metadata: run_metadata: 1,121 rows where technology = "smartseq", tissue_curation = "Trunk" and tissue_curation

1,121 rows where technology = "smartseq", tissue_curation = "Trunk" and tissue_curation_coarse = "Surface Structure"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	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
34548	34548	SRR32104353	SRX27449957	SRS23876478	SRP559533	PRJNA1214751	Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq]	GSE287815	Transcriptome Analysis	During vertebrate development the heart primarily arises from mesoderm with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives. Here by integrating bulk and single cell RNAseq with ATAC seq we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1 sox9a tfap2a and ets1. Notably we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.		24hpf TrunkNC 3	GSM8751790	source name:trunk NC tissue from somite 7 to somite 16\|tissue:trunk NC tissue from somite 7 to somite 16\|cell type:migratory trunk neural crest\|transgenic line:Tg 4.9sox10:eGFP\|age:24hpf\|fluorophore:GFP+\|geo loc name:missing\|collection date:missing	24hpf TrunkNC 3	Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples	trunk NC tissue from somite 7 to somite 16	mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.	tissue:trunk NC tissue from somite 7 to somite 16\|cell type:migratory trunk neural crest\|transgenic line:Tg 4.9sox10:eGFP\|age:24hpf\|fluorophore:GFP+	GSM8751790	GSM8751790: 24hpf TrunkNC 3; Danio rerio; RNA Seq	GSM8751790 r1	GSM8751790	1	mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP559533		Sox10+3_Trunk_24h_19733_R1_combined_filtered.fastq.gz	fastq	1792416000.0	35848320.0	GSM8751790 r1	0:50	A:512975947;C:383333260;G:389199848;T:506816777;N:90168	50	512975947	383333260	389199848	506816777	90168	SRX27449957	SRS23876478	SRA2058978	Martik Lab, Molecular and Cell Biology, University of California Berkeley	Martik Lab, Molecular and Cell Biology, University of California Berkeley							B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2025-01-23	Pharyngula	Embryo	Trunk	Surface Structure
34549	34549	SRR32104354	SRX27449956	SRS23876477	SRP559533	PRJNA1214751	Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq]	GSE287815	Transcriptome Analysis	During vertebrate development the heart primarily arises from mesoderm with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives. Here by integrating bulk and single cell RNAseq with ATAC seq we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1 sox9a tfap2a and ets1. Notably we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.		24hpf TrunkNC 2	GSM8751789	source name:trunk NC tissue from somite 7 to somite 16\|tissue:trunk NC tissue from somite 7 to somite 16\|cell type:migratory trunk neural crest\|transgenic line:Tg 4.9sox10:eGFP\|age:24hpf\|fluorophore:GFP+\|geo loc name:missing\|collection date:missing	24hpf TrunkNC 2	Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples	trunk NC tissue from somite 7 to somite 16	mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.	tissue:trunk NC tissue from somite 7 to somite 16\|cell type:migratory trunk neural crest\|transgenic line:Tg 4.9sox10:eGFP\|age:24hpf\|fluorophore:GFP+	GSM8751789	GSM8751789: 24hpf TrunkNC 2; Danio rerio; RNA Seq	GSM8751789 r1	GSM8751789	1	mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP559533		Sox10+2_Trunk_24h_19731_R1_combined_filtered.fastq.gz	fastq	1952754850.0	39055097.0	GSM8751789 r1	0:50	A:559564208;C:417671563;G:422591454;T:552829965;N:97660	50	559564208	417671563	422591454	552829965	97660	SRX27449956	SRS23876477	SRA2058978	Martik Lab, Molecular and Cell Biology, University of California Berkeley	Martik Lab, Molecular and Cell Biology, University of California Berkeley							B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2025-01-23	Pharyngula	Embryo	Trunk	Surface Structure
34550	34550	SRR32104355	SRX27449955	SRS23876476	SRP559533	PRJNA1214751	Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq]	GSE287815	Transcriptome Analysis	During vertebrate development the heart primarily arises from mesoderm with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives. Here by integrating bulk and single cell RNAseq with ATAC seq we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1 sox9a tfap2a and ets1. Notably we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.		24hpf TrunkNC 1	GSM8751788	source name:trunk NC tissue from somite 7 to somite 16\|tissue:trunk NC tissue from somite 7 to somite 16\|cell type:migratory trunk neural crest\|transgenic line:Tg 4.9sox10:eGFP\|age:24hpf\|fluorophore:GFP+\|geo loc name:missing\|collection date:missing	24hpf TrunkNC 1	Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples	trunk NC tissue from somite 7 to somite 16	mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.	tissue:trunk NC tissue from somite 7 to somite 16\|cell type:migratory trunk neural crest\|transgenic line:Tg 4.9sox10:eGFP\|age:24hpf\|fluorophore:GFP+	GSM8751788	GSM8751788: 24hpf TrunkNC 1; Danio rerio; RNA Seq	GSM8751788 r1	GSM8751788	1	mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP559533		Sox10+1_Trunk_24h_19729_R1_combined_filtered.fastq.gz	fastq	2086584450.0	41731689.0	GSM8751788 r1	0:50	A:588802695;C:455146722;G:460260703;T:582270728;N:103602	50	588802695	455146722	460260703	582270728	103602	SRX27449955	SRS23876476	SRA2058978	Martik Lab, Molecular and Cell Biology, University of California Berkeley	Martik Lab, Molecular and Cell Biology, University of California Berkeley							B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2025-01-23	Pharyngula	Embryo	Trunk	Surface Structure
57280	57280	SRR11302641	SRX7908670	SRS6316242	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s D22	GSM4410633	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s D22	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410633	GSM4410633: zebrafish 990s D22; Danio rerio; RNA Seq	GSM4410633		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410633	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_D22.bam	bam	14952235.0	302958.0	GSM4410633 r1	0:49.35	A:3811307;C:3645371;G:3617661;T:3873396;N:4500	49	3811307	3645371	3617661	3873396	4500	SRX7908670	SRS6316242	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96635	0.06324	0.87769	0.49502	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57281	57281	SRR11302640	SRX7908669	SRS6316243	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s D21	GSM4410632	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s D21	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410632	GSM4410632: zebrafish 990s D21; Danio rerio; RNA Seq	GSM4410632		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410632	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_D21.bam	bam	12301286.0	248613.0	GSM4410632 r1	0:49.48	A:3216338;C:2918960;G:2899913;T:3262285;N:3790	49	3216338	2918960	2899913	3262285	3790	SRX7908669	SRS6316243	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96446	0.11117	0.9137	0.51287	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57282	57282	SRR11302639	SRX7908668	SRS6316241	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s D20	GSM4410631	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s D20	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410631	GSM4410631: zebrafish 990s D20; Danio rerio; RNA Seq	GSM4410631		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410631	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_D20.bam	bam	13841010.0	280169.0	GSM4410631 r1	0:49.40	A:3567280;C:3336013;G:3310051;T:3623298;N:4368	49	3567280	3336013	3310051	3623298	4368	SRX7908668	SRS6316241	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96393	0.08232	0.92616	0.49002	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57283	57283	SRR11302638	SRX7908667	SRS6316240	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s D2	GSM4410630	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s D2	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410630	GSM4410630: zebrafish 990s D2; Danio rerio; RNA Seq	GSM4410630		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410630	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_D2.bam	bam	13249032.0	267250.0	GSM4410630 r1	0:49.58	A:3526925;C:3081325;G:3060212;T:3576643;N:3927	49	3526925	3081325	3060212	3576643	3927	SRX7908667	SRS6316240	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.95057	0.1848	0.92504	0.48003	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57284	57284	SRR11302637	SRX7908666	SRS6316237	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s D19	GSM4410629	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s D19	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410629	GSM4410629: zebrafish 990s D19; Danio rerio; RNA Seq	GSM4410629		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410629	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_D19.bam	bam	24639240.0	496686.0	GSM4410629 r1	0:49.61	A:6408578;C:5886841;G:5845099;T:6491229;N:7493	49	6408578	5886841	5845099	6491229	7493	SRX7908666	SRS6316237	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96339	0.06751	0.91198	0.46563	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57285	57285	SRR11302636	SRX7908665	SRS6316236	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s D18	GSM4410628	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s D18	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410628	GSM4410628: zebrafish 990s D18; Danio rerio; RNA Seq	GSM4410628		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410628	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_D18.bam	bam	6244321.0	125915.0	GSM4410628 r1	0:49.59	A:1600346;C:1515162;G:1505658;T:1621317;N:1838	49	1600346	1515162	1505658	1621317	1838	SRX7908665	SRS6316236	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96639	0.09462	0.93275	0.51899	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57286	57286	SRR11302635	SRX7908664	SRS6316239	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s D17	GSM4410627	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s D17	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410627	GSM4410627: zebrafish 990s D17; Danio rerio; RNA Seq	GSM4410627		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410627	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_D17.bam	bam	19546818.0	394040.0	GSM4410627 r1	0:49.61	A:5084961;C:4673304;G:4637984;T:5144779;N:5790	49	5084961	4673304	4637984	5144779	5790	SRX7908664	SRS6316239	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96388	0.09619	0.92419	0.46267	48	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57287	57287	SRR11302634	SRX7908663	SRS6316238	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s D16	GSM4410626	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s D16	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410626	GSM4410626: zebrafish 990s D16; Danio rerio; RNA Seq	GSM4410626		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410626	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_D16.bam	bam	35129013.0	708869.0	GSM4410626 r1	0:49.56	A:9128792;C:8378350;G:8324629;T:9287068;N:10174	49	9128792	8378350	8324629	9287068	10174	SRX7908663	SRS6316238	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96185	0.07724	0.91597	0.48886	41	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57288	57288	SRR11302633	SRX7908662	SRS6316235	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s D15	GSM4410625	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s D15	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410625	GSM4410625: zebrafish 990s D15; Danio rerio; RNA Seq	GSM4410625		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410625	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_D15.bam	bam	20555028.0	414281.0	GSM4410625 r1	0:49.62	A:5268027;C:4987353;G:4954575;T:5338793;N:6280	49	5268027	4987353	4954575	5338793	6280	SRX7908662	SRS6316235	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96672	0.07072	0.92295	0.48391	44	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57289	57289	SRR11302632	SRX7908661	SRS6316234	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s D14	GSM4410624	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s D14	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410624	GSM4410624: zebrafish 990s D14; Danio rerio; RNA Seq	GSM4410624		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410624	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_D14.bam	bam	25155383.0	507445.0	GSM4410624 r1	0:49.57	A:6589687;C:5956715;G:5911932;T:6689599;N:7450	49	6589687	5956715	5911932	6689599	7450	SRX7908661	SRS6316234	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.9592	0.1259	0.91175	0.47661	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57290	57290	SRR11302631	SRX7908660	SRS6316232	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s D13	GSM4410623	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s D13	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410623	GSM4410623: zebrafish 990s D13; Danio rerio; RNA Seq	GSM4410623		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410623	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_D13.bam	bam	26252350.0	529709.0	GSM4410623 r1	0:49.56	A:6824395;C:6273054;G:6234203;T:6912870;N:7828	49	6824395	6273054	6234203	6912870	7828	SRX7908660	SRS6316232	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96307	0.10084	0.90445	0.47847	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57291	57291	SRR11302630	SRX7908659	SRS6316233	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s D12	GSM4410622	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s D12	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410622	GSM4410622: zebrafish 990s D12; Danio rerio; RNA Seq	GSM4410622		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410622	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_D12.bam	bam	26274219.0	529278.0	GSM4410622 r1	0:49.64	A:6795815;C:6306706;G:6259822;T:6904582;N:7294	49	6795815	6306706	6259822	6904582	7294	SRX7908659	SRS6316233	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.95859	0.10058	0.90106	0.46651	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57292	57292	SRR11302629	SRX7908658	SRS6316231	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s D11	GSM4410621	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s D11	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410621	GSM4410621: zebrafish 990s D11; Danio rerio; RNA Seq	GSM4410621		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410621	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_D11.bam	bam	10464062.0	211250.0	GSM4410621 r1	0:49.53	A:2687251;C:2533437;G:2512865;T:2727443;N:3066	49	2687251	2533437	2512865	2727443	3066	SRX7908658	SRS6316231	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96414	0.06516	0.94255	0.53005	45	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57293	57293	SRR11302628	SRX7908657	SRS6316229	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s D10	GSM4410620	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s D10	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410620	GSM4410620: zebrafish 990s D10; Danio rerio; RNA Seq	GSM4410620		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410620	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_D10.bam	bam	22770979.0	459186.0	GSM4410620 r1	0:49.59	A:5826113;C:5533708;G:5495964;T:5908461;N:6733	49	5826113	5533708	5495964	5908461	6733	SRX7908657	SRS6316229	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96785	0.06209	0.90784	0.48004	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57294	57294	SRR11302627	SRX7908656	SRS6316230	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s D1	GSM4410619	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s D1	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410619	GSM4410619: zebrafish 990s D1; Danio rerio; RNA Seq	GSM4410619		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410619	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_D1.bam	bam	25924183.0	521171.0	GSM4410619 r1	0:49.74	A:6729937;C:6200705;G:6153858;T:6832585;N:7098	49	6729937	6200705	6153858	6832585	7098	SRX7908656	SRS6316230	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96292	0.10401	0.89721	0.48829	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57295	57295	SRR11302626	SRX7908655	SRS6316227	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s C9	GSM4410618	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s C9	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410618	GSM4410618: zebrafish 990s C9; Danio rerio; RNA Seq	GSM4410618		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410618	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_C9.bam	bam	24266046.0	489282.0	GSM4410618 r1	0:49.60	A:6303157;C:5796448;G:5758377;T:6400971;N:7093	49	6303157	5796448	5758377	6400971	7093	SRX7908655	SRS6316227	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96377	0.09952	0.93604	0.47909	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57296	57296	SRR11302625	SRX7908654	SRS6316228	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s C8	GSM4410617	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s C8	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410617	GSM4410617: zebrafish 990s C8; Danio rerio; RNA Seq	GSM4410617		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410617	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_C8.bam	bam	21899008.0	441712.0	GSM4410617 r1	0:49.58	A:5747348;C:5177667;G:5136928;T:5830424;N:6641	49	5747348	5177667	5136928	5830424	6641	SRX7908654	SRS6316228	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.95958	0.13065	0.92216	0.46914	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57297	57297	SRR11302624	SRX7908653	SRS6316226	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s C7	GSM4410616	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s C7	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410616	GSM4410616: zebrafish 990s C7; Danio rerio; RNA Seq	GSM4410616		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410616	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_C7.bam	bam	28404846.0	573859.0	GSM4410616 r1	0:49.50	A:7235244;C:6926753;G:6877946;T:7356336;N:8567	49	7235244	6926753	6877946	7356336	8567	SRX7908653	SRS6316226	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96435	0.06783	0.91492	0.48294	42	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57298	57298	SRR11302623	SRX7908652	SRS6316224	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s C6	GSM4410615	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s C6	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410615	GSM4410615: zebrafish 990s C6; Danio rerio; RNA Seq	GSM4410615		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410615	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_C6.bam	bam	18860719.0	381549.0	GSM4410615 r1	0:49.43	A:5074635;C:4333167;G:4301649;T:5145437;N:5831	49	5074635	4333167	4301649	5145437	5831	SRX7908652	SRS6316224	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.95523	0.16234	0.90329	0.47409	41	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57299	57299	SRR11302622	SRX7908651	SRS6316225	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s C5	GSM4410614	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s C5	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410614	GSM4410614: zebrafish 990s C5; Danio rerio; RNA Seq	GSM4410614		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410614	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_C5.bam	bam	15089981.0	304859.0	GSM4410614 r1	0:49.50	A:3951385;C:3573935;G:3555893;T:4003894;N:4874	49	3951385	3573935	3555893	4003894	4874	SRX7908651	SRS6316225	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96352	0.17134	0.93265	0.47004	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57300	57300	SRR11302621	SRX7908650	SRS6316222	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s C4	GSM4410613	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s C4	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410613	GSM4410613: zebrafish 990s C4; Danio rerio; RNA Seq	GSM4410613		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410613	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_C4.bam	bam	19269405.0	388669.0	GSM4410613 r1	0:49.58	A:5084174;C:4527015;G:4489207;T:5163246;N:5763	49	5084174	4527015	4489207	5163246	5763	SRX7908650	SRS6316222	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.95519	0.12584	0.91977	0.48712	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57301	57301	SRR11302620	SRX7908649	SRS6316223	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s C3	GSM4410612	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s C3	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410612	GSM4410612: zebrafish 990s C3; Danio rerio; RNA Seq	GSM4410612		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410612	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_C3.bam	bam	26296146.0	529798.0	GSM4410612 r1	0:49.63	A:6879183;C:6235952;G:6187938;T:6985257;N:7816	49	6879183	6235952	6187938	6985257	7816	SRX7908649	SRS6316223	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.9614	0.13063	0.92693	0.48691	44	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57302	57302	SRR11302619	SRX7908648	SRS6316221	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s C24	GSM4410611	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s C24	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410611	GSM4410611: zebrafish 990s C24; Danio rerio; RNA Seq	GSM4410611		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410611	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_C24.bam	bam	20420608.0	411528.0	GSM4410611 r1	0:49.62	A:5331504;C:4853719;G:4820428;T:5408957;N:6000	49	5331504	4853719	4820428	5408957	6000	SRX7908648	SRS6316221	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96386	0.11067	0.93474	0.44648	42	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57303	57303	SRR11302618	SRX7908647	SRS6316219	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s C23	GSM4410610	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s C23	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410610	GSM4410610: zebrafish 990s C23; Danio rerio; RNA Seq	GSM4410610		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410610	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_C23.bam	bam	35047445.0	705646.0	GSM4410610 r1	0:49.67	A:9165559;C:8316903;G:8242039;T:9312819;N:10125	49	9165559	8316903	8242039	9312819	10125	SRX7908647	SRS6316219	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.95667	0.08618	0.90662	0.48076	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57304	57304	SRR11302617	SRX7908646	SRS6316220	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s C22	GSM4410609	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s C22	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410609	GSM4410609: zebrafish 990s C22; Danio rerio; RNA Seq	GSM4410609		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410609	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_C22.bam	bam	26040133.0	524602.0	GSM4410609 r1	0:49.64	A:6788556;C:6199193;G:6157557;T:6887011;N:7816	49	6788556	6199193	6157557	6887011	7816	SRX7908646	SRS6316220	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.95869	0.11718	0.9027	0.4912	48	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57305	57305	SRR11302616	SRX7908645	SRS6316217	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s C21	GSM4410608	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s C21	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410608	GSM4410608: zebrafish 990s C21; Danio rerio; RNA Seq	GSM4410608		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410608	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_C21.bam	bam	27771299.0	564142.0	GSM4410608 r1	0:49.23	A:7277456;C:6567924;G:6520282;T:7397263;N:8374	49	7277456	6567924	6520282	7397263	8374	SRX7908645	SRS6316217	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96216	0.08311	0.92214	0.484	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57306	57306	SRR11302615	SRX7908644	SRS6316218	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s C20	GSM4410607	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s C20	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410607	GSM4410607: zebrafish 990s C20; Danio rerio; RNA Seq	GSM4410607		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410607	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_C20.bam	bam	12727564.0	257166.0	GSM4410607 r1	0:49.49	A:3253378;C:3091074;G:3068783;T:3310426;N:3903	49	3253378	3091074	3068783	3310426	3903	SRX7908644	SRS6316218	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96581	0.09966	0.92336	0.46559	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57307	57307	SRR11302614	SRX7908643	SRS6316216	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s C2	GSM4410606	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s C2	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410606	GSM4410606: zebrafish 990s C2; Danio rerio; RNA Seq	GSM4410606		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410606	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_C2.bam	bam	24641347.0	496145.0	GSM4410606 r1	0:49.67	A:6362402;C:5928362;G:5889128;T:6454430;N:7025	49	6362402	5928362	5889128	6454430	7025	SRX7908643	SRS6316216	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96422	0.09577	0.9095	0.47689	41	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57308	57308	SRR11302613	SRX7908642	SRS6316215	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s C19	GSM4410605	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s C19	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410605	GSM4410605: zebrafish 990s C19; Danio rerio; RNA Seq	GSM4410605		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410605	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_C19.bam	bam	35386657.0	712451.0	GSM4410605 r1	0:49.67	A:9180689;C:8467349;G:8402491;T:9325656;N:10472	49	9180689	8467349	8402491	9325656	10472	SRX7908642	SRS6316215	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96283	0.1015	0.87852	0.47362	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57309	57309	SRR11302612	SRX7908641	SRS6316214	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s C18	GSM4410604	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s C18	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410604	GSM4410604: zebrafish 990s C18; Danio rerio; RNA Seq	GSM4410604		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410604	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_C18.bam	bam	17769590.0	358461.0	GSM4410604 r1	0:49.57	A:4590943;C:4269740;G:4239656;T:4663920;N:5331	49	4590943	4269740	4239656	4663920	5331	SRX7908641	SRS6316214	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.9647	0.09031	0.93288	0.48597	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57310	57310	SRR11302611	SRX7908640	SRS6316213	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s C17	GSM4410603	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s C17	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410603	GSM4410603: zebrafish 990s C17; Danio rerio; RNA Seq	GSM4410603		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410603	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_C17.bam	bam	32426584.0	653000.0	GSM4410603 r1	0:49.66	A:8461669;C:7712485;G:7651317;T:8591564;N:9549	49	8461669	7712485	7651317	8591564	9549	SRX7908640	SRS6316213	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.9592	0.08874	0.91259	0.49461	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57311	57311	SRR11302610	SRX7908639	SRS6316212	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s C16	GSM4410602	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s C16	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410602	GSM4410602: zebrafish 990s C16; Danio rerio; RNA Seq	GSM4410602		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410602	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_C16.bam	bam	25635088.0	516511.0	GSM4410602 r1	0:49.63	A:6592405;C:6192402;G:6144035;T:6698710;N:7536	49	6592405	6192402	6144035	6698710	7536	SRX7908639	SRS6316212	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96488	0.06936	0.90636	0.48394	36	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57312	57312	SRR11302609	SRX7908638	SRS6316211	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s C15	GSM4410601	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s C15	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410601	GSM4410601: zebrafish 990s C15; Danio rerio; RNA Seq	GSM4410601		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410601	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_C15.bam	bam	24612894.0	495477.0	GSM4410601 r1	0:49.68	A:6387972;C:5887843;G:5848486;T:6481347;N:7246	49	6387972	5887843	5848486	6481347	7246	SRX7908638	SRS6316211	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96143	0.11709	0.91139	0.48454	40	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57313	57313	SRR11302608	SRX7908637	SRS6316210	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s C14	GSM4410600	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s C14	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410600	GSM4410600: zebrafish 990s C14; Danio rerio; RNA Seq	GSM4410600		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410600	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_C14.bam	bam	23180351.0	466251.0	GSM4410600 r1	0:49.72	A:6010197;C:5556779;G:5513064;T:6093732;N:6579	49	6010197	5556779	5513064	6093732	6579	SRX7908637	SRS6316210	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96353	0.10838	0.91863	0.4849	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57314	57314	SRR11302607	SRX7908636	SRS6316209	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s C13	GSM4410599	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s C13	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410599	GSM4410599: zebrafish 990s C13; Danio rerio; RNA Seq	GSM4410599		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410599	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_C13.bam	bam	29064624.0	585464.0	GSM4410599 r1	0:49.64	A:7486030;C:7009056;G:6957087;T:7604008;N:8443	49	7486030	7009056	6957087	7604008	8443	SRX7908636	SRS6316209	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96286	0.10457	0.92805	0.47785	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57315	57315	SRR11302606	SRX7908635	SRS6316208	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s C12	GSM4410598	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s C12	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410598	GSM4410598: zebrafish 990s C12; Danio rerio; RNA Seq	GSM4410598		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410598	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_C12.bam	bam	24139133.0	486052.0	GSM4410598 r1	0:49.66	A:6234424;C:5812036;G:5765520;T:6319939;N:7214	49	6234424	5812036	5765520	6319939	7214	SRX7908635	SRS6316208	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96519	0.07726	0.90713	0.4802	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57316	57316	SRR11302605	SRX7908634	SRS6316207	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s C11	GSM4410597	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s C11	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410597	GSM4410597: zebrafish 990s C11; Danio rerio; RNA Seq	GSM4410597		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410597	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_C11.bam	bam	16322856.0	329244.0	GSM4410597 r1	0:49.58	A:4485023;C:3646315;G:3622640;T:4563901;N:4977	49	4485023	3646315	3622640	4563901	4977	SRX7908634	SRS6316207	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.94782	0.31171	0.93539	0.48256	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57317	57317	SRR11302604	SRX7908633	SRS6316205	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s C10	GSM4410596	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s C10	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410596	GSM4410596: zebrafish 990s C10; Danio rerio; RNA Seq	GSM4410596		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410596	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_C10.bam	bam	21009208.0	423572.0	GSM4410596 r1	0:49.60	A:5465149;C:5010550;G:4980276;T:5546702;N:6531	49	5465149	5010550	4980276	5546702	6531	SRX7908633	SRS6316205	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96405	0.10732	0.92744	0.48269	39	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57318	57318	SRR11302603	SRX7908632	SRS6316206	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s C1	GSM4410595	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s C1	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410595	GSM4410595: zebrafish 990s C1; Danio rerio; RNA Seq	GSM4410595		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410595	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_C1.bam	bam	26901512.0	541337.0	GSM4410595 r1	0:49.69	A:6970707;C:6446413;G:6411599;T:7064656;N:8137	49	6970707	6446413	6411599	7064656	8137	SRX7908632	SRS6316206	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.9641	0.09528	0.92346	0.50558	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57319	57319	SRR11302602	SRX7908631	SRS6316202	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s B9	GSM4410594	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s B9	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410594	GSM4410594: zebrafish 990s B9; Danio rerio; RNA Seq	GSM4410594		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410594	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_B9.bam	bam	15426612.0	310884.0	GSM4410594 r1	0:49.62	A:4080022;C:3616468;G:3595348;T:4130253;N:4521	49	4080022	3616468	3595348	4130253	4521	SRX7908631	SRS6316202	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.95866	0.18239	0.93306	0.49468	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57320	57320	SRR11302601	SRX7908630	SRS6316204	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s B8	GSM4410593	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s B8	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410593	GSM4410593: zebrafish 990s B8; Danio rerio; RNA Seq	GSM4410593		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410593	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_B8.bam	bam	16209285.0	326585.0	GSM4410593 r1	0:49.63	A:4198717;C:3887458;G:3856999;T:4261238;N:4873	49	4198717	3887458	3856999	4261238	4873	SRX7908630	SRS6316204	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.95752	0.11124	0.93876	0.48231	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57321	57321	SRR11302600	SRX7908629	SRS6316200	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s B7	GSM4410592	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s B7	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410592	GSM4410592: zebrafish 990s B7; Danio rerio; RNA Seq	GSM4410592		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410592	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_B7.bam	bam	13053261.0	262841.0	GSM4410592 r1	0:49.66	A:3407078;C:3104309;G:3085740;T:3452172;N:3962	49	3407078	3104309	3085740	3452172	3962	SRX7908629	SRS6316200	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.9621	0.14005	0.94339	0.48716	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57322	57322	SRR11302599	SRX7908628	SRS6316203	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s B6	GSM4410591	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s B6	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410591	GSM4410591: zebrafish 990s B6; Danio rerio; RNA Seq	GSM4410591		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410591	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_B6.bam	bam	18688513.0	377150.0	GSM4410591 r1	0:49.55	A:4811790;C:4506958;G:4476764;T:4887270;N:5731	49	4811790	4506958	4476764	4887270	5731	SRX7908628	SRS6316203	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96323	0.09461	0.91492	0.4842	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57323	57323	SRR11302598	SRX7908627	SRS6316201	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s B5	GSM4410590	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s B5	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410590	GSM4410590: zebrafish 990s B5; Danio rerio; RNA Seq	GSM4410590		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410590	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_B5.bam	bam	23305863.0	469800.0	GSM4410590 r1	0:49.61	A:5996295;C:5637264;G:5603679;T:6061625;N:7000	49	5996295	5637264	5603679	6061625	7000	SRX7908627	SRS6316201	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96423	0.07727	0.91581	0.46864	48	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57324	57324	SRR11302597	SRX7908626	SRS6316197	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s B4	GSM4410589	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s B4	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410589	GSM4410589: zebrafish 990s B4; Danio rerio; RNA Seq	GSM4410589		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410589	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_B4.bam	bam	14198609.0	286330.0	GSM4410589 r1	0:49.59	A:3685085;C:3392571;G:3377981;T:3738614;N:4358	49	3685085	3392571	3377981	3738614	4358	SRX7908626	SRS6316197	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96687	0.12743	0.94134	0.50108	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57325	57325	SRR11302596	SRX7908625	SRS6316199	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s B3	GSM4410588	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s B3	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410588	GSM4410588: zebrafish 990s B3; Danio rerio; RNA Seq	GSM4410588		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410588	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_B3.bam	bam	21337200.0	430023.0	GSM4410588 r1	0:49.62	A:5500444;C:5141927;G:5111797;T:5576378;N:6654	49	5500444	5141927	5111797	5576378	6654	SRX7908625	SRS6316199	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96416	0.07969	0.90218	0.47964	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57326	57326	SRR11302595	SRX7908624	SRS6316198	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s B24	GSM4410587	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s B24	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410587	GSM4410587: zebrafish 990s B24; Danio rerio; RNA Seq	GSM4410587		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410587	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_B24.bam	bam	14884174.0	300927.0	GSM4410587 r1	0:49.46	A:3847326;C:3570345;G:3546698;T:3915410;N:4395	49	3847326	3570345	3546698	3915410	4395	SRX7908624	SRS6316198	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96401	0.10549	0.9389	0.47099	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57327	57327	SRR11302594	SRX7908623	SRS6316195	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s B23	GSM4410586	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s B23	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410586	GSM4410586: zebrafish 990s B23; Danio rerio; RNA Seq	GSM4410586		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410586	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_B23.bam	bam	21727602.0	437959.0	GSM4410586 r1	0:49.61	A:5617471;C:5219687;G:5183659;T:5700225;N:6560	49	5617471	5219687	5183659	5700225	6560	SRX7908623	SRS6316195	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96243	0.06801	0.877	0.50398	36	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57328	57328	SRR11302593	SRX7908622	SRS6316196	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s B22	GSM4410585	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s B22	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410585	GSM4410585: zebrafish 990s B22; Danio rerio; RNA Seq	GSM4410585		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410585	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_B22.bam	bam	14808460.0	298872.0	GSM4410585 r1	0:49.55	A:3814070;C:3570992;G:3546502;T:3872564;N:4332	49	3814070	3570992	3546502	3872564	4332	SRX7908622	SRS6316196	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96236	0.09761	0.93908	0.47544	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57329	57329	SRR11302592	SRX7908621	SRS6316192	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s B21	GSM4410584	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s B21	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410584	GSM4410584: zebrafish 990s B21; Danio rerio; RNA Seq	GSM4410584		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410584	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_B21.bam	bam	7756712.0	157032.0	GSM4410584 r1	0:49.40	A:2049070;C:1821395;G:1808619;T:2075260;N:2368	49	2049070	1821395	1808619	2075260	2368	SRX7908621	SRS6316192	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96154	0.21386	0.9403	0.52429	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57330	57330	SRR11302591	SRX7908620	SRS6316194	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s B20	GSM4410583	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s B20	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410583	GSM4410583: zebrafish 990s B20; Danio rerio; RNA Seq	GSM4410583		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410583	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_B20.bam	bam	16812241.0	340050.0	GSM4410583 r1	0:49.44	A:4301130;C:4085399;G:4056346;T:4364188;N:5178	49	4301130	4085399	4056346	4364188	5178	SRX7908620	SRS6316194	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96716	0.06463	0.91956	0.48441	46	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57331	57331	SRR11302590	SRX7908619	SRS6316193	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s B2	GSM4410582	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s B2	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410582	GSM4410582: zebrafish 990s B2; Danio rerio; RNA Seq	GSM4410582		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410582	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_B2.bam	bam	30944819.0	623277.0	GSM4410582 r1	0:49.65	A:8194727;C:7240383;G:7192797;T:8307778;N:9134	49	8194727	7240383	7192797	8307778	9134	SRX7908619	SRS6316193	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.9581	0.11638	0.89824	0.47307	38	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57332	57332	SRR11302589	SRX7908618	SRS6316191	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s B19	GSM4410581	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s B19	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410581	GSM4410581: zebrafish 990s B19; Danio rerio; RNA Seq	GSM4410581		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410581	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_B19.bam	bam	18557798.0	374931.0	GSM4410581 r1	0:49.50	A:4786927;C:4465486;G:4440781;T:4858904;N:5700	49	4786927	4465486	4440781	4858904	5700	SRX7908618	SRS6316191	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96412	0.07828	0.92125	0.49448	42	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57333	57333	SRR11302588	SRX7908617	SRS6316189	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s B18	GSM4410580	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s B18	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410580	GSM4410580: zebrafish 990s B18; Danio rerio; RNA Seq	GSM4410580		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410580	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_B18.bam	bam	23451188.0	472860.0	GSM4410580 r1	0:49.59	A:6035531;C:5661140;G:5621717;T:6125715;N:7085	49	6035531	5661140	5621717	6125715	7085	SRX7908617	SRS6316189	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.963	0.08656	0.90869	0.49805	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57334	57334	SRR11302587	SRX7908616	SRS6316188	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s B17	GSM4410579	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s B17	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410579	GSM4410579: zebrafish 990s B17; Danio rerio; RNA Seq	GSM4410579		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410579	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_B17.bam	bam	9008597.0	181598.0	GSM4410579 r1	0:49.61	A:2387290;C:2106785;G:2089721;T:2422047;N:2754	49	2387290	2106785	2089721	2422047	2754	SRX7908616	SRS6316188	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.95954	0.19762	0.94119	0.5018	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57335	57335	SRR11302586	SRX7908615	SRS6316190	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s B16	GSM4410578	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s B16	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410578	GSM4410578: zebrafish 990s B16; Danio rerio; RNA Seq	GSM4410578		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410578	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_B16.bam	bam	20217061.0	407523.0	GSM4410578 r1	0:49.61	A:5265904;C:4820615;G:4787256;T:5337241;N:6045	49	5265904	4820615	4787256	5337241	6045	SRX7908615	SRS6316190	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96128	0.10365	0.9231	0.47581	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57336	57336	SRR11302585	SRX7908614	SRS6316187	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s B15	GSM4410577	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s B15	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410577	GSM4410577: zebrafish 990s B15; Danio rerio; RNA Seq	GSM4410577		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410577	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_B15.bam	bam	16688538.0	336617.0	GSM4410577 r1	0:49.58	A:4274559;C:4055734;G:4027475;T:4325551;N:5219	49	4274559	4055734	4027475	4325551	5219	SRX7908614	SRS6316187	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.9665	0.07272	0.92851	0.48099	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57337	57337	SRR11302584	SRX7908613	SRS6316186	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s B14	GSM4410576	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s B14	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410576	GSM4410576: zebrafish 990s B14; Danio rerio; RNA Seq	GSM4410576		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410576	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_B14.bam	bam	7616235.0	154051.0	GSM4410576 r1	0:49.44	A:2056188;C:1739845;G:1728535;T:2089310;N:2357	49	2056188	1739845	1728535	2089310	2357	SRX7908613	SRS6316186	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.95879	0.27188	0.9373	0.52528	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57338	57338	SRR11302583	SRX7908612	SRS6316185	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s B13	GSM4410575	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s B13	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410575	GSM4410575: zebrafish 990s B13; Danio rerio; RNA Seq	GSM4410575		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410575	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_B13.bam	bam	17299086.0	348387.0	GSM4410575 r1	0:49.65	A:4463392;C:4164427;G:4139877;T:4526164;N:5226	49	4463392	4164427	4139877	4526164	5226	SRX7908612	SRS6316185	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.9635	0.10533	0.92977	0.48953	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57339	57339	SRR11302582	SRX7908611	SRS6316184	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s B12	GSM4410574	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s B12	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410574	GSM4410574: zebrafish 990s B12; Danio rerio; RNA Seq	GSM4410574		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410574	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_B12.bam	bam	23474956.0	472732.0	GSM4410574 r1	0:49.66	A:6063639;C:5645203;G:5610466;T:6148678;N:6970	49	6063639	5645203	5610466	6148678	6970	SRX7908611	SRS6316184	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96365	0.08835	0.92092	0.47208	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57340	57340	SRR11302581	SRX7908610	SRS6316183	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s B11	GSM4410573	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s B11	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410573	GSM4410573: zebrafish 990s B11; Danio rerio; RNA Seq	GSM4410573		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410573	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_B11.bam	bam	16035157.0	322934.0	GSM4410573 r1	0:49.65	A:4146889;C:3851858;G:3828619;T:4203084;N:4707	49	4146889	3851858	3828619	4203084	4707	SRX7908610	SRS6316183	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96384	0.11699	0.94093	0.47805	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57341	57341	SRR11302580	SRX7908609	SRS6316182	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s B10	GSM4410572	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s B10	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410572	GSM4410572: zebrafish 990s B10; Danio rerio; RNA Seq	GSM4410572		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410572	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_B10.bam	bam	14096551.0	284222.0	GSM4410572 r1	0:49.60	A:3618868;C:3414966;G:3392328;T:3665996;N:4393	49	3618868	3414966	3392328	3665996	4393	SRX7908609	SRS6316182	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96294	0.09185	0.94107	0.4874	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57342	57342	SRR11302579	SRX7908608	SRS6316181	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s B1	GSM4410571	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s B1	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410571	GSM4410571: zebrafish 990s B1; Danio rerio; RNA Seq	GSM4410571		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410571	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_B1.bam	bam	13856980.0	279102.0	GSM4410571 r1	0:49.65	A:3672204;C:3242179;G:3221658;T:3716850;N:4089	49	3672204	3242179	3221658	3716850	4089	SRX7908608	SRS6316181	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.95833	0.14516	0.93385	0.46308	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57343	57343	SRR11302578	SRX7908607	SRS6316180	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s A9	GSM4410570	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s A9	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410570	GSM4410570: zebrafish 990s A9; Danio rerio; RNA Seq	GSM4410570		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410570	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_A9.bam	bam	17075497.0	344121.0	GSM4410570 r1	0:49.62	A:4456792;C:4055609;G:4028161;T:4529646;N:5289	49	4456792	4055609	4028161	4529646	5289	SRX7908607	SRS6316180	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96232	0.1102	0.93671	0.50336	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57344	57344	SRR11302577	SRX7908606	SRS6316179	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s A8	GSM4410569	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s A8	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410569	GSM4410569: zebrafish 990s A8; Danio rerio; RNA Seq	GSM4410569		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410569	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_A8.bam	bam	16810326.0	339452.0	GSM4410569 r1	0:49.52	A:4372174;C:4016139;G:3987443;T:4429512;N:5058	49	4372174	4016139	3987443	4429512	5058	SRX7908606	SRS6316179	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96283	0.13767	0.93492	0.47721	45	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57345	57345	SRR11302576	SRX7908605	SRS6316178	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s A7	GSM4410568	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s A7	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410568	GSM4410568: zebrafish 990s A7; Danio rerio; RNA Seq	GSM4410568		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410568	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_A7.bam	bam	25404482.0	511925.0	GSM4410568 r1	0:49.63	A:6590510;C:6081778;G:6040538;T:6683960;N:7696	49	6590510	6081778	6040538	6683960	7696	SRX7908605	SRS6316178	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96145	0.09912	0.92198	0.47642	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57346	57346	SRR11302575	SRX7908604	SRS6316177	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s A6	GSM4410567	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s A6	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410567	GSM4410567: zebrafish 990s A6; Danio rerio; RNA Seq	GSM4410567		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410567	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_A6.bam	bam	13401980.0	270485.0	GSM4410567 r1	0:49.55	A:3452902;C:3229647;G:3208712;T:3506704;N:4015	49	3452902	3229647	3208712	3506704	4015	SRX7908604	SRS6316177	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.95931	0.09851	0.94111	0.48532	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57347	57347	SRR11302574	SRX7908603	SRS6316176	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s A5	GSM4410566	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s A5	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410566	GSM4410566: zebrafish 990s A5; Danio rerio; RNA Seq	GSM4410566		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410566	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_A5.bam	bam	17859359.0	359863.0	GSM4410566 r1	0:49.63	A:4661192;C:4250348;G:4214482;T:4728075;N:5262	49	4661192	4250348	4214482	4728075	5262	SRX7908603	SRS6316176	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96336	0.11509	0.93797	0.46297	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57348	57348	SRR11302573	SRX7908602	SRS6316174	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s A4	GSM4410565	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s A4	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410565	GSM4410565: zebrafish 990s A4; Danio rerio; RNA Seq	GSM4410565		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410565	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_A4.bam	bam	22326452.0	449827.0	GSM4410565 r1	0:49.63	A:5787211;C:5352678;G:5313520;T:5866507;N:6536	49	5787211	5352678	5313520	5866507	6536	SRX7908602	SRS6316174	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96139	0.08905	0.91851	0.48896	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57349	57349	SRR11302572	SRX7908601	SRS6316175	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s A3	GSM4410564	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s A3	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410564	GSM4410564: zebrafish 990s A3; Danio rerio; RNA Seq	GSM4410564		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410564	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_A3.bam	bam	21756925.0	438508.0	GSM4410564 r1	0:49.62	A:5650511;C:5205874;G:5163998;T:5730121;N:6421	49	5650511	5205874	5163998	5730121	6421	SRX7908601	SRS6316175	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96069	0.09546	0.92811	0.48483	41	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57350	57350	SRR11302571	SRX7908600	SRS6316173	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s A24	GSM4410563	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s A24	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410563	GSM4410563: zebrafish 990s A24; Danio rerio; RNA Seq	GSM4410563		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410563	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_A24.bam	bam	21902091.0	442251.0	GSM4410563 r1	0:49.52	A:5626608;C:5288084;G:5247861;T:5732839;N:6699	49	5626608	5288084	5247861	5732839	6699	SRX7908600	SRS6316173	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96433	0.08418	0.92139	0.48143	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57351	57351	SRR11302570	SRX7908599	SRS6316172	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s A23	GSM4410562	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s A23	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410562	GSM4410562: zebrafish 990s A23; Danio rerio; RNA Seq	GSM4410562		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410562	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_A23.bam	bam	24417258.0	491841.0	GSM4410562 r1	0:49.64	A:6380531;C:5798072;G:5754658;T:6476829;N:7168	49	6380531	5798072	5754658	6476829	7168	SRX7908599	SRS6316172	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.95974	0.11386	0.93141	0.46622	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57352	57352	SRR11302569	SRX7908598	SRS6316171	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s A22	GSM4410561	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s A22	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410561	GSM4410561: zebrafish 990s A22; Danio rerio; RNA Seq	GSM4410561		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410561	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_A22.bam	bam	23665999.0	476981.0	GSM4410561 r1	0:49.62	A:6081723;C:5713915;G:5678807;T:6184457;N:7097	49	6081723	5713915	5678807	6184457	7097	SRX7908598	SRS6316171	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96437	0.08101	0.91526	0.48297	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57353	57353	SRR11302568	SRX7908597	SRS6316170	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s A21	GSM4410560	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s A21	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410560	GSM4410560: zebrafish 990s A21; Danio rerio; RNA Seq	GSM4410560		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410560	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_A21.bam	bam	30119135.0	606292.0	GSM4410560 r1	0:49.68	A:7894692;C:7131349;G:7077245;T:8007295;N:8554	49	7894692	7131349	7077245	8007295	8554	SRX7908597	SRS6316170	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.95812	0.07769	0.91865	0.5021	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57354	57354	SRR11302567	SRX7908596	SRS6316169	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s A20	GSM4410559	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s A20	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410559	GSM4410559: zebrafish 990s A20; Danio rerio; RNA Seq	GSM4410559		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410559	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_A20.bam	bam	22478766.0	453258.0	GSM4410559 r1	0:49.59	A:5841447;C:5376978;G:5332083;T:5921650;N:6608	49	5841447	5376978	5332083	5921650	6608	SRX7908596	SRS6316169	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.95731	0.08786	0.92445	0.49535	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57355	57355	SRR11302566	SRX7908595	SRS6316168	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s A2	GSM4410558	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s A2	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410558	GSM4410558: zebrafish 990s A2; Danio rerio; RNA Seq	GSM4410558		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410558	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_A2.bam	bam	19088094.0	384444.0	GSM4410558 r1	0:49.65	A:4957048;C:4561438;G:4531806;T:5032248;N:5554	49	4957048	4561438	4531806	5032248	5554	SRX7908595	SRS6316168	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96252	0.09612	0.91705	0.48496	44	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57356	57356	SRR11302565	SRX7908594	SRS6316166	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s A19	GSM4410557	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s A19	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410557	GSM4410557: zebrafish 990s A19; Danio rerio; RNA Seq	GSM4410557		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410557	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_A19.bam	bam	8124990.0	163506.0	GSM4410557 r1	0:49.69	A:2093903;C:1958192;G:1942450;T:2128209;N:2236	49	2093903	1958192	1942450	2128209	2236	SRX7908594	SRS6316166	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96665	0.12458	0.92912	0.48872	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57357	57357	SRR11302564	SRX7908593	SRS6316165	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s A18	GSM4410556	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s A18	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410556	GSM4410556: zebrafish 990s A18; Danio rerio; RNA Seq	GSM4410556		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410556	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_A18.bam	bam	25879673.0	521145.0	GSM4410556 r1	0:49.66	A:6776528;C:6135214;G:6097496;T:6862874;N:7561	49	6776528	6135214	6097496	6862874	7561	SRX7908593	SRS6316165	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96168	0.1033	0.92206	0.47484	41	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57358	57358	SRR11302563	SRX7908592	SRS6316167	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s A17	GSM4410555	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s A17	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410555	GSM4410555: zebrafish 990s A17; Danio rerio; RNA Seq	GSM4410555		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410555	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_A17.bam	bam	9309002.0	188213.0	GSM4410555 r1	0:49.46	A:2409344;C:2231940;G:2215336;T:2449783;N:2599	49	2409344	2231940	2215336	2449783	2599	SRX7908592	SRS6316167	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96502	0.13802	0.91119	0.50636	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57359	57359	SRR11302562	SRX7908591	SRS6316164	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s A16	GSM4410554	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s A16	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410554	GSM4410554: zebrafish 990s A16; Danio rerio; RNA Seq	GSM4410554		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410554	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_A16.bam	bam	16920507.0	340982.0	GSM4410554 r1	0:49.62	A:4394092;C:4049044;G:4018535;T:4453777;N:5059	49	4394092	4049044	4018535	4453777	5059	SRX7908591	SRS6316164	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96043	0.10221	0.93829	0.47402	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57360	57360	SRR11302561	SRX7908590	SRS6316161	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s A15	GSM4410553	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s A15	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410553	GSM4410553: zebrafish 990s A15; Danio rerio; RNA Seq	GSM4410553		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410553	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_A15.bam	bam	17918600.0	360699.0	GSM4410553 r1	0:49.68	A:4634795;C:4306215;G:4271499;T:4700802;N:5289	49	4634795	4306215	4271499	4700802	5289	SRX7908590	SRS6316161	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.95965	0.11738	0.93259	0.48557	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57361	57361	SRR11302560	SRX7908589	SRS6316162	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s A14	GSM4410552	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s A14	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410552	GSM4410552: zebrafish 990s A14; Danio rerio; RNA Seq	GSM4410552		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410552	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_A14.bam	bam	20822358.0	419485.0	GSM4410552 r1	0:49.64	A:5356899;C:5024700;G:4992900;T:5441524;N:6335	49	5356899	5024700	4992900	5441524	6335	SRX7908589	SRS6316162	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96485	0.08984	0.91835	0.47886	48	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57362	57362	SRR11302559	SRX7908588	SRS6316163	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s A13	GSM4410551	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s A13	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410551	GSM4410551: zebrafish 990s A13; Danio rerio; RNA Seq	GSM4410551		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410551	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_A13.bam	bam	22307020.0	448645.0	GSM4410551 r1	0:49.72	A:5814033;C:5313315;G:5271355;T:5901627;N:6690	49	5814033	5313315	5271355	5901627	6690	SRX7908588	SRS6316163	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.95994	0.07073	0.8857	0.52499	41	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57363	57363	SRR11302558	SRX7908587	SRS6316160	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s A12	GSM4410550	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s A12	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410550	GSM4410550: zebrafish 990s A12; Danio rerio; RNA Seq	GSM4410550		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410550	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_A12.bam	bam	34433341.0	692689.0	GSM4410550 r1	0:49.71	A:8934183;C:8240756;G:8187452;T:9060756;N:10194	49	8934183	8240756	8187452	9060756	10194	SRX7908587	SRS6316160	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.9607	0.09578	0.8845	0.46372	34	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57364	57364	SRR11302557	SRX7908586	SRS6316159	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s A11	GSM4410549	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s A11	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410549	GSM4410549: zebrafish 990s A11; Danio rerio; RNA Seq	GSM4410549		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410549	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_A11.bam	bam	32209861.0	647541.0	GSM4410549 r1	0:49.74	A:8517449;C:7540744;G:7491730;T:8650464;N:9474	49	8517449	7540744	7491730	8650464	9474	SRX7908586	SRS6316159	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.95543	0.16659	0.90652	0.46702	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57365	57365	SRR11302556	SRX7908585	SRS6316157	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s A10	GSM4410548	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s A10	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410548	GSM4410548: zebrafish 990s A10; Danio rerio; RNA Seq	GSM4410548		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410548	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_A10.bam	bam	17585850.0	353845.0	GSM4410548 r1	0:49.70	A:4584784;C:4193009;G:4160432;T:4642486;N:5139	49	4584784	4193009	4160432	4642486	5139	SRX7908585	SRS6316157	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96442	0.09213	0.92904	0.49053	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57366	57366	SRR11302555	SRX7908584	SRS6316158	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 990s A1	GSM4410547	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 990s A1	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410547	GSM4410547: zebrafish 990s A1; Danio rerio; RNA Seq	GSM4410547		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410547	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_990s_A1.bam	bam	30957217.0	623412.0	GSM4410547 r1	0:49.66	A:8071976;C:7371031;G:7322241;T:8182691;N:9278	49	8071976	7371031	7322241	8182691	9278	SRX7908584	SRS6316158	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96362	0.08251	0.90711	0.46056	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57367	57367	SRR11302554	SRX7908583	SRS6316156	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 989s P9	GSM4410546	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 989s P9	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410546	GSM4410546: zebrafish 989s P9; Danio rerio; RNA Seq	GSM4410546		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410546	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_989s_P9.bam	bam	12678215.0	256714.0	GSM4410546 r1	0:49.39	A:3257099;C:3071672;G:3043362;T:3302984;N:3098	49	3257099	3071672	3043362	3302984	3098	SRX7908583	SRS6316156	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96426	0.09799	0.89345	0.48582	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57368	57368	SRR11302553	SRX7908582	SRS6316155	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 989s P8	GSM4410545	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 989s P8	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410545	GSM4410545: zebrafish 989s P8; Danio rerio; RNA Seq	GSM4410545		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410545	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_989s_P8.bam	bam	15876176.0	321452.0	GSM4410545 r1	0:49.39	A:4053984;C:3875508;G:3840669;T:4102053;N:3962	49	4053984	3875508	3840669	4102053	3962	SRX7908582	SRS6316155	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.9663	0.08158	0.90668	0.48539	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57369	57369	SRR11302552	SRX7908581	SRS6316154	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 989s P7	GSM4410544	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 989s P7	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410544	GSM4410544: zebrafish 989s P7; Danio rerio; RNA Seq	GSM4410544		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410544	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_989s_P7.bam	bam	24949009.0	504858.0	GSM4410544 r1	0:49.42	A:6459485;C:5999324;G:5945760;T:6538183;N:6257	49	6459485	5999324	5945760	6538183	6257	SRX7908581	SRS6316154	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96633	0.0893	0.89286	0.48428	37	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57370	57370	SRR11302551	SRX7908580	SRS6316153	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 989s P6	GSM4410543	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 989s P6	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410543	GSM4410543: zebrafish 989s P6; Danio rerio; RNA Seq	GSM4410543		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410543	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_989s_P6.bam	bam	15554547.0	314801.0	GSM4410543 r1	0:49.41	A:4006700;C:3757378;G:3727660;T:4058754;N:4055	49	4006700	3757378	3727660	4058754	4055	SRX7908580	SRS6316153	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96457	0.10212	0.91248	0.50459	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57371	57371	SRR11302550	SRX7908579	SRS6316152	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 989s P5	GSM4410542	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 989s P5	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410542	GSM4410542: zebrafish 989s P5; Danio rerio; RNA Seq	GSM4410542		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410542	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_989s_P5.bam	bam	14328454.0	289863.0	GSM4410542 r1	0:49.43	A:3660178;C:3495738;G:3458695;T:3710432;N:3411	49	3660178	3495738	3458695	3710432	3411	SRX7908579	SRS6316152	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96504	0.10406	0.9078	0.50053	45	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57372	57372	SRR11302549	SRX7908578	SRS6316151	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 989s P4	GSM4410541	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 989s P4	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410541	GSM4410541: zebrafish 989s P4; Danio rerio; RNA Seq	GSM4410541		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410541	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_989s_P4.bam	bam	18257797.0	369233.0	GSM4410541 r1	0:49.45	A:4655072;C:4457536;G:4426867;T:4713799;N:4523	49	4655072	4457536	4426867	4713799	4523	SRX7908578	SRS6316151	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96695	0.08182	0.90569	0.47694	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57373	57373	SRR11302548	SRX7908577	SRS6316149	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 989s P3	GSM4410540	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 989s P3	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410540	GSM4410540: zebrafish 989s P3; Danio rerio; RNA Seq	GSM4410540		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410540	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_989s_P3.bam	bam	13682928.0	276925.0	GSM4410540 r1	0:49.41	A:3473172;C:3359246;G:3328045;T:3519149;N:3316	49	3473172	3359246	3328045	3519149	3316	SRX7908577	SRS6316149	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96307	0.08688	0.90847	0.49011	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57374	57374	SRR11302547	SRX7908576	SRS6316150	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 989s P22	GSM4410539	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 989s P22	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410539	GSM4410539: zebrafish 989s P22; Danio rerio; RNA Seq	GSM4410539		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410539	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_989s_P22.bam	bam	23275586.0	470623.0	GSM4410539 r1	0:49.46	A:6029395;C:5591130;G:5532121;T:6117340;N:5600	49	6029395	5591130	5532121	6117340	5600	SRX7908576	SRS6316150	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.95984	0.07881	0.9023	0.50517	41	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57375	57375	SRR11302546	SRX7908575	SRS6316146	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 989s P21	GSM4410538	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 989s P21	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410538	GSM4410538: zebrafish 989s P21; Danio rerio; RNA Seq	GSM4410538		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410538	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_989s_P21.bam	bam	7951757.0	161237.0	GSM4410538 r1	0:49.32	A:2065167;C:1903244;G:1885731;T:2095662;N:1953	49	2065167	1903244	1885731	2095662	1953	SRX7908575	SRS6316146	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96234	0.19054	0.90266	0.49557	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure
57376	57376	SRR11302545	SRX7908574	SRS6316148	SRP252691	PRJNA612443	Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis	GSE146923	Transcriptome Analysis	Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing	pubmed:32483144	zebrafish 989s P20	GSM4410537	source name:zebrafish\|tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	zebrafish 989s P20	bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples	zebrafish	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	tissue:embryo trunk\|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry\|age:48 hpf	GSM4410537	GSM4410537: zebrafish 989s P20; Danio rerio; RNA Seq	GSM4410537		1	FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol	GEO Accession:GSM4410537	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP252691	intentional duplicate\|dangling references:treat as unmapped	zebrafish_989s_P20.bam	bam	16692869.0	338021.0	GSM4410537 r1	0:49.38	A:4320881;C:4010465;G:3976013;T:4381218;N:4292	49	4320881	4010465	3976013	4381218	4292	SRX7908574	SRS6316148	SRA1054549	GEO	Betsholtz, ICMC - MedH, Karolinska Institutet	1	0.96252	0.09142	0.90025	0.50002	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Sweden	2020-03-13	Hatching	Embryo	Trunk	Surface Structure

Advanced export

JSON shape: default, array, newline-delimited

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");;