebrate jaw and middle ear yet the cellular mechanisms by which this occurs have remained unclear. Here we show that Endothelin1 Edn1 signaling accelerates mesenchymal condensation and subsequent cartilage formation in the lower face through antagonism of Jagged Notch signaling and Prrx1 transcription factors. A genomic analysis of facial skeletal precursors in mutants and overexpression embryos reveals that Jagged Notch signaling represses genes that are strongly induced as pharyngeal arch neural crest derived cells begin skeletal differentiation. In wild types initial Jagged Notch repression dorsally ensures that barx1+ condensations and cartilage differentiation occur first in ventral intermediate zones of the pharyngeal arches. Reduced Jagged Notch signaling results in an expansion of pre cartilage condensations in the upper face with loss of barx1 partially restoring dorsal cartilage shapes in jag1b mutants. Further by studying new mutants for zebrafish prrx1a and prrx1b we find that Prrx1 genes function in parallel to Jagged Notch signaling to restrict the formation of dorsal barx1+ pre cartilage condensations. Consistently combined losses of jag1b and prrx1a/b robustly rescue ventral barx1+ condensations and lower facial cartilage development in edn1 mutants. Together our work suggests that Edn1 works through parallel inhibition of Jagged Notch and Prrx1 pathways to promote an earlier and more extensive establishment of cartilage condensations in the lower face. Overall design: We performed RNAseq on FACS sorted neural crest derived pharyngeal arch cells fli1a:GFP; sox10:DsRed double positive from wild type embryos at 3 different stages 20 28 and 36 hpf and embryos with altered levels of Edn1 and Notch signaling edn1 mutants and hsp70I:Gal4; UAS:Edn1 transgenics; jag1b mutants dibenzazepine treated embryos and hsp70I:Gal4; UAS:NICD transgenics. We also sequenced RNA from heat shocked UAS:Edn1+ and hsp…	pubmed:27058748	hspEdn1 36hpf DP	GSM1876259	source name:Pharyngeal arches\|tissue:Pharyngeal arches\|developmental stage:embryo\|age:36 hpf\|genotype:hspGal4 ; UASEdn1\|treatment:Heat shocked	hspEdn1 36hpf DP	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the RPKM values. Genome build: GRCz10 Supplementary files format and content: csv text files include RPKM values for each gene in each sample	Pharyngeal arches		GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		tissue:Pharyngeal arches\|developmental stage:embryo\|age:36 hpf\|genotype:hspGal4 ; UASEdn1\|treatment:Heat shocked	GSM1876259	GSM1876259: hspEdn1 36hpf DP; Danio rerio; RNA Seq	GSM1876259		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM1876259	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP063659		GC-63_L000_R1_001.fastq.gz GC-63_L000_R2_001.fastq.gz	fastq fastq	8241464016.0	54220158.0	GSM1876259 r1	0:76 1:76	A:2338801834;C:1581411340;G:1652427014;T:2666281574;N:2542254	76	76			2338801834	1581411340	1652427014	2666281574	2542254	SRX1240720	SRS1067359	SRA297650	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.88843	0.85822	0.15095	0.14812	0.75978	0.7751	0.49125	0.48482	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2015-09-14	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
39925	39925	SRR2392490	SRX1240719	SRS1067360	SRP063659	PRJNA295533	Accelerated cartilage differentiation distinguishes the lower from the upper vertebrate face	GSE72985	Transcriptome Analysis	Distinct shaping of the upper versus lower facial skeleton is essential for function of the vertebrate jaw and middle ear yet the cellular mechanisms by which this occurs have remained unclear. Here we show that Endothelin1 Edn1 signaling accelerates mesenchymal condensation and subsequent cartilage formation in the lower face through antagonism of Jagged Notch signaling and Prrx1 transcription factors. A genomic analysis of facial skeletal precursors in mutants and overexpression embryos reveals that Jagged Notch signaling represses genes that are strongly induced as pharyngeal arch neural crest derived cells begin skeletal differentiation. In wild types initial Jagged Notch repression dorsally ensures that barx1+ condensations and cartilage differentiation occur first in ventral intermediate zones of the pharyngeal arches. Reduced Jagged Notch signaling results in an expansion of pre cartilage condensations in the upper face with loss of barx1 partially restoring dorsal cartilage shapes in jag1b mutants. Further by studying new mutants for zebrafish prrx1a and prrx1b we find that Prrx1 genes function in parallel to Jagged Notch signaling to restrict the formation of dorsal barx1+ pre cartilage condensations. Consistently combined losses of jag1b and prrx1a/b robustly rescue ventral barx1+ condensations and lower facial cartilage development in edn1 mutants. Together our work suggests that Edn1 works through parallel inhibition of Jagged Notch and Prrx1 pathways to promote an earlier and more extensive establishment of cartilage condensations in the lower face. Overall design: We performed RNAseq on FACS sorted neural crest derived pharyngeal arch cells fli1a:GFP; sox10:DsRed double positive from wild type embryos at 3 different stages 20 28 and 36 hpf and embryos with altered levels of Edn1 and Notch signaling edn1 mutants and hsp70I:Gal4; UAS:Edn1 transgenics; jag1b mutants dibenzazepine treated embryos and hsp70I:Gal4; UAS:NICD transgenics. We also sequenced RNA from heat shocked UAS:Edn1+ and hsp…	pubmed:27058748	hspNICD 36hpf DP	GSM1876258	source name:Pharyngeal arches\|tissue:Pharyngeal arches\|developmental stage:embryo\|age:36 hpf\|genotype:hspGal4 ; UASNICD\|treatment:Heat shocked	hspNICD 36hpf DP	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the RPKM values. Genome build: GRCz10 Supplementary files format and content: csv text files include RPKM values for each gene in each sample	Pharyngeal arches		GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		tissue:Pharyngeal arches\|developmental stage:embryo\|age:36 hpf\|genotype:hspGal4 ; UASNICD\|treatment:Heat shocked	GSM1876258	GSM1876258: hspNICD 36hpf DP; Danio rerio; RNA Seq	GSM1876258		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM1876258	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP063659		GC-71_L000_R1_001.fastq.gz GC-71_L000_R2_001.fastq.gz	fastq fastq	8181679072.0	53826836.0	GSM1876258 r1	0:76 1:76	A:2319439232;C:1614438452;G:1687303013;T:2557951732;N:2546643	76	76			2319439232	1614438452	1687303013	2557951732	2546643	SRX1240719	SRS1067360	SRA297650	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.90043	0.87604	0.13901	0.13824	0.74937	0.76777	0.48827	0.47857	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2015-09-14	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
39926	39926	SRR2392489	SRX1240718	SRS1067361	SRP063659	PRJNA295533	Accelerated cartilage differentiation distinguishes the lower from the upper vertebrate face	GSE72985	Transcriptome Analysis	Distinct shaping of the upper versus lower facial skeleton is essential for function of the vertebrate jaw and middle ear yet the cellular mechanisms by which this occurs have remained unclear. Here we show that Endothelin1 Edn1 signaling accelerates mesenchymal condensation and subsequent cartilage formation in the lower face through antagonism of Jagged Notch signaling and Prrx1 transcription factors. A genomic analysis of facial skeletal precursors in mutants and overexpression embryos reveals that Jagged Notch signaling represses genes that are strongly induced as pharyngeal arch neural crest derived cells begin skeletal differentiation. In wild types initial Jagged Notch repression dorsally ensures that barx1+ condensations and cartilage differentiation occur first in ventral intermediate zones of the pharyngeal arches. Reduced Jagged Notch signaling results in an expansion of pre cartilage condensations in the upper face with loss of barx1 partially restoring dorsal cartilage shapes in jag1b mutants. Further by studying new mutants for zebrafish prrx1a and prrx1b we find that Prrx1 genes function in parallel to Jagged Notch signaling to restrict the formation of dorsal barx1+ pre cartilage condensations. Consistently combined losses of jag1b and prrx1a/b robustly rescue ventral barx1+ condensations and lower facial cartilage development in edn1 mutants. Together our work suggests that Edn1 works through parallel inhibition of Jagged Notch and Prrx1 pathways to promote an earlier and more extensive establishment of cartilage condensations in the lower face. Overall design: We performed RNAseq on FACS sorted neural crest derived pharyngeal arch cells fli1a:GFP; sox10:DsRed double positive from wild type embryos at 3 different stages 20 28 and 36 hpf and embryos with altered levels of Edn1 and Notch signaling edn1 mutants and hsp70I:Gal4; UAS:Edn1 transgenics; jag1b mutants dibenzazepine treated embryos and hsp70I:Gal4; UAS:NICD transgenics. We also sequenced RNA from heat shocked UAS:Edn1+ and hsp…	pubmed:27058748	DBZ 36hpf DP	GSM1876257	source name:Pharyngeal arches\|tissue:Pharyngeal arches\|developmental stage:embryo\|age:36 hpf\|genotype:WT\|treatment:DBZ treated	DBZ 36hpf DP	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the RPKM values. Genome build: GRCz10 Supplementary files format and content: csv text files include RPKM values for each gene in each sample	Pharyngeal arches		GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		tissue:Pharyngeal arches\|developmental stage:embryo\|age:36 hpf\|genotype:WT\|treatment:DBZ treated	GSM1876257	GSM1876257: DBZ 36hpf DP; Danio rerio; RNA Seq	GSM1876257		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM1876257	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP063659		GC-41_L000_R1_001.fastq.gz GC-41_L000_R2_001.fastq.gz	fastq fastq	10477585112.0	68931481.0	GSM1876257 r1	0:76 1:76	A:3034271232;C:2011126753;G:2224836663;T:3203537953;N:3812511	76	76			3034271232	2011126753	2224836663	3203537953	3812511	SRX1240718	SRS1067361	SRA297650	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.86576	0.91066	0.12989	0.13947	0.77273	0.78804	0.49193	0.49239	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2015-09-14	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
39927	39927	SRR2392488	SRX1240717	SRS1067362	SRP063659	PRJNA295533	Accelerated cartilage differentiation distinguishes the lower from the upper vertebrate face	GSE72985	Transcriptome Analysis	Distinct shaping of the upper versus lower facial skeleton is essential for function of the vertebrate jaw and middle ear yet the cellular mechanisms by which this occurs have remained unclear. Here we show that Endothelin1 Edn1 signaling accelerates mesenchymal condensation and subsequent cartilage formation in the lower face through antagonism of Jagged Notch signaling and Prrx1 transcription factors. A genomic analysis of facial skeletal precursors in mutants and overexpression embryos reveals that Jagged Notch signaling represses genes that are strongly induced as pharyngeal arch neural crest derived cells begin skeletal differentiation. In wild types initial Jagged Notch repression dorsally ensures that barx1+ condensations and cartilage differentiation occur first in ventral intermediate zones of the pharyngeal arches. Reduced Jagged Notch signaling results in an expansion of pre cartilage condensations in the upper face with loss of barx1 partially restoring dorsal cartilage shapes in jag1b mutants. Further by studying new mutants for zebrafish prrx1a and prrx1b we find that Prrx1 genes function in parallel to Jagged Notch signaling to restrict the formation of dorsal barx1+ pre cartilage condensations. Consistently combined losses of jag1b and prrx1a/b robustly rescue ventral barx1+ condensations and lower facial cartilage development in edn1 mutants. Together our work suggests that Edn1 works through parallel inhibition of Jagged Notch and Prrx1 pathways to promote an earlier and more extensive establishment of cartilage condensations in the lower face. Overall design: We performed RNAseq on FACS sorted neural crest derived pharyngeal arch cells fli1a:GFP; sox10:DsRed double positive from wild type embryos at 3 different stages 20 28 and 36 hpf and embryos with altered levels of Edn1 and Notch signaling edn1 mutants and hsp70I:Gal4; UAS:Edn1 transgenics; jag1b mutants dibenzazepine treated embryos and hsp70I:Gal4; UAS:NICD transgenics. We also sequenced RNA from heat shocked UAS:Edn1+ and hsp…	pubmed:27058748	jag1b 36hpf DP	GSM1876256	source name:Pharyngeal arches\|tissue:Pharyngeal arches\|developmental stage:embryo\|age:36 hpf\|genotype:jag1b / \|treatment:Genotyped	jag1b 36hpf DP	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the RPKM values. Genome build: GRCz10 Supplementary files format and content: csv text files include RPKM values for each gene in each sample	Pharyngeal arches		GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		tissue:Pharyngeal arches\|developmental stage:embryo\|age:36 hpf\|genotype:jag1b / \|treatment:Genotyped	GSM1876256	GSM1876256: jag1b 36hpf DP; Danio rerio; RNA Seq	GSM1876256		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM1876256	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP063659		GC-61_L000_R2_001.fastq.gz GC-61_L000_R1_001.fastq.gz	fastq fastq	7981914592.0	52512596.0	GSM1876256 r1	0:76 1:76	A:2278594852;C:1520667450;G:1610295025;T:2569901477;N:2455788	76	76			2278594852	1520667450	1610295025	2569901477	2455788	SRX1240717	SRS1067362	SRA297650	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.88292	0.85134	0.15785	0.15494	0.7643	0.78222	0.5054	0.49691	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2015-09-14	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
39928	39928	SRR2392487	SRX1240716	SRS1067363	SRP063659	PRJNA295533	Accelerated cartilage differentiation distinguishes the lower from the upper vertebrate face	GSE72985	Transcriptome Analysis	Distinct shaping of the upper versus lower facial skeleton is essential for function of the vertebrate jaw and middle ear yet the cellular mechanisms by which this occurs have remained unclear. Here we show that Endothelin1 Edn1 signaling accelerates mesenchymal condensation and subsequent cartilage formation in the lower face through antagonism of Jagged Notch signaling and Prrx1 transcription factors. A genomic analysis of facial skeletal precursors in mutants and overexpression embryos reveals that Jagged Notch signaling represses genes that are strongly induced as pharyngeal arch neural crest derived cells begin skeletal differentiation. In wild types initial Jagged Notch repression dorsally ensures that barx1+ condensations and cartilage differentiation occur first in ventral intermediate zones of the pharyngeal arches. Reduced Jagged Notch signaling results in an expansion of pre cartilage condensations in the upper face with loss of barx1 partially restoring dorsal cartilage shapes in jag1b mutants. Further by studying new mutants for zebrafish prrx1a and prrx1b we find that Prrx1 genes function in parallel to Jagged Notch signaling to restrict the formation of dorsal barx1+ pre cartilage condensations. Consistently combined losses of jag1b and prrx1a/b robustly rescue ventral barx1+ condensations and lower facial cartilage development in edn1 mutants. Together our work suggests that Edn1 works through parallel inhibition of Jagged Notch and Prrx1 pathways to promote an earlier and more extensive establishment of cartilage condensations in the lower face. Overall design: We performed RNAseq on FACS sorted neural crest derived pharyngeal arch cells fli1a:GFP; sox10:DsRed double positive from wild type embryos at 3 different stages 20 28 and 36 hpf and embryos with altered levels of Edn1 and Notch signaling edn1 mutants and hsp70I:Gal4; UAS:Edn1 transgenics; jag1b mutants dibenzazepine treated embryos and hsp70I:Gal4; UAS:NICD transgenics. We also sequenced RNA from heat shocked UAS:Edn1+ and hsp…	pubmed:27058748	edn1 36hpf DP	GSM1876255	source name:Pharyngeal arches\|tissue:Pharyngeal arches\|developmental stage:embryo\|age:36 hpf\|genotype:edn1 / \|treatment:N1	edn1 36hpf DP	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the RPKM values. Genome build: GRCz10 Supplementary files format and content: csv text files include RPKM values for each gene in each sample	Pharyngeal arches		GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		tissue:Pharyngeal arches\|developmental stage:embryo\|age:36 hpf\|genotype:edn1 / \|treatment:N1	GSM1876255	GSM1876255: edn1 36hpf DP; Danio rerio; RNA Seq	GSM1876255		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM1876255	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP063659		GC-34_CAGATC_L008_R1_001.fastq.gz GC-34_CAGATC_L008_R2_001.fastq.gz	fastq fastq	3805470400.0	38054704.0	GSM1876255 r1	0:50 1:50	A:1039863232;C:811509659;G:855601660;T:1094752796;N:3743053	50	50			1039863232	811509659	855601660	1094752796	3743053	SRX1240716	SRS1067363	SRA297650	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.90373	0.77103	0.11765	0.1006	0.75982	0.77565	0.48596	0.4847	50	50	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2015-09-14	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
39929	39929	SRR2392486	SRX1240715	SRS1067364	SRP063659	PRJNA295533	Accelerated cartilage differentiation distinguishes the lower from the upper vertebrate face	GSE72985	Transcriptome Analysis	Distinct shaping of the upper versus lower facial skeleton is essential for function of the vertebrate jaw and middle ear yet the cellular mechanisms by which this occurs have remained unclear. Here we show that Endothelin1 Edn1 signaling accelerates mesenchymal condensation and subsequent cartilage formation in the lower face through antagonism of Jagged Notch signaling and Prrx1 transcription factors. A genomic analysis of facial skeletal precursors in mutants and overexpression embryos reveals that Jagged Notch signaling represses genes that are strongly induced as pharyngeal arch neural crest derived cells begin skeletal differentiation. In wild types initial Jagged Notch repression dorsally ensures that barx1+ condensations and cartilage differentiation occur first in ventral intermediate zones of the pharyngeal arches. Reduced Jagged Notch signaling results in an expansion of pre cartilage condensations in the upper face with loss of barx1 partially restoring dorsal cartilage shapes in jag1b mutants. Further by studying new mutants for zebrafish prrx1a and prrx1b we find that Prrx1 genes function in parallel to Jagged Notch signaling to restrict the formation of dorsal barx1+ pre cartilage condensations. Consistently combined losses of jag1b and prrx1a/b robustly rescue ventral barx1+ condensations and lower facial cartilage development in edn1 mutants. Together our work suggests that Edn1 works through parallel inhibition of Jagged Notch and Prrx1 pathways to promote an earlier and more extensive establishment of cartilage condensations in the lower face. Overall design: We performed RNAseq on FACS sorted neural crest derived pharyngeal arch cells fli1a:GFP; sox10:DsRed double positive from wild type embryos at 3 different stages 20 28 and 36 hpf and embryos with altered levels of Edn1 and Notch signaling edn1 mutants and hsp70I:Gal4; UAS:Edn1 transgenics; jag1b mutants dibenzazepine treated embryos and hsp70I:Gal4; UAS:NICD transgenics. We also sequenced RNA from heat shocked UAS:Edn1+ and hsp…	pubmed:27058748	WT 28hpf DP	GSM1876254	source name:Pharyngeal arches\|tissue:Pharyngeal arches\|developmental stage:embryo\|age:28 hpf\|genotype:WT\|treatment:N1	WT 28hpf DP	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the RPKM values. Genome build: GRCz10 Supplementary files format and content: csv text files include RPKM values for each gene in each sample	Pharyngeal arches		GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		tissue:Pharyngeal arches\|developmental stage:embryo\|age:28 hpf\|genotype:WT\|treatment:N1	GSM1876254	GSM1876254: WT 28hpf DP; Danio rerio; RNA Seq	GSM1876254		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM1876254	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP063659		GC-53_L000_R1_001.fastq.gz GC-53_L000_R2_001.fastq.gz	fastq fastq	8894656200.0	58517475.0	GSM1876254 r1	0:76 1:76	A:2518354811;C:1741233873;G:1824297464;T:2807980201;N:2789851	76	76			2518354811	1741233873	1824297464	2807980201	2789851	SRX1240715	SRS1067364	SRA297650	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.89587	0.86799	0.11918	0.11489	0.74846	0.76528	0.49754	0.49063	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2015-09-14	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
39931	39931	SRR2392484	SRX1240713	SRS1067366	SRP063659	PRJNA295533	Accelerated cartilage differentiation distinguishes the lower from the upper vertebrate face	GSE72985	Transcriptome Analysis	Distinct shaping of the upper versus lower facial skeleton is essential for function of the vertebrate jaw and middle ear yet the cellular mechanisms by which this occurs have remained unclear. Here we show that Endothelin1 Edn1 signaling accelerates mesenchymal condensation and subsequent cartilage formation in the lower face through antagonism of Jagged Notch signaling and Prrx1 transcription factors. A genomic analysis of facial skeletal precursors in mutants and overexpression embryos reveals that Jagged Notch signaling represses genes that are strongly induced as pharyngeal arch neural crest derived cells begin skeletal differentiation. In wild types initial Jagged Notch repression dorsally ensures that barx1+ condensations and cartilage differentiation occur first in ventral intermediate zones of the pharyngeal arches. Reduced Jagged Notch signaling results in an expansion of pre cartilage condensations in the upper face with loss of barx1 partially restoring dorsal cartilage shapes in jag1b mutants. Further by studying new mutants for zebrafish prrx1a and prrx1b we find that Prrx1 genes function in parallel to Jagged Notch signaling to restrict the formation of dorsal barx1+ pre cartilage condensations. Consistently combined losses of jag1b and prrx1a/b robustly rescue ventral barx1+ condensations and lower facial cartilage development in edn1 mutants. Together our work suggests that Edn1 works through parallel inhibition of Jagged Notch and Prrx1 pathways to promote an earlier and more extensive establishment of cartilage condensations in the lower face. Overall design: We performed RNAseq on FACS sorted neural crest derived pharyngeal arch cells fli1a:GFP; sox10:DsRed double positive from wild type embryos at 3 different stages 20 28 and 36 hpf and embryos with altered levels of Edn1 and Notch signaling edn1 mutants and hsp70I:Gal4; UAS:Edn1 transgenics; jag1b mutants dibenzazepine treated embryos and hsp70I:Gal4; UAS:NICD transgenics. We also sequenced RNA from heat shocked UAS:Edn1+ and hsp…	pubmed:27058748	WT 36hpf DP	GSM1876252	source name:Pharyngeal arches\|tissue:Pharyngeal arches\|developmental stage:embryo\|age:36 hpf\|genotype:WT\|treatment:N1	WT 36hpf DP	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the RPKM values. Genome build: GRCz10 Supplementary files format and content: csv text files include RPKM values for each gene in each sample	Pharyngeal arches		GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		tissue:Pharyngeal arches\|developmental stage:embryo\|age:36 hpf\|genotype:WT\|treatment:N1	GSM1876252	GSM1876252: WT 36hpf DP; Danio rerio; RNA Seq	GSM1876252		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM1876252	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP063659		GC-24_ATTCCT_L001_R1_001.fastq.gz GC-24_ATTCCT_L001_R2_001.fastq.gz	fastq fastq	5577850800.0	55778508.0	GSM1876252 r1	0:50 1:50	A:1539279722;C:1164400006;G:1236602222;T:1636301311;N:1267539	50	50			1539279722	1164400006	1236602222	1636301311	1267539	SRX1240713	SRS1067366	SRA297650	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.90764	0.74515	0.17719	0.14848	0.75566	0.77737	0.49598	0.48654	50	50	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2015-09-14	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
41312	41312	SRR4199307	SRX2148087	SRS1679265	SRP087617	PRJNA342262	Proliferation independent regulation of organ size by Notch signaling	GSE86571	Transcriptome Analysis	Purpose: To identify genes that are transcriptionally controlled by Notch signaling during zebrafish lateral line proneuromast formation. Methods: We isolated primordium cells from dissected tails of 36 hpf TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd and sibling TgcldnB:GFP;TgcldnB:gal4 embryos by FACS and performed RNASeq analysis. Results: Using an optimized data analysis workflow we mapped about 26 million sequence reads per sample to the zebrafish genome build danRer10 and identified 32 105 transcripts in the dissociated tails of WT and NICD zebrafish with TopHat workflow. Approximately 2% of the transcripts showed differential expression between the WT and NICD tails with a fold change =0.5 and p value <0.01. Conclusion: RNASeq analyses revealed that Notch signaling cell autonomously induces apical constriction and cell adhesion. Overall design: Zebrafish lateral line mRNA profiles of 36 hours wild type WT and NICD embryos were generated in triplicate using HiSeq 2500 Illumina.	pubmed:28085667	NICD rep3	GSM2306087	source name:dissociated embryo tails\|strain:TgcldnB:GFP; TgcldnB:gal4 x TgUAS:nicd\|tissue:dissociated embryo tails\|age:36 hpf	NICD rep3	Illumina CASAVA 1.8.2 software used for basecalling. Sequenced reads were mapped to danRer10 whole genome using tophat v2.0.13 with parameters p 8 transcriptome index G o no coverage search The fragments per kilobase of transcript per million mapped reads FPKM values were generated using Cufflinks version 2.2.1 with parameters p 4 g o. Reads were counted on danRer10 Ensembl transcripts from UCSC using HTSeq version 0.6.1 with parameters m intersection nonempty s no f bam. Genome build: danRer10 from UCSC Supplementary files format and content: Two tab delimited text files: one includes raw counts of sequencing reads for each Sample one includes FPKM values for each Sample.	dissociated embryo tails	Zebrafish embryos positive for GFP were selected.	Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.	Zebrafish embryos were raised for 36 hpf in the 28.5C incubator.	strain:TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd\|tissue:dissociated embryo tails\|age:36 hpf	GSM2306087	GSM2306087: NICD rep3; Danio rerio; RNA Seq	GSM2306087		1	Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.	GEO Accession:GSM2306087	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP087617		mutant3.fastq.gz	fastq	1706861931.0	33467881.0	GSM2306087 r1	0:51 1:0	A:400027681;C:444926525;G:399939257;T:461913972;N:54496	51	0			400027681	444926525	399939257	461913972	54496	SRX2148087	SRS1679265	SRA464955	GEO	Stowers Institute for Medical Research	1	0.75848		0.06958		0.73616		0.47901		51		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2016-09-08	Pharyngula	Embryo	Tail	Multi-system
41313	41313	SRR4199306	SRX2148086	SRS1679264	SRP087617	PRJNA342262	Proliferation independent regulation of organ size by Notch signaling	GSE86571	Transcriptome Analysis	Purpose: To identify genes that are transcriptionally controlled by Notch signaling during zebrafish lateral line proneuromast formation. Methods: We isolated primordium cells from dissected tails of 36 hpf TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd and sibling TgcldnB:GFP;TgcldnB:gal4 embryos by FACS and performed RNASeq analysis. Results: Using an optimized data analysis workflow we mapped about 26 million sequence reads per sample to the zebrafish genome build danRer10 and identified 32 105 transcripts in the dissociated tails of WT and NICD zebrafish with TopHat workflow. Approximately 2% of the transcripts showed differential expression between the WT and NICD tails with a fold change =0.5 and p value <0.01. Conclusion: RNASeq analyses revealed that Notch signaling cell autonomously induces apical constriction and cell adhesion. Overall design: Zebrafish lateral line mRNA profiles of 36 hours wild type WT and NICD embryos were generated in triplicate using HiSeq 2500 Illumina.	pubmed:28085667	NICD rep2	GSM2306086	source name:dissociated embryo tails\|strain:TgcldnB:GFP; TgcldnB:gal4 x TgUAS:nicd\|tissue:dissociated embryo tails\|age:36 hpf	NICD rep2	Illumina CASAVA 1.8.2 software used for basecalling. Sequenced reads were mapped to danRer10 whole genome using tophat v2.0.13 with parameters p 8 transcriptome index G o no coverage search The fragments per kilobase of transcript per million mapped reads FPKM values were generated using Cufflinks version 2.2.1 with parameters p 4 g o. Reads were counted on danRer10 Ensembl transcripts from UCSC using HTSeq version 0.6.1 with parameters m intersection nonempty s no f bam. Genome build: danRer10 from UCSC Supplementary files format and content: Two tab delimited text files: one includes raw counts of sequencing reads for each Sample one includes FPKM values for each Sample.	dissociated embryo tails	Zebrafish embryos positive for GFP were selected.	Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.	Zebrafish embryos were raised for 36 hpf in the 28.5C incubator.	strain:TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd\|tissue:dissociated embryo tails\|age:36 hpf	GSM2306086	GSM2306086: NICD rep2; Danio rerio; RNA Seq	GSM2306086		1	Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.	GEO Accession:GSM2306086	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP087617		mutant2.fastq.gz	fastq	1745551857.0	34226507.0	GSM2306086 r1	0:51 1:0	A:414724753;C:449494336;G:403529006;T:477747391;N:56371	51	0			414724753	449494336	403529006	477747391	56371	SRX2148086	SRS1679264	SRA464955	GEO	Stowers Institute for Medical Research	1	0.77355		0.08842		0.71674		0.48589		51		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2016-09-08	Pharyngula	Embryo	Tail	Multi-system
41314	41314	SRR4199305	SRX2148085	SRS1679263	SRP087617	PRJNA342262	Proliferation independent regulation of organ size by Notch signaling	GSE86571	Transcriptome Analysis	Purpose: To identify genes that are transcriptionally controlled by Notch signaling during zebrafish lateral line proneuromast formation. Methods: We isolated primordium cells from dissected tails of 36 hpf TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd and sibling TgcldnB:GFP;TgcldnB:gal4 embryos by FACS and performed RNASeq analysis. Results: Using an optimized data analysis workflow we mapped about 26 million sequence reads per sample to the zebrafish genome build danRer10 and identified 32 105 transcripts in the dissociated tails of WT and NICD zebrafish with TopHat workflow. Approximately 2% of the transcripts showed differential expression between the WT and NICD tails with a fold change =0.5 and p value <0.01. Conclusion: RNASeq analyses revealed that Notch signaling cell autonomously induces apical constriction and cell adhesion. Overall design: Zebrafish lateral line mRNA profiles of 36 hours wild type WT and NICD embryos were generated in triplicate using HiSeq 2500 Illumina.	pubmed:28085667	NICD rep1	GSM2306085	source name:dissociated embryo tails\|strain:TgcldnB:GFP; TgcldnB:gal4 x TgUAS:nicd\|tissue:dissociated embryo tails\|age:36 hpf	NICD rep1	Illumina CASAVA 1.8.2 software used for basecalling. Sequenced reads were mapped to danRer10 whole genome using tophat v2.0.13 with parameters p 8 transcriptome index G o no coverage search The fragments per kilobase of transcript per million mapped reads FPKM values were generated using Cufflinks version 2.2.1 with parameters p 4 g o. Reads were counted on danRer10 Ensembl transcripts from UCSC using HTSeq version 0.6.1 with parameters m intersection nonempty s no f bam. Genome build: danRer10 from UCSC Supplementary files format and content: Two tab delimited text files: one includes raw counts of sequencing reads for each Sample one includes FPKM values for each Sample.	dissociated embryo tails	Zebrafish embryos positive for GFP were selected.	Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.	Zebrafish embryos were raised for 36 hpf in the 28.5C incubator.	strain:TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd\|tissue:dissociated embryo tails\|age:36 hpf	GSM2306085	GSM2306085: NICD rep1; Danio rerio; RNA Seq	GSM2306085		1	Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.	GEO Accession:GSM2306085	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP087617		mutant1.fastq.gz	fastq	1606289064.0	31495864.0	GSM2306085 r1	0:51 1:0	A:383363329;C:409816147;G:373853062;T:439205035;N:51491	51	0			383363329	409816147	373853062	439205035	51491	SRX2148085	SRS1679263	SRA464955	GEO	Stowers Institute for Medical Research	1	0.80199		0.09405		0.71382		0.48651		51		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2016-09-08	Pharyngula	Embryo	Tail	Multi-system
41315	41315	SRR4199304	SRX2148084	SRS1679262	SRP087617	PRJNA342262	Proliferation independent regulation of organ size by Notch signaling	GSE86571	Transcriptome Analysis	Purpose: To identify genes that are transcriptionally controlled by Notch signaling during zebrafish lateral line proneuromast formation. Methods: We isolated primordium cells from dissected tails of 36 hpf TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd and sibling TgcldnB:GFP;TgcldnB:gal4 embryos by FACS and performed RNASeq analysis. Results: Using an optimized data analysis workflow we mapped about 26 million sequence reads per sample to the zebrafish genome build danRer10 and identified 32 105 transcripts in the dissociated tails of WT and NICD zebrafish with TopHat workflow. Approximately 2% of the transcripts showed differential expression between the WT and NICD tails with a fold change =0.5 and p value <0.01. Conclusion: RNASeq analyses revealed that Notch signaling cell autonomously induces apical constriction and cell adhesion. Overall design: Zebrafish lateral line mRNA profiles of 36 hours wild type WT and NICD embryos were generated in triplicate using HiSeq 2500 Illumina.	pubmed:28085667	WT rep3	GSM2306084	source name:dissociated embryo tails\|strain:Tgcldnb:lynGFPzf106\|tissue:dissociated embryo tails\|age:36 hpf type	WT rep3	Illumina CASAVA 1.8.2 software used for basecalling. Sequenced reads were mapped to danRer10 whole genome using tophat v2.0.13 with parameters p 8 transcriptome index G o no coverage search The fragments per kilobase of transcript per million mapped reads FPKM values were generated using Cufflinks version 2.2.1 with parameters p 4 g o. Reads were counted on danRer10 Ensembl transcripts from UCSC using HTSeq version 0.6.1 with parameters m intersection nonempty s no f bam. Genome build: danRer10 from UCSC Supplementary files format and content: Two tab delimited text files: one includes raw counts of sequencing reads for each Sample one includes FPKM values for each Sample.	dissociated embryo tails	Zebrafish embryos positive for GFP were selected.	Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.	Zebrafish embryos were raised for 36 hpf in the 28.5C incubator.	strain:Tgcldnb:lynGFPzf106\|tissue:dissociated embryo tails\|age:36 hpf type	GSM2306084	GSM2306084: WT rep3; Danio rerio; RNA Seq	GSM2306084		1	Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.	GEO Accession:GSM2306084	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP087617		WT3.fastq.gz	fastq	1621399650.0	31792150.0	GSM2306084 r1	0:51 1:0	A:394689371;C:400826196;G:384059217;T:441773624;N:51242	51	0			394689371	400826196	384059217	441773624	51242	SRX2148084	SRS1679262	SRA464955	GEO	Stowers Institute for Medical Research	1	0.87053		0.08236		0.7218		0.4831		51		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2016-09-08	Pharyngula	Embryo	Tail	Multi-system
41316	41316	SRR4199303	SRX2148083	SRS1679261	SRP087617	PRJNA342262	Proliferation independent regulation of organ size by Notch signaling	GSE86571	Transcriptome Analysis	Purpose: To identify genes that are transcriptionally controlled by Notch signaling during zebrafish lateral line proneuromast formation. Methods: We isolated primordium cells from dissected tails of 36 hpf TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd and sibling TgcldnB:GFP;TgcldnB:gal4 embryos by FACS and performed RNASeq analysis. Results: Using an optimized data analysis workflow we mapped about 26 million sequence reads per sample to the zebrafish genome build danRer10 and identified 32 105 transcripts in the dissociated tails of WT and NICD zebrafish with TopHat workflow. Approximately 2% of the transcripts showed differential expression between the WT and NICD tails with a fold change =0.5 and p value <0.01. Conclusion: RNASeq analyses revealed that Notch signaling cell autonomously induces apical constriction and cell adhesion. Overall design: Zebrafish lateral line mRNA profiles of 36 hours wild type WT and NICD embryos were generated in triplicate using HiSeq 2500 Illumina.	pubmed:28085667	WT rep2	GSM2306083	source name:dissociated embryo tails\|strain:Tgcldnb:lynGFPzf106\|tissue:dissociated embryo tails\|age:36 hpf type	WT rep2	Illumina CASAVA 1.8.2 software used for basecalling. Sequenced reads were mapped to danRer10 whole genome using tophat v2.0.13 with parameters p 8 transcriptome index G o no coverage search The fragments per kilobase of transcript per million mapped reads FPKM values were generated using Cufflinks version 2.2.1 with parameters p 4 g o. Reads were counted on danRer10 Ensembl transcripts from UCSC using HTSeq version 0.6.1 with parameters m intersection nonempty s no f bam. Genome build: danRer10 from UCSC Supplementary files format and content: Two tab delimited text files: one includes raw counts of sequencing reads for each Sample one includes FPKM values for each Sample.	dissociated embryo tails	Zebrafish embryos positive for GFP were selected.	Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.	Zebrafish embryos were raised for 36 hpf in the 28.5C incubator.	strain:Tgcldnb:lynGFPzf106\|tissue:dissociated embryo tails\|age:36 hpf type	GSM2306083	GSM2306083: WT rep2; Danio rerio; RNA Seq	GSM2306083		1	Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.	GEO Accession:GSM2306083	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP087617		WT2.fastq.gz	fastq	1626903774.0	31900074.0	GSM2306083 r1	0:51 1:0	A:394214874;C:407655291;G:379120984;T:445859413;N:53212	51	0			394214874	407655291	379120984	445859413	53212	SRX2148083	SRS1679261	SRA464955	GEO	Stowers Institute for Medical Research	1	0.81975		0.09539		0.70869		0.4872		51		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2016-09-08	Pharyngula	Embryo	Tail	Multi-system
41317	41317	SRR4199302	SRX2148082	SRS1679260	SRP087617	PRJNA342262	Proliferation independent regulation of organ size by Notch signaling	GSE86571	Transcriptome Analysis	Purpose: To identify genes that are transcriptionally controlled by Notch signaling during zebrafish lateral line proneuromast formation. Methods: We isolated primordium cells from dissected tails of 36 hpf TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd and sibling TgcldnB:GFP;TgcldnB:gal4 embryos by FACS and performed RNASeq analysis. Results: Using an optimized data analysis workflow we mapped about 26 million sequence reads per sample to the zebrafish genome build danRer10 and identified 32 105 transcripts in the dissociated tails of WT and NICD zebrafish with TopHat workflow. Approximately 2% of the transcripts showed differential expression between the WT and NICD tails with a fold change =0.5 and p value <0.01. Conclusion: RNASeq analyses revealed that Notch signaling cell autonomously induces apical constriction and cell adhesion. Overall design: Zebrafish lateral line mRNA profiles of 36 hours wild type WT and NICD embryos were generated in triplicate using HiSeq 2500 Illumina.	pubmed:28085667	WT rep1	GSM2306082	source name:dissociated embryo tails\|strain:Tgcldnb:lynGFPzf106\|tissue:dissociated embryo tails\|age:36 hpf type	WT rep1	Illumina CASAVA 1.8.2 software used for basecalling. Sequenced reads were mapped to danRer10 whole genome using tophat v2.0.13 with parameters p 8 transcriptome index G o no coverage search The fragments per kilobase of transcript per million mapped reads FPKM values were generated using Cufflinks version 2.2.1 with parameters p 4 g o. Reads were counted on danRer10 Ensembl transcripts from UCSC using HTSeq version 0.6.1 with parameters m intersection nonempty s no f bam. Genome build: danRer10 from UCSC Supplementary files format and content: Two tab delimited text files: one includes raw counts of sequencing reads for each Sample one includes FPKM values for each Sample.	dissociated embryo tails	Zebrafish embryos positive for GFP were selected.	Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.	Zebrafish embryos were raised for 36 hpf in the 28.5C incubator.	strain:Tgcldnb:lynGFPzf106\|tissue:dissociated embryo tails\|age:36 hpf type	GSM2306082	GSM2306082: WT rep1; Danio rerio; RNA Seq	GSM2306082		1	Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.	GEO Accession:GSM2306082	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP087617		WT1.fastq.gz	fastq	1646867622.0	32291522.0	GSM2306082 r1	0:51 1:0	A:400030238;C:412959654;G:377713613;T:456111038;N:53079	51	0			400030238	412959654	377713613	456111038	53079	SRX2148082	SRS1679260	SRA464955	GEO	Stowers Institute for Medical Research	1	0.81411		0.10419		0.70621		0.48075		51		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2016-09-08	Pharyngula	Embryo	Tail	Multi-system
41879	41879	SRR5320530	SRX2619935	SRS2029898	SRP101558	PRJNA378498	Functional Analysis of Regional Gene Expression in Zebrafish Craniofacial Development	GSE95812	Transcriptome Analysis	Patterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite their significance for craniofacial development how genetic programs drive this regionalization remains poorly understood. Here we use combinatorial labeling of zebrafish cranial neural crest derived cells CNCCs to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin1 Edn1 signaling in the intermediate joint forming region yet a surprisingly minor role in ventral most regions. Analysis of co variance across multiple sequencing experiments further reveals clusters of co regulated genes with in situ hybridization confirming the expression of novel genes with domain specific expression. We then performed mutational analysis of a number of these genes which uncovered antagonistic functions of two Edn1 targets follistatin a fsta and emx2 in regulating cartilaginous joints in the hyoid arch. Our unbiased discovery and functional analysis of genes with regional expression in arch CNCCs reveals complex regulation by Edn1 and points to novel candidates for craniofacial disorders. Overall design: mRNA profiles of 3 distinct populations of zebrafish pharyngeal arch cells isolated using FACS from 36 hpf wild type WT zebrafish. fli1a:GFP+;sox10:DsRed and fli1a:GFP ;sox10:DsRed+ populations were also isolated at the same time and sequenced as controls 3 replicate each. Additionally there are mRNA profiles of zebrafish pharyngeal arches all domains combined isolated by FACS from 36 hpf zebrafish with the following genotypes: edn1 / 2 replicates jag1b / jag1b+/+ control hsp70I:Gal4; UAS:Edn1 hsp70I:Gal4; UAS:Nicd and hsp70I:Gal4 control.	pubmed:28705894	hspGal4 fli1a sox10	GSM2526409	tissue:Pharyngeal arches\|developmental stage:36 hpf\|genotype:hspGal4\|treatment:Heat shocked	hspGal4 fli1a sox10	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the TPM values. Genome build: GRCz10 Supplementary files format and content: csv text files include TPM values for each gene in each sample	Pharyngeal arches		GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		developmental stage:36 hpf\|genotype:hspGal4\|treatment:Heat shocked	GSM2526409	GSM2526409: hspGal4 fli1a sox10; Danio rerio; RNA Seq	GSM2526409		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM2526409	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP101558				12101492616.0	79615083.0	GSM2526409 r1	0:76 1:76	A:3579849331;C:2226140960;G:2397001824;T:3898240336;N:260165	76	76			3579849331	2226140960	2397001824	3898240336	260165	SRX2619935	SRS2029898	SRA543392	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.85984	0.92526	0.14429	0.15831	0.76226	0.77816	0.50873	0.50352	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2017-03-08	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
41880	41880	SRR5320529	SRX2619934	SRS2029897	SRP101558	PRJNA378498	Functional Analysis of Regional Gene Expression in Zebrafish Craniofacial Development	GSE95812	Transcriptome Analysis	Patterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite their significance for craniofacial development how genetic programs drive this regionalization remains poorly understood. Here we use combinatorial labeling of zebrafish cranial neural crest derived cells CNCCs to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin1 Edn1 signaling in the intermediate joint forming region yet a surprisingly minor role in ventral most regions. Analysis of co variance across multiple sequencing experiments further reveals clusters of co regulated genes with in situ hybridization confirming the expression of novel genes with domain specific expression. We then performed mutational analysis of a number of these genes which uncovered antagonistic functions of two Edn1 targets follistatin a fsta and emx2 in regulating cartilaginous joints in the hyoid arch. Our unbiased discovery and functional analysis of genes with regional expression in arch CNCCs reveals complex regulation by Edn1 and points to novel candidates for craniofacial disorders. Overall design: mRNA profiles of 3 distinct populations of zebrafish pharyngeal arch cells isolated using FACS from 36 hpf wild type WT zebrafish. fli1a:GFP+;sox10:DsRed and fli1a:GFP ;sox10:DsRed+ populations were also isolated at the same time and sequenced as controls 3 replicate each. Additionally there are mRNA profiles of zebrafish pharyngeal arches all domains combined isolated by FACS from 36 hpf zebrafish with the following genotypes: edn1 / 2 replicates jag1b / jag1b+/+ control hsp70I:Gal4; UAS:Edn1 hsp70I:Gal4; UAS:Nicd and hsp70I:Gal4 control.	pubmed:28705894	hspNICD fli1a sox10	GSM2526408	tissue:Pharyngeal arches\|developmental stage:36 hpf\|genotype:hspGal4 ; UASNICD\|treatment:Heat shocked	hspNICD fli1a sox10	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the TPM values. Genome build: GRCz10 Supplementary files format and content: csv text files include TPM values for each gene in each sample	Pharyngeal arches		GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		developmental stage:36 hpf\|genotype:hspGal4 ; UASNICD\|treatment:Heat shocked	GSM2526408	GSM2526408: hspNICD fli1a sox10; Danio rerio; RNA Seq	GSM2526408		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM2526408	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP101558				8181679072.0	53826836.0	GSM2526408 r1												SRX2619934	SRS2029897	SRA543392	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.83613	0.71682	0.12705	0.11094	0.74158	0.75611	0.48765	0.48307	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2017-03-08	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
41881	41881	SRR5320528	SRX2619933	SRS2029896	SRP101558	PRJNA378498	Functional Analysis of Regional Gene Expression in Zebrafish Craniofacial Development	GSE95812	Transcriptome Analysis	Patterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite their significance for craniofacial development how genetic programs drive this regionalization remains poorly understood. Here we use combinatorial labeling of zebrafish cranial neural crest derived cells CNCCs to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin1 Edn1 signaling in the intermediate joint forming region yet a surprisingly minor role in ventral most regions. Analysis of co variance across multiple sequencing experiments further reveals clusters of co regulated genes with in situ hybridization confirming the expression of novel genes with domain specific expression. We then performed mutational analysis of a number of these genes which uncovered antagonistic functions of two Edn1 targets follistatin a fsta and emx2 in regulating cartilaginous joints in the hyoid arch. Our unbiased discovery and functional analysis of genes with regional expression in arch CNCCs reveals complex regulation by Edn1 and points to novel candidates for craniofacial disorders. Overall design: mRNA profiles of 3 distinct populations of zebrafish pharyngeal arch cells isolated using FACS from 36 hpf wild type WT zebrafish. fli1a:GFP+;sox10:DsRed and fli1a:GFP ;sox10:DsRed+ populations were also isolated at the same time and sequenced as controls 3 replicate each. Additionally there are mRNA profiles of zebrafish pharyngeal arches all domains combined isolated by FACS from 36 hpf zebrafish with the following genotypes: edn1 / 2 replicates jag1b / jag1b+/+ control hsp70I:Gal4; UAS:Edn1 hsp70I:Gal4; UAS:Nicd and hsp70I:Gal4 control.	pubmed:28705894	hspEdn1 fli1a sox10	GSM2526407	tissue:Pharyngeal arches\|developmental stage:36 hpf\|genotype:hspGal4 ; UASEdn1\|treatment:Heat shocked	hspEdn1 fli1a sox10	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the TPM values. Genome build: GRCz10 Supplementary files format and content: csv text files include TPM values for each gene in each sample	Pharyngeal arches		GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		developmental stage:36 hpf\|genotype:hspGal4 ; UASEdn1\|treatment:Heat shocked	GSM2526407	GSM2526407: hspEdn1 fli1a sox10; Danio rerio; RNA Seq	GSM2526407		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM2526407	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP101558				8241464016.0	54220158.0	GSM2526407 r1	0:76 1:76	A:2338801834;C:1581411340;G:1652427014;T:2666281574;N:2542254	76	76			2338801834	1581411340	1652427014	2666281574	2542254	SRX2619933	SRS2029896	SRA543392	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.8884	0.85826	0.15095	0.14838	0.75958	0.77538	0.49126	0.48522	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2017-03-08	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
41882	41882	SRR5320527	SRX2619932	SRS2029895	SRP101558	PRJNA378498	Functional Analysis of Regional Gene Expression in Zebrafish Craniofacial Development	GSE95812	Transcriptome Analysis	Patterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite their significance for craniofacial development how genetic programs drive this regionalization remains poorly understood. Here we use combinatorial labeling of zebrafish cranial neural crest derived cells CNCCs to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin1 Edn1 signaling in the intermediate joint forming region yet a surprisingly minor role in ventral most regions. Analysis of co variance across multiple sequencing experiments further reveals clusters of co regulated genes with in situ hybridization confirming the expression of novel genes with domain specific expression. We then performed mutational analysis of a number of these genes which uncovered antagonistic functions of two Edn1 targets follistatin a fsta and emx2 in regulating cartilaginous joints in the hyoid arch. Our unbiased discovery and functional analysis of genes with regional expression in arch CNCCs reveals complex regulation by Edn1 and points to novel candidates for craniofacial disorders. Overall design: mRNA profiles of 3 distinct populations of zebrafish pharyngeal arch cells isolated using FACS from 36 hpf wild type WT zebrafish. fli1a:GFP+;sox10:DsRed and fli1a:GFP ;sox10:DsRed+ populations were also isolated at the same time and sequenced as controls 3 replicate each. Additionally there are mRNA profiles of zebrafish pharyngeal arches all domains combined isolated by FACS from 36 hpf zebrafish with the following genotypes: edn1 / 2 replicates jag1b / jag1b+/+ control hsp70I:Gal4; UAS:Edn1 hsp70I:Gal4; UAS:Nicd and hsp70I:Gal4 control.	pubmed:28705894	jag1b++ fli1a sox10	GSM2526406	tissue:Pharyngeal arches\|developmental stage:36 hpf\|genotype:jag1b+/+\|treatment:Genotyped	jag1b++ fli1a sox10	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the TPM values. Genome build: GRCz10 Supplementary files format and content: csv text files include TPM values for each gene in each sample	Pharyngeal arches		GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		developmental stage:36 hpf\|genotype:jag1b+/+\|treatment:Genotyped	GSM2526406	GSM2526406: jag1b++ fli1a sox10; Danio rerio; RNA Seq	GSM2526406		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM2526406	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP101558				9196789944.0	60505197.0	GSM2526406 r1	0:76 1:76	A:2617231956;C:1761629764;G:1849570227;T:2965452565;N:2905432	76	76			2617231956	1761629764	1849570227	2965452565	2905432	SRX2619932	SRS2029895	SRA543392	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.87578	0.84631	0.14233	0.13848	0.7641	0.78602	0.49727	0.49394	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2017-03-08	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
41883	41883	SRR5320526	SRX2619931	SRS2029894	SRP101558	PRJNA378498	Functional Analysis of Regional Gene Expression in Zebrafish Craniofacial Development	GSE95812	Transcriptome Analysis	Patterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite their significance for craniofacial development how genetic programs drive this regionalization remains poorly understood. Here we use combinatorial labeling of zebrafish cranial neural crest derived cells CNCCs to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin1 Edn1 signaling in the intermediate joint forming region yet a surprisingly minor role in ventral most regions. Analysis of co variance across multiple sequencing experiments further reveals clusters of co regulated genes with in situ hybridization confirming the expression of novel genes with domain specific expression. We then performed mutational analysis of a number of these genes which uncovered antagonistic functions of two Edn1 targets follistatin a fsta and emx2 in regulating cartilaginous joints in the hyoid arch. Our unbiased discovery and functional analysis of genes with regional expression in arch CNCCs reveals complex regulation by Edn1 and points to novel candidates for craniofacial disorders. Overall design: mRNA profiles of 3 distinct populations of zebrafish pharyngeal arch cells isolated using FACS from 36 hpf wild type WT zebrafish. fli1a:GFP+;sox10:DsRed and fli1a:GFP ;sox10:DsRed+ populations were also isolated at the same time and sequenced as controls 3 replicate each. Additionally there are mRNA profiles of zebrafish pharyngeal arches all domains combined isolated by FACS from 36 hpf zebrafish with the following genotypes: edn1 / 2 replicates jag1b / jag1b+/+ control hsp70I:Gal4; UAS:Edn1 hsp70I:Gal4; UAS:Nicd and hsp70I:Gal4 control.	pubmed:28705894	jag1b fli1a sox10	GSM2526405	tissue:Pharyngeal arches\|developmental stage:36 hpf\|genotype:jag1b / \|treatment:Genotyped	jag1b fli1a sox10	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the TPM values. Genome build: GRCz10 Supplementary files format and content: csv text files include TPM values for each gene in each sample	Pharyngeal arches		GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		developmental stage:36 hpf\|genotype:jag1b / \|treatment:Genotyped	GSM2526405	GSM2526405: jag1b fli1a sox10; Danio rerio; RNA Seq	GSM2526405		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM2526405	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP101558				7981914592.0	52512596.0	GSM2526405 r1	0:76 1:76	A:2278594852;C:1520667450;G:1610295025;T:2569901477;N:2455788	76	76			2278594852	1520667450	1610295025	2569901477	2455788	SRX2619931	SRS2029894	SRA543392	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.88292	0.85135	0.1578	0.15478	0.76435	0.78175	0.50571	0.49719	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2017-03-08	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
41884	41884	SRR5320525	SRX2619930	SRS2029893	SRP101558	PRJNA378498	Functional Analysis of Regional Gene Expression in Zebrafish Craniofacial Development	GSE95812	Transcriptome Analysis	Patterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite their significance for craniofacial development how genetic programs drive this regionalization remains poorly understood. Here we use combinatorial labeling of zebrafish cranial neural crest derived cells CNCCs to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin1 Edn1 signaling in the intermediate joint forming region yet a surprisingly minor role in ventral most regions. Analysis of co variance across multiple sequencing experiments further reveals clusters of co regulated genes with in situ hybridization confirming the expression of novel genes with domain specific expression. We then performed mutational analysis of a number of these genes which uncovered antagonistic functions of two Edn1 targets follistatin a fsta and emx2 in regulating cartilaginous joints in the hyoid arch. Our unbiased discovery and functional analysis of genes with regional expression in arch CNCCs reveals complex regulation by Edn1 and points to novel candidates for craniofacial disorders. Overall design: mRNA profiles of 3 distinct populations of zebrafish pharyngeal arch cells isolated using FACS from 36 hpf wild type WT zebrafish. fli1a:GFP+;sox10:DsRed and fli1a:GFP ;sox10:DsRed+ populations were also isolated at the same time and sequenced as controls 3 replicate each. Additionally there are mRNA profiles of zebrafish pharyngeal arches all domains combined isolated by FACS from 36 hpf zebrafish with the following genotypes: edn1 / 2 replicates jag1b / jag1b+/+ control hsp70I:Gal4; UAS:Edn1 hsp70I:Gal4; UAS:Nicd and hsp70I:Gal4 control.	pubmed:28705894	edn1 fli1a sox10 2	GSM2526404	tissue:Pharyngeal arches\|developmental stage:36 hpf\|genotype:edn1 / \|treatment:Genotyped	edn1 fli1a sox10 2	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the TPM values. Genome build: GRCz10 Supplementary files format and content: csv text files include TPM values for each gene in each sample	Pharyngeal arches		GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		developmental stage:36 hpf\|genotype:edn1 / \|treatment:Genotyped	GSM2526404	GSM2526404: edn1 fli1a sox10 2; Danio rerio; RNA Seq	GSM2526404		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM2526404	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP101558		GC-805_L000_R1_001.fastq.gz GC-805_L000_R2_001.fastq.gz	fastq fastq	8083094760.0	53178255.0	GSM2526404 r1	0:76 1:76	A:2289691443;C:1736629919;G:1749357479;T:2306964200;N:451719	76	76			2289691443	1736629919	1749357479	2306964200	451719	SRX2619930	SRS2029893	SRA543392	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.9383	0.92923	0.13857	0.13758	0.73641	0.74416	0.44748	0.48421	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2017-03-08	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
41885	41885	SRR5320524	SRX2619929	SRS2029892	SRP101558	PRJNA378498	Functional Analysis of Regional Gene Expression in Zebrafish Craniofacial Development	GSE95812	Transcriptome Analysis	Patterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite their significance for craniofacial development how genetic programs drive this regionalization remains poorly understood. Here we use combinatorial labeling of zebrafish cranial neural crest derived cells CNCCs to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin1 Edn1 signaling in the intermediate joint forming region yet a surprisingly minor role in ventral most regions. Analysis of co variance across multiple sequencing experiments further reveals clusters of co regulated genes with in situ hybridization confirming the expression of novel genes with domain specific expression. We then performed mutational analysis of a number of these genes which uncovered antagonistic functions of two Edn1 targets follistatin a fsta and emx2 in regulating cartilaginous joints in the hyoid arch. Our unbiased discovery and functional analysis of genes with regional expression in arch CNCCs reveals complex regulation by Edn1 and points to novel candidates for craniofacial disorders. Overall design: mRNA profiles of 3 distinct populations of zebrafish pharyngeal arch cells isolated using FACS from 36 hpf wild type WT zebrafish. fli1a:GFP+;sox10:DsRed and fli1a:GFP ;sox10:DsRed+ populations were also isolated at the same time and sequenced as controls 3 replicate each. Additionally there are mRNA profiles of zebrafish pharyngeal arches all domains combined isolated by FACS from 36 hpf zebrafish with the following genotypes: edn1 / 2 replicates jag1b / jag1b+/+ control hsp70I:Gal4; UAS:Edn1 hsp70I:Gal4; UAS:Nicd and hsp70I:Gal4 control.	pubmed:28705894	edn1 fli1a sox10 1	GSM2526403	tissue:Pharyngeal arches\|developmental stage:36 hpf\|genotype:edn1 / \|treatment:Genotyped	edn1 fli1a sox10 1	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the TPM values. Genome build: GRCz10 Supplementary files format and content: csv text files include TPM values for each gene in each sample	Pharyngeal arches		GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		developmental stage:36 hpf\|genotype:edn1 / \|treatment:Genotyped	GSM2526403	GSM2526403: edn1 fli1a sox10 1; Danio rerio; RNA Seq	GSM2526403		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM2526403	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP101558				3805470400.0	38054704.0	GSM2526403 r1	0:50 1:50	A:1039863232;C:811509659;G:855601660;T:1094752796;N:3743053	50	50			1039863232	811509659	855601660	1094752796	3743053	SRX2619929	SRS2029892	SRA543392	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.90375	0.77106	0.11778	0.10051	0.76037	0.77571	0.48632	0.48462	50	50	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2017-03-08	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
41892	41892	SRR5320517	SRX2619922	SRS2029885	SRP101558	PRJNA378498	Functional Analysis of Regional Gene Expression in Zebrafish Craniofacial Development	GSE95812	Transcriptome Analysis	Patterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite their significance for craniofacial development how genetic programs drive this regionalization remains poorly understood. Here we use combinatorial labeling of zebrafish cranial neural crest derived cells CNCCs to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin1 Edn1 signaling in the intermediate joint forming region yet a surprisingly minor role in ventral most regions. Analysis of co variance across multiple sequencing experiments further reveals clusters of co regulated genes with in situ hybridization confirming the expression of novel genes with domain specific expression. We then performed mutational analysis of a number of these genes which uncovered antagonistic functions of two Edn1 targets follistatin a fsta and emx2 in regulating cartilaginous joints in the hyoid arch. Our unbiased discovery and functional analysis of genes with regional expression in arch CNCCs reveals complex regulation by Edn1 and points to novel candidates for craniofacial disorders. Overall design: mRNA profiles of 3 distinct populations of zebrafish pharyngeal arch cells isolated using FACS from 36 hpf wild type WT zebrafish. fli1a:GFP+;sox10:DsRed and fli1a:GFP ;sox10:DsRed+ populations were also isolated at the same time and sequenced as controls 3 replicate each. Additionally there are mRNA profiles of zebrafish pharyngeal arches all domains combined isolated by FACS from 36 hpf zebrafish with the following genotypes: edn1 / 2 replicates jag1b / jag1b+/+ control hsp70I:Gal4; UAS:Edn1 hsp70I:Gal4; UAS:Nicd and hsp70I:Gal4 control.	pubmed:28705894	WT hand2 sox10 2	GSM2526396	tissue:Pharyngeal arches\|developmental stage:36 hpf\|genotype:WT\|treatment:N1	WT hand2 sox10 2	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the TPM values. Genome build: GRCz10 Supplementary files format and content: csv text files include TPM values for each gene in each sample	Pharyngeal arches		GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		developmental stage:36 hpf\|genotype:WT\|treatment:N1	GSM2526396	GSM2526396: WT hand2 sox10 2; Danio rerio; RNA Seq	GSM2526396		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM2526396	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP101558		GC-99_L000_R1_001.fastq.gz GC-99_L000_R2_001.fastq.gz	fastq fastq	5678291208.0	37357179.0	GSM2526396 r1	0:76 1:76	A:1598205402;C:1219592650;G:1242882414;T:1613938733;N:3672009	76	76			1598205402	1219592650	1242882414	1613938733	3672009	SRX2619922	SRS2029885	SRA543392	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.95476	0.95009	0.12808	0.12848	0.74602	0.76008	0.45997	0.46118	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2017-03-08	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
41893	41893	SRR5320516	SRX2619921	SRS2029884	SRP101558	PRJNA378498	Functional Analysis of Regional Gene Expression in Zebrafish Craniofacial Development	GSE95812	Transcriptome Analysis	Patterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite their significance for craniofacial development how genetic programs drive this regionalization remains poorly understood. Here we use combinatorial labeling of zebrafish cranial neural crest derived cells CNCCs to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin1 Edn1 signaling in the intermediate joint forming region yet a surprisingly minor role in ventral most regions. Analysis of co variance across multiple sequencing experiments further reveals clusters of co regulated genes with in situ hybridization confirming the expression of novel genes with domain specific expression. We then performed mutational analysis of a number of these genes which uncovered antagonistic functions of two Edn1 targets follistatin a fsta and emx2 in regulating cartilaginous joints in the hyoid arch. Our unbiased discovery and functional analysis of genes with regional expression in arch CNCCs reveals complex regulation by Edn1 and points to novel candidates for craniofacial disorders. Overall design: mRNA profiles of 3 distinct populations of zebrafish pharyngeal arch cells isolated using FACS from 36 hpf wild type WT zebrafish. fli1a:GFP+;sox10:DsRed and fli1a:GFP ;sox10:DsRed+ populations were also isolated at the same time and sequenced as controls 3 replicate each. Additionally there are mRNA profiles of zebrafish pharyngeal arches all domains combined isolated by FACS from 36 hpf zebrafish with the following genotypes: edn1 / 2 replicates jag1b / jag1b+/+ control hsp70I:Gal4; UAS:Edn1 hsp70I:Gal4; UAS:Nicd and hsp70I:Gal4 control.	pubmed:28705894	WT hand2 sox10 1	GSM2526395	tissue:Pharyngeal arches\|developmental stage:36 hpf\|genotype:WT\|treatment:N1	WT hand2 sox10 1	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the TPM values. Genome build: GRCz10 Supplementary files format and content: csv text files include TPM values for each gene in each sample	Pharyngeal arches		GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		developmental stage:36 hpf\|genotype:WT\|treatment:N1	GSM2526395	GSM2526395: WT hand2 sox10 1; Danio rerio; RNA Seq	GSM2526395		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM2526395	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP101558		GC-32_ACTGAT_L008_R1_001.fastq.gz GC-32_ACTGAT_L008_R2_001.fastq.gz	fastq fastq	4507512700.0	45075127.0	GSM2526395 r1	0:50 1:50	A:1231085820;C:944462783;G:1008951826;T:1318567555;N:4444716	50	50			1231085820	944462783	1008951826	1318567555	4444716	SRX2619921	SRS2029884	SRA543392	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.9285	0.75484	0.0986	0.08168	0.75751	0.77863	0.49299	0.48494	50	50	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2017-03-08	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
41894	41894	SRR5320515	SRX2619920	SRS2029883	SRP101558	PRJNA378498	Functional Analysis of Regional Gene Expression in Zebrafish Craniofacial Development	GSE95812	Transcriptome Analysis	Patterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite their significance for craniofacial development how genetic programs drive this regionalization remains poorly understood. Here we use combinatorial labeling of zebrafish cranial neural crest derived cells CNCCs to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin1 Edn1 signaling in the intermediate joint forming region yet a surprisingly minor role in ventral most regions. Analysis of co variance across multiple sequencing experiments further reveals clusters of co regulated genes with in situ hybridization confirming the expression of novel genes with domain specific expression. We then performed mutational analysis of a number of these genes which uncovered antagonistic functions of two Edn1 targets follistatin a fsta and emx2 in regulating cartilaginous joints in the hyoid arch. Our unbiased discovery and functional analysis of genes with regional expression in arch CNCCs reveals complex regulation by Edn1 and points to novel candidates for craniofacial disorders. Overall design: mRNA profiles of 3 distinct populations of zebrafish pharyngeal arch cells isolated using FACS from 36 hpf wild type WT zebrafish. fli1a:GFP+;sox10:DsRed and fli1a:GFP ;sox10:DsRed+ populations were also isolated at the same time and sequenced as controls 3 replicate each. Additionally there are mRNA profiles of zebrafish pharyngeal arches all domains combined isolated by FACS from 36 hpf zebrafish with the following genotypes: edn1 / 2 replicates jag1b / jag1b+/+ control hsp70I:Gal4; UAS:Edn1 hsp70I:Gal4; UAS:Nicd and hsp70I:Gal4 control.	pubmed:28705894	WT dlx5a sox10	GSM2526394	tissue:Pharyngeal arches\|developmental stage:36 hpf\|genotype:WT\|treatment:N1	WT dlx5a sox10	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the TPM values. Genome build: GRCz10 Supplementary files format and content: csv text files include TPM values for each gene in each sample	Pharyngeal arches		GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		developmental stage:36 hpf\|genotype:WT\|treatment:N1	GSM2526394	GSM2526394: WT dlx5a sox10; Danio rerio; RNA Seq	GSM2526394		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM2526394	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP101558		GC-807_L000_R1_001.fastq.gz GC-807_L000_R2_001.fastq.gz	fastq fastq	8131381360.0	53495930.0	GSM2526394 r1	0:76 1:76	A:2329666125;C:1728067909;G:1735452315;T:2337737035;N:457976	76	76			2329666125	1728067909	1735452315	2337737035	457976	SRX2619920	SRS2029883	SRA543392	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.94883	0.93771	0.12915	0.12662	0.75112	0.7597	0.48692	0.48304	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2017-03-08	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
41895	41895	SRR5320514	SRX2619919	SRS2029882	SRP101558	PRJNA378498	Functional Analysis of Regional Gene Expression in Zebrafish Craniofacial Development	GSE95812	Transcriptome Analysis	Patterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite their significance for craniofacial development how genetic programs drive this regionalization remains poorly understood. Here we use combinatorial labeling of zebrafish cranial neural crest derived cells CNCCs to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin1 Edn1 signaling in the intermediate joint forming region yet a surprisingly minor role in ventral most regions. Analysis of co variance across multiple sequencing experiments further reveals clusters of co regulated genes with in situ hybridization confirming the expression of novel genes with domain specific expression. We then performed mutational analysis of a number of these genes which uncovered antagonistic functions of two Edn1 targets follistatin a fsta and emx2 in regulating cartilaginous joints in the hyoid arch. Our unbiased discovery and functional analysis of genes with regional expression in arch CNCCs reveals complex regulation by Edn1 and points to novel candidates for craniofacial disorders. Overall design: mRNA profiles of 3 distinct populations of zebrafish pharyngeal arch cells isolated using FACS from 36 hpf wild type WT zebrafish. fli1a:GFP+;sox10:DsRed and fli1a:GFP ;sox10:DsRed+ populations were also isolated at the same time and sequenced as controls 3 replicate each. Additionally there are mRNA profiles of zebrafish pharyngeal arches all domains combined isolated by FACS from 36 hpf zebrafish with the following genotypes: edn1 / 2 replicates jag1b / jag1b+/+ control hsp70I:Gal4; UAS:Edn1 hsp70I:Gal4; UAS:Nicd and hsp70I:Gal4 control.	pubmed:28705894	WT fli1a sox10 3	GSM2526393	tissue:Pharyngeal arches\|developmental stage:36 hpf\|genotype:WT\|treatment:N1	WT fli1a sox10 3	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the TPM values. Genome build: GRCz10 Supplementary files format and content: csv text files include TPM values for each gene in each sample	Pharyngeal arches		GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		developmental stage:36 hpf\|genotype:WT\|treatment:N1	GSM2526393	GSM2526393: WT fli1a sox10 3; Danio rerio; RNA Seq	GSM2526393		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM2526393	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP101558		GC-94_L000_R1_001.fastq.gz GC-94_L000_R2_001.fastq.gz	fastq fastq	7177187832.0	47218341.0	GSM2526393 r1	0:76 1:76	A:1987437090;C:1523180428;G:1579096104;T:2080512802;N:6961408	76	76			1987437090	1523180428	1579096104	2080512802	6961408	SRX2619919	SRS2029882	SRA543392	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.9383	0.92453	0.13099	0.12672	0.74152	0.76055	0.47365	0.46661	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2017-03-08	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
41896	41896	SRR5320513	SRX2619918	SRS2029881	SRP101558	PRJNA378498	Functional Analysis of Regional Gene Expression in Zebrafish Craniofacial Development	GSE95812	Transcriptome Analysis	Patterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite their significance for craniofacial development how genetic programs drive this regionalization remains poorly understood. Here we use combinatorial labeling of zebrafish cranial neural crest derived cells CNCCs to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin1 Edn1 signaling in the intermediate joint forming region yet a surprisingly minor role in ventral most regions. Analysis of co variance across multiple sequencing experiments further reveals clusters of co regulated genes with in situ hybridization confirming the expression of novel genes with domain specific expression. We then performed mutational analysis of a number of these genes which uncovered antagonistic functions of two Edn1 targets follistatin a fsta and emx2 in regulating cartilaginous joints in the hyoid arch. Our unbiased discovery and functional analysis of genes with regional expression in arch CNCCs reveals complex regulation by Edn1 and points to novel candidates for craniofacial disorders. Overall design: mRNA profiles of 3 distinct populations of zebrafish pharyngeal arch cells isolated using FACS from 36 hpf wild type WT zebrafish. fli1a:GFP+;sox10:DsRed and fli1a:GFP ;sox10:DsRed+ populations were also isolated at the same time and sequenced as controls 3 replicate each. Additionally there are mRNA profiles of zebrafish pharyngeal arches all domains combined isolated by FACS from 36 hpf zebrafish with the following genotypes: edn1 / 2 replicates jag1b / jag1b+/+ control hsp70I:Gal4; UAS:Edn1 hsp70I:Gal4; UAS:Nicd and hsp70I:Gal4 control.	pubmed:28705894	WT fli1a sox10 2	GSM2526392	tissue:Pharyngeal arches\|developmental stage:36 hpf\|genotype:WT\|treatment:N1	WT fli1a sox10 2	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the TPM values. Genome build: GRCz10 Supplementary files format and content: csv text files include TPM values for each gene in each sample	Pharyngeal arches		GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		developmental stage:36 hpf\|genotype:WT\|treatment:N1	GSM2526392	GSM2526392: WT fli1a sox10 2; Danio rerio; RNA Seq	GSM2526392		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM2526392	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP101558		GC-804_L000_R1_001.fastq.gz GC-804_L000_R2_001.fastq.gz	fastq fastq	7744827272.0	50952811.0	GSM2526392 r1	0:76 1:76	A:2194582167;C:1674810287;G:1681888119;T:2193114686;N:432013	76	76			2194582167	1674810287	1681888119	2193114686	432013	SRX2619918	SRS2029881	SRA543392	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.94738	0.94045	0.1245	0.12381	0.7389	0.74955	0.47046	0.47075	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2017-03-08	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
41897	41897	SRR5320512	SRX2619917	SRS2029880	SRP101558	PRJNA378498	Functional Analysis of Regional Gene Expression in Zebrafish Craniofacial Development	GSE95812	Transcriptome Analysis	Patterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite their significance for craniofacial development how genetic programs drive this regionalization remains poorly understood. Here we use combinatorial labeling of zebrafish cranial neural crest derived cells CNCCs to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin1 Edn1 signaling in the intermediate joint forming region yet a surprisingly minor role in ventral most regions. Analysis of co variance across multiple sequencing experiments further reveals clusters of co regulated genes with in situ hybridization confirming the expression of novel genes with domain specific expression. We then performed mutational analysis of a number of these genes which uncovered antagonistic functions of two Edn1 targets follistatin a fsta and emx2 in regulating cartilaginous joints in the hyoid arch. Our unbiased discovery and functional analysis of genes with regional expression in arch CNCCs reveals complex regulation by Edn1 and points to novel candidates for craniofacial disorders. Overall design: mRNA profiles of 3 distinct populations of zebrafish pharyngeal arch cells isolated using FACS from 36 hpf wild type WT zebrafish. fli1a:GFP+;sox10:DsRed and fli1a:GFP ;sox10:DsRed+ populations were also isolated at the same time and sequenced as controls 3 replicate each. Additionally there are mRNA profiles of zebrafish pharyngeal arches all domains combined isolated by FACS from 36 hpf zebrafish with the following genotypes: edn1 / 2 replicates jag1b / jag1b+/+ control hsp70I:Gal4; UAS:Edn1 hsp70I:Gal4; UAS:Nicd and hsp70I:Gal4 control.	pubmed:28705894	WT fli1a sox10 1	GSM2526391	tissue:Pharyngeal arches\|developmental stage:36 hpf\|genotype:WT\|treatment:N1	WT fli1a sox10 1	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the TPM values. Genome build: GRCz10 Supplementary files format and content: csv text files include TPM values for each gene in each sample	Pharyngeal arches		GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		developmental stage:36 hpf\|genotype:WT\|treatment:N1	GSM2526391	GSM2526391: WT fli1a sox10 1; Danio rerio; RNA Seq	GSM2526391		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM2526391	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP101558				5577850800.0	55778508.0	GSM2526391 r1	0:50 1:50	A:1539279722;C:1164400006;G:1236602222;T:1636301311;N:1267539	50	50			1539279722	1164400006	1236602222	1636301311	1267539	SRX2619917	SRS2029880	SRA543392	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.90764	0.74518	0.17723	0.14872	0.75546	0.77741	0.49639	0.48675	50	50	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2017-03-08	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
42954	42954	SRR5855387	SRX3024626	SRS2373891	SRP113259	PRJNA395253	Nr2f transcription factors promote the identity of the vertebrate upper jaw	GSE101719	Transcriptome Analysis	The jaws are complementary in form and function but develop asymmetrically as the lower but not upper jaw bone forms around a prominent cartilage template. How such differences in skeletal composition are patterned is unclear. Here we identify four Nuclear receptor 2f genes nr2f1a nr2f1b nr2f2 and nr2f5 as enriched in zebrafish upper jaw precursors. Whereas loss of Nr2f genes results in expansion of upper jaw cartilage to resemble that of the lower jaw Nr2f5 misexpression inhibits lower jaw cartilage formation. Genome wide analyses show that Nr2f genes prevent expansion of lower jaw associated gene expression into the upper jaw territory. Further restriction of Nr2f expression by Endothelin1 signaling is critical for lower jaw development as reducing Nr2f dosage fully restores lower jaw development in edn1 mutants. We propose that Nr2f genes drive jaw asymmetry by limiting early cartilage differentiation in the upper jaw to preserve more precursors for later osteogenesis. Overall design: Zebrafish pharyngeal arch cells expressing both fli1a:GFP and sox10:DsRed were isolated by FACS from 36 hpf nr2f2; nr2f5 double mutant embryos 2 replicates: n = 37 & 84; 18 858 & 30 655 cells sox10:Gal4+ embryos n = 69; 86 517 cells sox10:Gal4; UAS:Nr2f5 embryos n = 84; 56 866 cells.	pubmed:29358039	sox10:Gal4 fli1a:GFP+ sox10:DsRed+	GSM2713941	tissue:pharyngeal arch cells\|Stage:36 hpf\|genotype/variation:sox10:Gal4\|identification:fin biopsies taken at 24 hpf genotyped for Gal4 and the UAS allele	sox10:Gal4 fli1a:GFP+ sox10:DsRed+	Raw sequencing data in Fastq format were imported into Partek Flow® for alignment and quantification. In pre alignment QC the reads from all samples were generally of high quality with the average quality score for each sample exceeding 33. The reads were then trimmed at both ends based on the Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. Trimmed reads were aligned to the Danio rerio GRCz10 genome assembly Emsembl v80 using the TopHat 2 algorithm. Aligned reads were quantified with the Partek E/M algorithm using default parameters to generate TPM values. Genome build: GRCz10 Supplementary files format and content: The csv text files have the TPM values for each gene in each sample.	pharyngeal arch cells		GFP/DsRed double positive cells populations were collected into RLT lysis buffer Qiagen and total RNA was immediately extracted using the RNeasy Micro kit Qiagen according to the manufacturer’s instructions. The purified RNA was evaluated for quality and quantity on a BioAnalyzer Pico RNA chip Agilent Santa Clara CA and then reverse transcribed into cDNA using the SMARTer kit Clontech Mountain View CA. cDNA amplification was adjusted based on the RNA input quantity and the size and amount of generated cDNA was measured by BioAnalyzer. The samples were sonicated on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommendations. DNA libraries were assembled using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA with NextFlex adapters Bioo Scientific Austin TX. Libraries were assessed by Bioanalyzer and quantified using qPCR Kapa Library Quantification kit. Sequencing was performed on a NextSeq 500 75 bp paired end reads Illumina San Diego CA. Library construction and sequencing were performed at the USC Molecular Genomics Core at the USC Norris Comprehensive Cancer Center.	Embryos were maintained at 28.5 degrees C until 27 hpf and then transferred to 22 degrees C to slow their development. Embryos were dissociated and sorted once they achieved morphological criteria corresponding to the standard 36 hpf stage	Stage:36 hpf\|genotype/variation:sox10:Gal4\|identification:fin biopsies taken at 24 hpf genotyped for Gal4 and the UAS allele	GSM2713941	GSM2713941: sox10:Gal4 fli1a:GFP+ sox10:DsRed+; Danio rerio; RNA Seq	GSM2713941		1	GFP/DsRed double positive cells populations were collected into RLT lysis buffer Qiagen and total RNA was immediately extracted using the RNeasy Micro kit Qiagen according to the manufacturer’s instructions. The purified RNA was evaluated for quality and quantity on a BioAnalyzer Pico RNA chip Agilent Santa Clara CA and then reverse transcribed into cDNA using the SMARTer kit Clontech Mountain View CA. cDNA amplification was adjusted based on the RNA input quantity and the size and amount of generated cDNA was measured by BioAnalyzer. The samples were sonicated on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommendations. DNA libraries were assembled using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA with NextFlex adapters Bioo Scientific Austin TX. Libraries were assessed by Bioanalyzer and quantified using qPCR Kapa Library Quantification kit. Sequencing was performed on a NextSeq 500 75 bp paired end reads Illumina San Diego CA. Library construction and sequencing were performed at the USC Molecular Genomics Core at the USC Norris Comprehensive Cancer Center.	GEO Accession:GSM2713941	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP113259		sox10Gal4_GC104_S5_R2_001.fastq.gz sox10Gal4_GC104_S5_R1_001.fastq.gz	fastq fastq	5174277752.0	34041301.0	GSM2713941 r1	0:76 1:76	A:829112690;C:1697763956;G:1785211548;T:861259657;N:929901	76	76			829112690	1697763956	1785211548	861259657	929901	SRX3024626	SRS2373891	SRA589735	GEO	Crump Lab, Stem Cell Biology and Regenerative Medicine, University of Southern California	2	0.89781	0.89904	0.07767	0.07318	0.83378	0.84287	0.79941	0.84864	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2017-07-20	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
42955	42955	SRR5855386	SRX3024625	SRS2373890	SRP113259	PRJNA395253	Nr2f transcription factors promote the identity of the vertebrate upper jaw	GSE101719	Transcriptome Analysis	The jaws are complementary in form and function but develop asymmetrically as the lower but not upper jaw bone forms around a prominent cartilage template. How such differences in skeletal composition are patterned is unclear. Here we identify four Nuclear receptor 2f genes nr2f1a nr2f1b nr2f2 and nr2f5 as enriched in zebrafish upper jaw precursors. Whereas loss of Nr2f genes results in expansion of upper jaw cartilage to resemble that of the lower jaw Nr2f5 misexpression inhibits lower jaw cartilage formation. Genome wide analyses show that Nr2f genes prevent expansion of lower jaw associated gene expression into the upper jaw territory. Further restriction of Nr2f expression by Endothelin1 signaling is critical for lower jaw development as reducing Nr2f dosage fully restores lower jaw development in edn1 mutants. We propose that Nr2f genes drive jaw asymmetry by limiting early cartilage differentiation in the upper jaw to preserve more precursors for later osteogenesis. Overall design: Zebrafish pharyngeal arch cells expressing both fli1a:GFP and sox10:DsRed were isolated by FACS from 36 hpf nr2f2; nr2f5 double mutant embryos 2 replicates: n = 37 & 84; 18 858 & 30 655 cells sox10:Gal4+ embryos n = 69; 86 517 cells sox10:Gal4; UAS:Nr2f5 embryos n = 84; 56 866 cells.	pubmed:29358039	sox10:Gal4; UAS:Nr2f5 fli1a:GFP+ sox10:DsRed+	GSM2713940	tissue:pharyngeal arch cells\|Stage:36 hpf\|genotype/variation:sox10:Gal4; UAS:Nr2f5\|identification:fin biopsies taken at 24 hpf genotyped for Gal4 and the UAS allele	sox10:Gal4; UAS:Nr2f5 fli1a:GFP+ sox10:DsRed+	Raw sequencing data in Fastq format were imported into Partek Flow® for alignment and quantification. In pre alignment QC the reads from all samples were generally of high quality with the average quality score for each sample exceeding 33. The reads were then trimmed at both ends based on the Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. Trimmed reads were aligned to the Danio rerio GRCz10 genome assembly Emsembl v80 using the TopHat 2 algorithm. Aligned reads were quantified with the Partek E/M algorithm using default parameters to generate TPM values. Genome build: GRCz10 Supplementary files format and content: The csv text files have the TPM values for each gene in each sample.	pharyngeal arch cells		GFP/DsRed double positive cells populations were collected into RLT lysis buffer Qiagen and total RNA was immediately extracted using the RNeasy Micro kit Qiagen according to the manufacturer’s instructions. The purified RNA was evaluated for quality and quantity on a BioAnalyzer Pico RNA chip Agilent Santa Clara CA and then reverse transcribed into cDNA using the SMARTer kit Clontech Mountain View CA. cDNA amplification was adjusted based on the RNA input quantity and the size and amount of generated cDNA was measured by BioAnalyzer. The samples were sonicated on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommendations. DNA libraries were assembled using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA with NextFlex adapters Bioo Scientific Austin TX. Libraries were assessed by Bioanalyzer and quantified using qPCR Kapa Library Quantification kit. Sequencing was performed on a NextSeq 500 75 bp paired end reads Illumina San Diego CA. Library construction and sequencing were performed at the USC Molecular Genomics Core at the USC Norris Comprehensive Cancer Center.	Embryos were maintained at 28.5 degrees C until 27 hpf and then transferred to 22 degrees C to slow their development. Embryos were dissociated and sorted once they achieved morphological criteria corresponding to the standard 36 hpf stage	Stage:36 hpf\|genotype/variation:sox10:Gal4; UAS:Nr2f5\|identification:fin biopsies taken at 24 hpf genotyped for Gal4 and the UAS allele	GSM2713940	GSM2713940: sox10:Gal4; UAS:Nr2f5 fli1a:GFP+ sox10:DsRed+; Danio rerio; RNA Seq	GSM2713940		1	GFP/DsRed double positive cells populations were collected into RLT lysis buffer Qiagen and total RNA was immediately extracted using the RNeasy Micro kit Qiagen according to the manufacturer’s instructions. The purified RNA was evaluated for quality and quantity on a BioAnalyzer Pico RNA chip Agilent Santa Clara CA and then reverse transcribed into cDNA using the SMARTer kit Clontech Mountain View CA. cDNA amplification was adjusted based on the RNA input quantity and the size and amount of generated cDNA was measured by BioAnalyzer. The samples were sonicated on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommendations. DNA libraries were assembled using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA with NextFlex adapters Bioo Scientific Austin TX. Libraries were assessed by Bioanalyzer and quantified using qPCR Kapa Library Quantification kit. Sequencing was performed on a NextSeq 500 75 bp paired end reads Illumina San Diego CA. Library construction and sequencing were performed at the USC Molecular Genomics Core at the USC Norris Comprehensive Cancer Center.	GEO Accession:GSM2713940	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP113259		sox10Gal4UASNr2f5_GC103_S4_R1_001.fastq.gz sox10Gal4UASNr2f5_GC103_S4_R2_001.fastq.gz	fastq fastq	1876943424.0	12348312.0	GSM2713940 r1	0:76 1:76	A:277876402;C:637297214;G:668302099;T:293137389;N:330320	76	76			277876402	637297214	668302099	293137389	330320	SRX3024625	SRS2373890	SRA589735	GEO	Crump Lab, Stem Cell Biology and Regenerative Medicine, University of Southern California	2	0.95473	0.94996	0.08065	0.07608	0.84177	0.85127	0.82239	0.8689	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2017-07-20	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
42956	42956	SRR5855385	SRX3024624	SRS2373889	SRP113259	PRJNA395253	Nr2f transcription factors promote the identity of the vertebrate upper jaw	GSE101719	Transcriptome Analysis	The jaws are complementary in form and function but develop asymmetrically as the lower but not upper jaw bone forms around a prominent cartilage template. How such differences in skeletal composition are patterned is unclear. Here we identify four Nuclear receptor 2f genes nr2f1a nr2f1b nr2f2 and nr2f5 as enriched in zebrafish upper jaw precursors. Whereas loss of Nr2f genes results in expansion of upper jaw cartilage to resemble that of the lower jaw Nr2f5 misexpression inhibits lower jaw cartilage formation. Genome wide analyses show that Nr2f genes prevent expansion of lower jaw associated gene expression into the upper jaw territory. Further restriction of Nr2f expression by Endothelin1 signaling is critical for lower jaw development as reducing Nr2f dosage fully restores lower jaw development in edn1 mutants. We propose that Nr2f genes drive jaw asymmetry by limiting early cartilage differentiation in the upper jaw to preserve more precursors for later osteogenesis. Overall design: Zebrafish pharyngeal arch cells expressing both fli1a:GFP and sox10:DsRed were isolated by FACS from 36 hpf nr2f2; nr2f5 double mutant embryos 2 replicates: n = 37 & 84; 18 858 & 30 655 cells sox10:Gal4+ embryos n = 69; 86 517 cells sox10:Gal4; UAS:Nr2f5 embryos n = 84; 56 866 cells.	pubmed:29358039	nr2f2; nr2f5 mutant 2 fli1a:GFP+ sox10:DsRed+	GSM2713939	tissue:pharyngeal arch cells\|Stage:36 hpf\|genotype/variation:nr2f2; nr2f5 mutant\|identification:ocular coloboma	nr2f2; nr2f5 mutant 2 fli1a:GFP+ sox10:DsRed+	Raw sequencing data in Fastq format were imported into Partek Flow® for alignment and quantification. In pre alignment QC the reads from all samples were generally of high quality with the average quality score for each sample exceeding 33. The reads were then trimmed at both ends based on the Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. Trimmed reads were aligned to the Danio rerio GRCz10 genome assembly Emsembl v80 using the TopHat 2 algorithm. Aligned reads were quantified with the Partek E/M algorithm using default parameters to generate TPM values. Genome build: GRCz10 Supplementary files format and content: The csv text files have the TPM values for each gene in each sample.	pharyngeal arch cells		GFP/DsRed double positive cells populations were collected into RLT lysis buffer Qiagen and total RNA was immediately extracted using the RNeasy Micro kit Qiagen according to the manufacturer’s instructions. The purified RNA was evaluated for quality and quantity on a BioAnalyzer Pico RNA chip Agilent Santa Clara CA and then reverse transcribed into cDNA using the SMARTer kit Clontech Mountain View CA. cDNA amplification was adjusted based on the RNA input quantity and the size and amount of generated cDNA was measured by BioAnalyzer. The samples were sonicated on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommendations. DNA libraries were assembled using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA with NextFlex adapters Bioo Scientific Austin TX. Libraries were assessed by Bioanalyzer and quantified using qPCR Kapa Library Quantification kit. Sequencing was performed on a NextSeq 500 75 bp paired end reads Illumina San Diego CA. Library construction and sequencing were performed at the USC Molecular Genomics Core at the USC Norris Comprehensive Cancer Center.	Embryos were maintained at 28.5 degrees C until 27 hpf and then transferred to 22 degrees C to slow their development. Embryos were dissociated and sorted once they achieved morphological criteria corresponding to the standard 36 hpf stage	Stage:36 hpf\|genotype/variation:nr2f2; nr2f5 mutant\|identification:ocular coloboma	GSM2713939	GSM2713939: nr2f2; nr2f5 mutant 2 fli1a:GFP+ sox10:DsRed+; Danio rerio; RNA Seq	GSM2713939		1	GFP/DsRed double positive cells populations were collected into RLT lysis buffer Qiagen and total RNA was immediately extracted using the RNeasy Micro kit Qiagen according to the manufacturer’s instructions. The purified RNA was evaluated for quality and quantity on a BioAnalyzer Pico RNA chip Agilent Santa Clara CA and then reverse transcribed into cDNA using the SMARTer kit Clontech Mountain View CA. cDNA amplification was adjusted based on the RNA input quantity and the size and amount of generated cDNA was measured by BioAnalyzer. The samples were sonicated on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommendations. DNA libraries were assembled using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA with NextFlex adapters Bioo Scientific Austin TX. Libraries were assessed by Bioanalyzer and quantified using qPCR Kapa Library Quantification kit. Sequencing was performed on a NextSeq 500 75 bp paired end reads Illumina San Diego CA. Library construction and sequencing were performed at the USC Molecular Genomics Core at the USC Norris Comprehensive Cancer Center.	GEO Accession:GSM2713939	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP113259		nr2f25mut2_GC102_S3_R1_001.fastq.gz nr2f25mut2_GC102_S3_R2_001.fastq.gz	fastq fastq	4425393512.0	29114431.0	GSM2713939 r1	0:76 1:76	A:742522706;C:1435550593;G:1473779857;T:772748815;N:791541	76	76			742522706	1435550593	1473779857	772748815	791541	SRX3024624	SRS2373889	SRA589735	GEO	Crump Lab, Stem Cell Biology and Regenerative Medicine, University of Southern California	2	0.83264	0.83706	0.0728	0.07018	0.85208	0.85823	0.81134	0.83008	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2017-07-20	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
42957	42957	SRR5855384	SRX3024623	SRS2373888	SRP113259	PRJNA395253	Nr2f transcription factors promote the identity of the vertebrate upper jaw	GSE101719	Transcriptome Analysis	The jaws are complementary in form and function but develop asymmetrically as the lower but not upper jaw bone forms around a prominent cartilage template. How such differences in skeletal composition are patterned is unclear. Here we identify four Nuclear receptor 2f genes nr2f1a nr2f1b nr2f2 and nr2f5 as enriched in zebrafish upper jaw precursors. Whereas loss of Nr2f genes results in expansion of upper jaw cartilage to resemble that of the lower jaw Nr2f5 misexpression inhibits lower jaw cartilage formation. Genome wide analyses show that Nr2f genes prevent expansion of lower jaw associated gene expression into the upper jaw territory. Further restriction of Nr2f expression by Endothelin1 signaling is critical for lower jaw development as reducing Nr2f dosage fully restores lower jaw development in edn1 mutants. We propose that Nr2f genes drive jaw asymmetry by limiting early cartilage differentiation in the upper jaw to preserve more precursors for later osteogenesis. Overall design: Zebrafish pharyngeal arch cells expressing both fli1a:GFP and sox10:DsRed were isolated by FACS from 36 hpf nr2f2; nr2f5 double mutant embryos 2 replicates: n = 37 & 84; 18 858 & 30 655 cells sox10:Gal4+ embryos n = 69; 86 517 cells sox10:Gal4; UAS:Nr2f5 embryos n = 84; 56 866 cells.	pubmed:29358039	nr2f2; nr2f5 mutant 1 fli1a:GFP+ sox10:DsRed+	GSM2713938	tissue:pharyngeal arch cells\|Stage:36 hpf\|genotype/variation:nr2f2; nr2f5 mutant\|identification:ocular coloboma	nr2f2; nr2f5 mutant 1 fli1a:GFP+ sox10:DsRed+	Raw sequencing data in Fastq format were imported into Partek Flow® for alignment and quantification. In pre alignment QC the reads from all samples were generally of high quality with the average quality score for each sample exceeding 33. The reads were then trimmed at both ends based on the Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. Trimmed reads were aligned to the Danio rerio GRCz10 genome assembly Emsembl v80 using the TopHat 2 algorithm. Aligned reads were quantified with the Partek E/M algorithm using default parameters to generate TPM values. Genome build: GRCz10 Supplementary files format and content: The csv text files have the TPM values for each gene in each sample.	pharyngeal arch cells		GFP/DsRed double positive cells populations were collected into RLT lysis buffer Qiagen and total RNA was immediately extracted using the RNeasy Micro kit Qiagen according to the manufacturer’s instructions. The purified RNA was evaluated for quality and quantity on a BioAnalyzer Pico RNA chip Agilent Santa Clara CA and then reverse transcribed into cDNA using the SMARTer kit Clontech Mountain View CA. cDNA amplification was adjusted based on the RNA input quantity and the size and amount of generated cDNA was measured by BioAnalyzer. The samples were sonicated on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommendations. DNA libraries were assembled using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA with NextFlex adapters Bioo Scientific Austin TX. Libraries were assessed by Bioanalyzer and quantified using qPCR Kapa Library Quantification kit. Sequencing was performed on a NextSeq 500 75 bp paired end reads Illumina San Diego CA. Library construction and sequencing were performed at the USC Molecular Genomics Core at the USC Norris Comprehensive Cancer Center.	Embryos were maintained at 28.5 degrees C until 27 hpf and then transferred to 22 degrees C to slow their development. Embryos were dissociated and sorted once they achieved morphological criteria corresponding to the standard 36 hpf stage	Stage:36 hpf\|genotype/variation:nr2f2; nr2f5 mutant\|identification:ocular coloboma	GSM2713938	GSM2713938: nr2f2; nr2f5 mutant 1 fli1a:GFP+ sox10:DsRed+; Danio rerio; RNA Seq	GSM2713938		1	GFP/DsRed double positive cells populations were collected into RLT lysis buffer Qiagen and total RNA was immediately extracted using the RNeasy Micro kit Qiagen according to the manufacturer’s instructions. The purified RNA was evaluated for quality and quantity on a BioAnalyzer Pico RNA chip Agilent Santa Clara CA and then reverse transcribed into cDNA using the SMARTer kit Clontech Mountain View CA. cDNA amplification was adjusted based on the RNA input quantity and the size and amount of generated cDNA was measured by BioAnalyzer. The samples were sonicated on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommendations. DNA libraries were assembled using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA with NextFlex adapters Bioo Scientific Austin TX. Libraries were assessed by Bioanalyzer and quantified using qPCR Kapa Library Quantification kit. Sequencing was performed on a NextSeq 500 75 bp paired end reads Illumina San Diego CA. Library construction and sequencing were performed at the USC Molecular Genomics Core at the USC Norris Comprehensive Cancer Center.	GEO Accession:GSM2713938	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP113259		nr2f25mut1_GC101_S2_R1_001.fastq.gz nr2f25mut1_GC101_S2_R2_001.fastq.gz	fastq fastq	4981028448.0	32769924.0	GSM2713938 r1	0:76 1:76	A:840950063;C:1614355757;G:1644774381;T:880078202;N:870045	76	76			840950063	1614355757	1644774381	880078202	870045	SRX3024623	SRS2373888	SRA589735	GEO	Crump Lab, Stem Cell Biology and Regenerative Medicine, University of Southern California	2	0.92321	0.92152	0.11945	0.11592	0.82627	0.83368	0.7663	0.79383	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2017-07-20	Pharyngula	Embryo	Pharyngeal Arch	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

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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");;