{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where technology = \"smartseq\" and tissue_curation_coarse = \"Surface Structure\"", "rows": [[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.", null, null, null, "24hpf TrunkNC 3", "GSM8751790", null, "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", null, "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\u2122 Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq\u00ae v4 Ultra\u00ae 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.", null, "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. 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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.", null, null, null, "24hpf TrunkNC 2", "GSM8751789", null, "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", null, "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\u2122 Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq\u00ae v4 Ultra\u00ae 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.", null, "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\u2122 Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq\u00ae v4 Ultra\u00ae 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP559533", null, null, "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, null, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2025-01-23", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [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.", null, null, null, "24hpf TrunkNC 1", "GSM8751788", null, "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", null, "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\u2122 Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq\u00ae v4 Ultra\u00ae 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.", null, "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\u2122 Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq\u00ae v4 Ultra\u00ae 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP559533", null, null, "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, null, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2025-01-23", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [51228, "SRR8591752", "SRX5391965", "SRS4379795", "SRP186291", "PRJNA523219", "Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs", "GSE126763", "Transcriptome Analysis", "In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.", null, "pubmed:31006648", null, "T cells 3", "GSM3612324", null, "source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tglck:DsRedx", "T cells 3", "Raw reads were first aligned to zebrafish reference genome danRer10\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10\u00a0 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish epidermis", null, "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", null, "tissue:epidermis|Stage:adult|transgenic line:Tglck:DsRedx", "GSM3612324", "GSM3612324: T cells 3; Danio rerio; RNA Seq", "GSM3612324", null, "1", "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", "GEO Accession:GSM3612324", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP186291", null, null, "T_cells_3_R2.fq.gz T_cells_3_R1.fq.gz", "fastq fastq", 11144333100.0, 37147777.0, "GSM3612324 r1", "0:150 1:150", "A:3499952862;C:2003192621;G:2060397654;T:3580454183;N:335780", 150, 150, null, null, 3499952862, 2003192621, 2060397654, 3580454183, 335780, "SRX5391965", "SRS4379795", "SRA850414", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.7813, 0.78015, 0.18285, 0.17813, 0.83978, 0.84051, 0.5593, 0.449, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "nebnext", "sc", "single_cell_plate", "smartseq", null, "China", "2019-02-19", "Adult", "Adult", "Skin", "Surface Structure"], [51229, "SRR8591751", "SRX5391964", "SRS4379794", "SRP186291", "PRJNA523219", "Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs", "GSE126763", "Transcriptome Analysis", "In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.", null, "pubmed:31006648", null, "T cells 2", "GSM3612323", null, "source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tglck:DsRedx", "T cells 2", "Raw reads were first aligned to zebrafish reference genome danRer10\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10\u00a0 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish epidermis", null, "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", null, "tissue:epidermis|Stage:adult|transgenic line:Tglck:DsRedx", "GSM3612323", "GSM3612323: T cells 2; Danio rerio; RNA Seq", "GSM3612323", null, "1", "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. 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As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.", null, "pubmed:31006648", null, "T cells 1", "GSM3612322", null, "source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tglck:DsRedx", "T cells 1", "Raw reads were first aligned to zebrafish reference genome danRer10\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10\u00a0 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish epidermis", null, "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", null, "tissue:epidermis|Stage:adult|transgenic line:Tglck:DsRedx", "GSM3612322", "GSM3612322: T cells 1; Danio rerio; RNA Seq", "GSM3612322", null, "1", "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. 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As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.", null, "pubmed:31006648", null, "Neutrophils 3", "GSM3612321", null, "source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tglyz:GFP", "Neutrophils 3", "Raw reads were first aligned to zebrafish reference genome danRer10\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10\u00a0 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish epidermis", null, "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", null, "tissue:epidermis|Stage:adult|transgenic line:Tglyz:GFP", "GSM3612321", "GSM3612321: Neutrophils 3; Danio rerio; RNA Seq", "GSM3612321", null, "1", "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", "GEO Accession:GSM3612321", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP186291", null, null, "Neutrophils_3_R1.fq.gz Neutrophils_3_R2.fq.gz", "fastq fastq", 8692700700.0, 28975669.0, "GSM3612321 r1", "0:150 1:150", "A:2652684352;C:1652069995;G:1735457120;T:2652129934;N:359299", 150, 150, null, null, 2652684352, 1652069995, 1735457120, 2652129934, 359299, "SRX5391962", "SRS4379792", "SRA850414", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.8145, 0.81686, 0.10965, 0.10808, 0.92713, 0.92744, 0.55607, 0.57186, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "nebnext", "sc", "single_cell_plate", "smartseq", null, "China", "2019-02-19", "Adult", "Adult", "Skin", "Surface Structure"], [51232, "SRR8591748", "SRX5391961", "SRS4379791", "SRP186291", "PRJNA523219", "Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs", "GSE126763", "Transcriptome Analysis", "In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.", null, "pubmed:31006648", null, "Neutrophils 2", "GSM3612320", null, "source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tglyz:GFP", "Neutrophils 2", "Raw reads were first aligned to zebrafish reference genome danRer10\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10\u00a0 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish epidermis", null, "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", null, "tissue:epidermis|Stage:adult|transgenic line:Tglyz:GFP", "GSM3612320", "GSM3612320: Neutrophils 2; Danio rerio; RNA Seq", "GSM3612320", null, "1", "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", "GEO Accession:GSM3612320", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP186291", null, null, "Neutrophils_2_R1.fq.gz Neutrophils_2_R2.fq.gz", "fastq fastq", 7327680000.0, 24425600.0, "GSM3612320 r1", "0:150 1:150", "A:2187183417;C:1429377098;G:1474177623;T:2236324081;N:617781", 150, 150, null, null, 2187183417, 1429377098, 1474177623, 2236324081, 617781, "SRX5391961", "SRS4379791", "SRA850414", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.84825, 0.84925, 0.11406, 0.11367, 0.91244, 0.91277, 0.54443, 0.52025, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "nebnext", "sc", "single_cell_plate", "smartseq", null, "China", "2019-02-19", "Adult", "Adult", "Skin", "Surface Structure"], [51233, "SRR8591747", "SRX5391960", "SRS4379790", "SRP186291", "PRJNA523219", "Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs", "GSE126763", "Transcriptome Analysis", "In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.", null, "pubmed:31006648", null, "Neutrophils 1", "GSM3612319", null, "source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tglyz:GFP", "Neutrophils 1", "Raw reads were first aligned to zebrafish reference genome danRer10\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10\u00a0 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish epidermis", null, "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", null, "tissue:epidermis|Stage:adult|transgenic line:Tglyz:GFP", "GSM3612319", "GSM3612319: Neutrophils 1; Danio rerio; RNA Seq", "GSM3612319", null, "1", "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", "GEO Accession:GSM3612319", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP186291", null, null, "Neutrophils_1_R1.fq.gz Neutrophils_1_R2.fq.gz", "fastq fastq", 12087825300.0, 40292751.0, "GSM3612319 r1", "0:150 1:150", "A:3327151170;C:2523891980;G:2588985485;T:3644916170;N:2880495", 150, 150, null, null, 3327151170, 2523891980, 2588985485, 3644916170, 2880495, "SRX5391960", "SRS4379790", "SRA850414", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.88642, 0.88127, 0.10539, 0.10565, 0.85151, 0.85451, 0.45008, 0.4553, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "nebnext", "sc", "single_cell_plate", "smartseq", null, "China", "2019-02-19", "Adult", "Adult", "Skin", "Surface Structure"], [51234, "SRR8591746", "SRX5391959", "SRS4379789", "SRP186291", "PRJNA523219", "Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs", "GSE126763", "Transcriptome Analysis", "In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.", null, "pubmed:31006648", null, "MLCs 4", "GSM3612318", null, "source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP", "MLCs 4", "Raw reads were first aligned to zebrafish reference genome danRer10\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10\u00a0 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish epidermis", null, "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", null, "tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP", "GSM3612318", "GSM3612318: MLCs 4; Danio rerio; RNA Seq", "GSM3612318", null, "1", "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", "GEO Accession:GSM3612318", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP186291", null, null, "MLCs_4_R2.fq.gz MLCs_4_R1.fq.gz", "fastq fastq", 8636325300.0, 28787751.0, "GSM3612318 r1", "0:150 1:150", "A:2653500651;C:1647706630;G:1681001556;T:2652196955;N:1919508", 150, 150, null, null, 2653500651, 1647706630, 1681001556, 2652196955, 1919508, "SRX5391959", "SRS4379789", "SRA850414", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.82279, 0.82455, 0.10092, 0.10051, 0.87625, 0.87411, 0.64616, 0.67509, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "nebnext", "sc", "single_cell_plate", "smartseq", null, "China", "2019-02-19", "Adult", "Adult", "Skin", "Surface Structure"], [51235, "SRR8591745", "SRX5391958", "SRS4379788", "SRP186291", "PRJNA523219", "Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs", "GSE126763", "Transcriptome Analysis", "In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.", null, "pubmed:31006648", null, "MLCs 3", "GSM3612317", null, "source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP", "MLCs 3", "Raw reads were first aligned to zebrafish reference genome danRer10\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10\u00a0 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish epidermis", null, "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", null, "tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP", "GSM3612317", "GSM3612317: MLCs 3; Danio rerio; RNA Seq", "GSM3612317", null, "1", "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", "GEO Accession:GSM3612317", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP186291", null, null, "MLCs_3_R1.fq.gz MLCs_3_R2.fq.gz", "fastq fastq", 9768968700.0, 32563229.0, "GSM3612317 r1", "0:150 1:150", "A:2993731360;C:1868928141;G:1920209904;T:2983932349;N:2166946", 150, 150, null, null, 2993731360, 1868928141, 1920209904, 2983932349, 2166946, "SRX5391958", "SRS4379788", "SRA850414", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.80623, 0.80159, 0.09971, 0.09865, 0.85754, 0.85677, 0.57368, 0.57722, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "nebnext", "sc", "single_cell_plate", "smartseq", null, "China", "2019-02-19", "Adult", "Adult", "Skin", "Surface Structure"], [51236, "SRR8591744", "SRX5391957", "SRS4379787", "SRP186291", "PRJNA523219", "Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs", "GSE126763", "Transcriptome Analysis", "In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.", null, "pubmed:31006648", null, "MLCs 2", "GSM3612316", null, "source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP", "MLCs 2", "Raw reads were first aligned to zebrafish reference genome danRer10\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10\u00a0 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish epidermis", null, "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", null, "tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP", "GSM3612316", "GSM3612316: MLCs 2; Danio rerio; RNA Seq", "GSM3612316", null, "1", "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", "GEO Accession:GSM3612316", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP186291", null, null, "MLCs_2_R2.fq.gz MLCs_2_R1.fq.gz", "fastq fastq", 13514398200.0, 45047994.0, "GSM3612316 r1", "0:150 1:150", "A:3741759684;C:2708870921;G:2854612129;T:4207496675;N:1658791", 150, 150, null, null, 3741759684, 2708870921, 2854612129, 4207496675, 1658791, "SRX5391957", "SRS4379787", "SRA850414", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.85592, 0.84009, 0.10566, 0.10231, 0.85904, 0.86689, 0.46757, 0.54817, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "nebnext", "sc", "single_cell_plate", "smartseq", null, "China", "2019-02-19", "Adult", "Adult", "Skin", "Surface Structure"], [51237, "SRR8591743", "SRX5391956", "SRS4379786", "SRP186291", "PRJNA523219", "Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs", "GSE126763", "Transcriptome Analysis", "In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.", null, "pubmed:31006648", null, "MLCs 1", "GSM3612315", null, "source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP", "MLCs 1", "Raw reads were first aligned to zebrafish reference genome danRer10\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10\u00a0 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish epidermis", null, "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", null, "tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP", "GSM3612315", "GSM3612315: MLCs 1; Danio rerio; RNA Seq", "GSM3612315", null, "1", "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", "GEO Accession:GSM3612315", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP186291", null, null, "MLCs_1_R1.fq.gz MLCs_1_R2.fq.gz", "fastq fastq", 6037864832.0, 20003506.0, "GSM3612315 r1", "0:150.92 1:150.92", "A:1818516368;C:1085016023;G:1139951931;T:1985307132;N:9073378", 150, 150, null, null, 1818516368, 1085016023, 1139951931, 1985307132, 9073378, "SRX5391956", "SRS4379786", "SRA850414", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.74163, 0.65034, 0.20675, 0.17721, 0.85285, 0.87409, 0.66103, 0.66629, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "nebnext", "sc", "single_cell_plate", "smartseq", null, "China", "2019-02-19", "Adult", "Adult", "Skin", "Surface Structure"], [51238, "SRR8591742", "SRX5391955", "SRS4379784", "SRP186291", "PRJNA523219", "Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs", "GSE126763", "Transcriptome Analysis", "In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.", null, "pubmed:31006648", null, "Keratinocytes 3", "GSM3612314", null, "source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tgkrt4:lyn GFP", "Keratinocytes 3", "Raw reads were first aligned to zebrafish reference genome danRer10\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10\u00a0 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish epidermis", null, "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", null, "tissue:epidermis|Stage:adult|transgenic line:Tgkrt4:lyn GFP", "GSM3612314", "GSM3612314: Keratinocytes 3; Danio rerio; RNA Seq", "GSM3612314", null, "1", "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", "GEO Accession:GSM3612314", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP186291", null, null, "Keratinocytes_3_R1.fq.gz Keratinocytes_3_R2.fq.gz", "fastq fastq", 7155019200.0, 23850064.0, "GSM3612314 r1", "0:150 1:150", "A:2267290727;C:1304084105;G:1335196968;T:2248029844;N:417556", 150, 150, null, null, 2267290727, 1304084105, 1335196968, 2248029844, 417556, "SRX5391955", "SRS4379784", "SRA850414", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.77684, 0.75758, 0.12563, 0.12043, 0.87606, 0.87618, 0.63846, 0.64712, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "nebnext", "sc", "single_cell_plate", "smartseq", null, "China", "2019-02-19", "Adult", "Adult", "Skin", "Surface Structure"], [51239, "SRR8591741", "SRX5391954", "SRS4379785", "SRP186291", "PRJNA523219", "Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs", "GSE126763", "Transcriptome Analysis", "In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.", null, "pubmed:31006648", null, "Keratinocytes 2", "GSM3612313", null, "source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tgkrt4:lyn GFP", "Keratinocytes 2", "Raw reads were first aligned to zebrafish reference genome danRer10\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10\u00a0 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish epidermis", null, "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", null, "tissue:epidermis|Stage:adult|transgenic line:Tgkrt4:lyn GFP", "GSM3612313", "GSM3612313: Keratinocytes 2; Danio rerio; RNA Seq", "GSM3612313", null, "1", "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", "GEO Accession:GSM3612313", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP186291", null, null, "Keratinocytes_2_R1.fq.gz Keratinocytes_2_R2.fq.gz", "fastq fastq", 6456398100.0, 21521327.0, "GSM3612313 r1", "0:150 1:150", "A:2077468795;C:1142603883;G:1144675726;T:2084897858;N:6751838", 150, 150, null, null, 2077468795, 1142603883, 1144675726, 2084897858, 6751838, "SRX5391954", "SRS4379785", "SRA850414", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.74005, 0.73114, 0.1187, 0.11653, 0.8604, 0.85985, 0.56777, 0.56778, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "nebnext", "sc", "single_cell_plate", "smartseq", null, "China", "2019-02-19", "Adult", "Adult", "Skin", "Surface Structure"], [51240, "SRR8591740", "SRX5391953", "SRS4379783", "SRP186291", "PRJNA523219", "Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs", "GSE126763", "Transcriptome Analysis", "In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.", null, "pubmed:31006648", null, "Keratinocytes 1", "GSM3612312", null, "source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tgkrt4:lyn GFP", "Keratinocytes 1", "Raw reads were first aligned to zebrafish reference genome danRer10\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10\u00a0 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish epidermis", null, "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", null, "tissue:epidermis|Stage:adult|transgenic line:Tgkrt4:lyn GFP", "GSM3612312", "GSM3612312: Keratinocytes 1; Danio rerio; RNA Seq", "GSM3612312", null, "1", "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", "GEO Accession:GSM3612312", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP186291", null, null, "Keratinocytes_1_R2.fq.gz Keratinocytes_1_R1.fq.gz", "fastq fastq", 13235365200.0, 44117884.0, "GSM3612312 r1", "0:150 1:150", "A:3733277705;C:2648363624;G:2742826351;T:4109351172;N:1546348", 150, 150, null, null, 3733277705, 2648363624, 2742826351, 4109351172, 1546348, "SRX5391953", "SRS4379783", "SRA850414", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.83183, 0.82563, 0.13916, 0.13781, 0.86048, 0.86517, 0.46753, 0.45399, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "nebnext", "sc", "single_cell_plate", "smartseq", null, "China", "2019-02-19", "Adult", "Adult", "Skin", "Surface Structure"], [51241, "SRR8591739", "SRX5391952", "SRS4379782", "SRP186291", "PRJNA523219", "Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs", "GSE126763", "Transcriptome Analysis", "In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.", null, "pubmed:31006648", null, "cLCs 4", "GSM3612311", null, "source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP", "cLCs 4", "Raw reads were first aligned to zebrafish reference genome danRer10\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10\u00a0 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish epidermis", null, "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", null, "tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP", "GSM3612311", "GSM3612311: cLCs 4; Danio rerio; RNA Seq", "GSM3612311", null, "1", "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", "GEO Accession:GSM3612311", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP186291", null, null, "cLCs_4_R1.fq.gz cLCs_4_R2.fq.gz", "fastq fastq", 8713251600.0, 29044172.0, "GSM3612311 r1", "0:150 1:150", "A:2637859361;C:1663768374;G:1739990329;T:2671283369;N:350167", 150, 150, null, null, 2637859361, 1663768374, 1739990329, 2671283369, 350167, "SRX5391952", "SRS4379782", "SRA850414", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.82506, 0.82564, 0.14826, 0.14636, 0.92133, 0.92194, 0.64203, 0.64155, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "nebnext", "sc", "single_cell_plate", "smartseq", null, "China", "2019-02-19", "Adult", "Adult", "Skin", "Surface Structure"], [51242, "SRR8591738", "SRX5391951", "SRS4379781", "SRP186291", "PRJNA523219", "Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs", "GSE126763", "Transcriptome Analysis", "In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.", null, "pubmed:31006648", null, "cLCs 3", "GSM3612310", null, "source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP", "cLCs 3", "Raw reads were first aligned to zebrafish reference genome danRer10\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10\u00a0 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish epidermis", null, "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", null, "tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP", "GSM3612310", "GSM3612310: cLCs 3; Danio rerio; RNA Seq", "GSM3612310", null, "1", "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", "GEO Accession:GSM3612310", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP186291", null, null, "cLCs_3_R2.fq.gz cLCs_3_R1.fq.gz", "fastq fastq", 8085762300.0, 26952541.0, "GSM3612310 r1", "0:150 1:150", "A:2358914181;C:1670033364;G:1711269394;T:2345255094;N:290267", 150, 150, null, null, 2358914181, 1670033364, 1711269394, 2345255094, 290267, "SRX5391951", "SRS4379781", "SRA850414", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.80361, 0.80478, 0.06011, 0.06067, 0.90666, 0.90613, 0.43542, 0.42737, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "nebnext", "sc", "single_cell_plate", "smartseq", null, "China", "2019-02-19", "Adult", "Adult", "Skin", "Surface Structure"], [51243, "SRR8591737", "SRX5391950", "SRS4379780", "SRP186291", "PRJNA523219", "Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs", "GSE126763", "Transcriptome Analysis", "In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.", null, "pubmed:31006648", null, "cLCs 2", "GSM3612309", null, "source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP", "cLCs 2", "Raw reads were first aligned to zebrafish reference genome danRer10\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10\u00a0 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish epidermis", null, "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", null, "tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP", "GSM3612309", "GSM3612309: cLCs 2; Danio rerio; RNA Seq", "GSM3612309", null, "1", "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", "GEO Accession:GSM3612309", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP186291", null, null, "cLCs_2_R2.fq.gz cLCs_2_R1.fq.gz", "fastq fastq", 14035834800.0, 46786116.0, "GSM3612309 r1", "0:150 1:150", "A:3886956713;C:2808123594;G:3002545528;T:4337287271;N:921694", 150, 150, null, null, 3886956713, 2808123594, 3002545528, 4337287271, 921694, "SRX5391950", "SRS4379780", "SRA850414", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.80521, 0.79346, 0.13916, 0.13314, 0.88061, 0.88872, 0.5212, 0.54523, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "nebnext", "sc", "single_cell_plate", "smartseq", null, "China", "2019-02-19", "Adult", "Adult", "Skin", "Surface Structure"], [51244, "SRR8591736", "SRX5391949", "SRS4379779", "SRP186291", "PRJNA523219", "Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs", "GSE126763", "Transcriptome Analysis", "In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.", null, "pubmed:31006648", null, "cLCs 1", "GSM3612308", null, "source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP", "cLCs 1", "Raw reads were first aligned to zebrafish reference genome danRer10\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10\u00a0 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish epidermis", null, "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", null, "tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP", "GSM3612308", "GSM3612308: cLCs 1; Danio rerio; RNA Seq", "GSM3612308", null, "1", "Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.", "GEO Accession:GSM3612308", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP186291", null, null, "cLCs_1_R1.fq.gz cLCs_1_R2.fq.gz", "fastq fastq", 6917825858.0, 22926042.0, "GSM3612308 r1", "0:150.87 1:150.87", "A:2168007671;C:1152140252;G:1228288198;T:2358773829;N:10615908", 150, 150, null, null, 2168007671, 1152140252, 1228288198, 2358773829, 10615908, "SRX5391949", "SRS4379779", "SRA850414", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.6965, 0.66301, 0.20956, 0.19509, 0.8521, 0.86218, 0.6102, 0.59061, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "nebnext", "sc", "single_cell_plate", "smartseq", null, "China", "2019-02-19", "Adult", "Adult", "Skin", "Surface Structure"], [51261, "SRR8632324", "SRX5431025", "SRS4411020", "SRP186864", "PRJNA524286", "The miR 199 CDK2 axis modulates neutrophil migration and systemic inflammation", "GSE127174", "Transcriptome Analysis", "We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils and RNAseq for identification of mRNA targets of miRNA 199 in neutrophils Overall design: for miRNA profiles we compared the miRNA present in zebrafish neutrophils and keratinocytes to the whole embryo. for miR 199 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR199 or vector control", null, "pubmed:31451657", null, "Krt4+", "GSM3629719", null, "source name:keratinocytes|strain background:AB|gentoype/variation:wild type|tissue:keratinocytes", "Krt4+", "Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina HiSeq 2500 for Samples 1 5 in Illumina HiSeq 4000 for Samples 6 11. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter: for Samples 1 5: \u201c alignEndsType EndToEnd outFilterMismatchNmax 1 outFilterMultimapScoreRange 0 outFilterMultimapNmax 10 outSAMunmapped Within outFilterScoreMinOverLread 0 outFilterMatchNminOverLread 0 outFilterMatchNmin 16 alignSJDBoverhangMin 1000\u201d for Samples 6 11: \u201c outSAMmapqUnique 60\u201d. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5: \u201c s 1 \u2013Q 10\u201d for Samples 6 11 \" p Q 10\". The data was filtered: for Samples 1 5 using read count > 10 in more than 1 of the samples; for Samples 6 11 using read count per million CPM > 0.5 in more than 3 of the samples normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts", "keratinocytes", "transgenic zebrafish lines were used to produce embryos. For miRNA profiling transgenic lines expressing GFP in either neutrophils or apical keratincyes were used. For miR 199 target discovery transgenic lines expressing miR 199 or a vector control together with a GFP reporter were used.", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories Inc..", "zebrafish embryos were grown to 3 dpf in embryonic media", "strain background:AB|gentoype/variation:wild type|tissue:keratinocytes", "GSM3629719", "GSM3629719: Krt4+; Danio rerio; RNA Seq", "GSM3629719", null, "1", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories Inc..", "GEO Accession:GSM3629719", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP186864", null, null, "krt4.fastq.gz", "fastq", 101078150.0, 2021563.0, "GSM3629719 r1", "0:50", "A:18002613;C:22778088;G:30701792;T:29589610;N:6047", 50, null, null, null, 18002613, 22778088, 30701792, 29589610, 6047, "SRX5431025", "SRS4411020", "SRA852308", "GEO", "Department of Biological Sciences, Purdue University", 1, 0.05911, null, 0.00807, null, 0.97461, null, 0.77586, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "smartseq", null, "United States", "2019-02-26", "Larval", "Larval", "Skin", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s D22", "GSM4410633", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410633", "GSM4410633: zebrafish 990s D22; Danio rerio; RNA Seq", "GSM4410633", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410633", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 3811307, 3645371, 3617661, 3873396, 4500, "SRX7908670", "SRS6316242", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96635, null, 0.06324, null, 0.87769, null, 0.49502, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s D21", "GSM4410632", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410632", "GSM4410632: zebrafish 990s D21; Danio rerio; RNA Seq", "GSM4410632", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410632", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 3216338, 2918960, 2899913, 3262285, 3790, "SRX7908669", "SRS6316243", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96446, null, 0.11117, null, 0.9137, null, 0.51287, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s D20", "GSM4410631", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410631", "GSM4410631: zebrafish 990s D20; Danio rerio; RNA Seq", "GSM4410631", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410631", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 3567280, 3336013, 3310051, 3623298, 4368, "SRX7908668", "SRS6316241", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96393, null, 0.08232, null, 0.92616, null, 0.49002, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s D2", "GSM4410630", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410630", "GSM4410630: zebrafish 990s D2; Danio rerio; RNA Seq", "GSM4410630", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410630", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 3526925, 3081325, 3060212, 3576643, 3927, "SRX7908667", "SRS6316240", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.95057, null, 0.1848, null, 0.92504, null, 0.48003, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s D19", "GSM4410629", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410629", "GSM4410629: zebrafish 990s D19; Danio rerio; RNA Seq", "GSM4410629", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410629", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 6408578, 5886841, 5845099, 6491229, 7493, "SRX7908666", "SRS6316237", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96339, null, 0.06751, null, 0.91198, null, 0.46563, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s D18", "GSM4410628", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410628", "GSM4410628: zebrafish 990s D18; Danio rerio; RNA Seq", "GSM4410628", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410628", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 1600346, 1515162, 1505658, 1621317, 1838, "SRX7908665", "SRS6316236", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96639, null, 0.09462, null, 0.93275, null, 0.51899, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s D17", "GSM4410627", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410627", "GSM4410627: zebrafish 990s D17; Danio rerio; RNA Seq", "GSM4410627", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410627", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 5084961, 4673304, 4637984, 5144779, 5790, "SRX7908664", "SRS6316239", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96388, null, 0.09619, null, 0.92419, null, 0.46267, null, 48, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s D16", "GSM4410626", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410626", "GSM4410626: zebrafish 990s D16; Danio rerio; RNA Seq", "GSM4410626", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410626", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 9128792, 8378350, 8324629, 9287068, 10174, "SRX7908663", "SRS6316238", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96185, null, 0.07724, null, 0.91597, null, 0.48886, null, 41, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s D15", "GSM4410625", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410625", "GSM4410625: zebrafish 990s D15; Danio rerio; RNA Seq", "GSM4410625", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410625", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 5268027, 4987353, 4954575, 5338793, 6280, "SRX7908662", "SRS6316235", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96672, null, 0.07072, null, 0.92295, null, 0.48391, null, 44, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s D14", "GSM4410624", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410624", "GSM4410624: zebrafish 990s D14; Danio rerio; RNA Seq", "GSM4410624", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410624", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 6589687, 5956715, 5911932, 6689599, 7450, "SRX7908661", "SRS6316234", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.9592, null, 0.1259, null, 0.91175, null, 0.47661, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s D13", "GSM4410623", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410623", "GSM4410623: zebrafish 990s D13; Danio rerio; RNA Seq", "GSM4410623", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410623", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 6824395, 6273054, 6234203, 6912870, 7828, "SRX7908660", "SRS6316232", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96307, null, 0.10084, null, 0.90445, null, 0.47847, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s D12", "GSM4410622", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410622", "GSM4410622: zebrafish 990s D12; Danio rerio; RNA Seq", "GSM4410622", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410622", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 6795815, 6306706, 6259822, 6904582, 7294, "SRX7908659", "SRS6316233", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.95859, null, 0.10058, null, 0.90106, null, 0.46651, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s D11", "GSM4410621", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410621", "GSM4410621: zebrafish 990s D11; Danio rerio; RNA Seq", "GSM4410621", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410621", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 2687251, 2533437, 2512865, 2727443, 3066, "SRX7908658", "SRS6316231", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96414, null, 0.06516, null, 0.94255, null, 0.53005, null, 45, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s D10", "GSM4410620", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410620", "GSM4410620: zebrafish 990s D10; Danio rerio; RNA Seq", "GSM4410620", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410620", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 5826113, 5533708, 5495964, 5908461, 6733, "SRX7908657", "SRS6316229", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96785, null, 0.06209, null, 0.90784, null, 0.48004, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s D1", "GSM4410619", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410619", "GSM4410619: zebrafish 990s D1; Danio rerio; RNA Seq", "GSM4410619", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410619", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 6729937, 6200705, 6153858, 6832585, 7098, "SRX7908656", "SRS6316230", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96292, null, 0.10401, null, 0.89721, null, 0.48829, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s C9", "GSM4410618", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410618", "GSM4410618: zebrafish 990s C9; Danio rerio; RNA Seq", "GSM4410618", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410618", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 6303157, 5796448, 5758377, 6400971, 7093, "SRX7908655", "SRS6316227", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96377, null, 0.09952, null, 0.93604, null, 0.47909, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s C8", "GSM4410617", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410617", "GSM4410617: zebrafish 990s C8; Danio rerio; RNA Seq", "GSM4410617", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410617", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 5747348, 5177667, 5136928, 5830424, 6641, "SRX7908654", "SRS6316228", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.95958, null, 0.13065, null, 0.92216, null, 0.46914, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s C7", "GSM4410616", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410616", "GSM4410616: zebrafish 990s C7; Danio rerio; RNA Seq", "GSM4410616", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410616", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 7235244, 6926753, 6877946, 7356336, 8567, "SRX7908653", "SRS6316226", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96435, null, 0.06783, null, 0.91492, null, 0.48294, null, 42, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s C6", "GSM4410615", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410615", "GSM4410615: zebrafish 990s C6; Danio rerio; RNA Seq", "GSM4410615", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410615", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 5074635, 4333167, 4301649, 5145437, 5831, "SRX7908652", "SRS6316224", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.95523, null, 0.16234, null, 0.90329, null, 0.47409, null, 41, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s C5", "GSM4410614", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410614", "GSM4410614: zebrafish 990s C5; Danio rerio; RNA Seq", "GSM4410614", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410614", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 3951385, 3573935, 3555893, 4003894, 4874, "SRX7908651", "SRS6316225", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96352, null, 0.17134, null, 0.93265, null, 0.47004, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s C4", "GSM4410613", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410613", "GSM4410613: zebrafish 990s C4; Danio rerio; RNA Seq", "GSM4410613", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410613", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 5084174, 4527015, 4489207, 5163246, 5763, "SRX7908650", "SRS6316222", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.95519, null, 0.12584, null, 0.91977, null, 0.48712, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s C3", "GSM4410612", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410612", "GSM4410612: zebrafish 990s C3; Danio rerio; RNA Seq", "GSM4410612", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410612", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 6879183, 6235952, 6187938, 6985257, 7816, "SRX7908649", "SRS6316223", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.9614, null, 0.13063, null, 0.92693, null, 0.48691, null, 44, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s C24", "GSM4410611", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410611", "GSM4410611: zebrafish 990s C24; Danio rerio; RNA Seq", "GSM4410611", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410611", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 5331504, 4853719, 4820428, 5408957, 6000, "SRX7908648", "SRS6316221", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96386, null, 0.11067, null, 0.93474, null, 0.44648, null, 42, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s C23", "GSM4410610", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410610", "GSM4410610: zebrafish 990s C23; Danio rerio; RNA Seq", "GSM4410610", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410610", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 9165559, 8316903, 8242039, 9312819, 10125, "SRX7908647", "SRS6316219", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.95667, null, 0.08618, null, 0.90662, null, 0.48076, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s C22", "GSM4410609", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410609", "GSM4410609: zebrafish 990s C22; Danio rerio; RNA Seq", "GSM4410609", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410609", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 6788556, 6199193, 6157557, 6887011, 7816, "SRX7908646", "SRS6316220", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.95869, null, 0.11718, null, 0.9027, null, 0.4912, null, 48, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s C21", "GSM4410608", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410608", "GSM4410608: zebrafish 990s C21; Danio rerio; RNA Seq", "GSM4410608", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410608", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 7277456, 6567924, 6520282, 7397263, 8374, "SRX7908645", "SRS6316217", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96216, null, 0.08311, null, 0.92214, null, 0.484, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s C20", "GSM4410607", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410607", "GSM4410607: zebrafish 990s C20; Danio rerio; RNA Seq", "GSM4410607", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410607", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 3253378, 3091074, 3068783, 3310426, 3903, "SRX7908644", "SRS6316218", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96581, null, 0.09966, null, 0.92336, null, 0.46559, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s C2", "GSM4410606", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410606", "GSM4410606: zebrafish 990s C2; Danio rerio; RNA Seq", "GSM4410606", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410606", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 6362402, 5928362, 5889128, 6454430, 7025, "SRX7908643", "SRS6316216", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96422, null, 0.09577, null, 0.9095, null, 0.47689, null, 41, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s C19", "GSM4410605", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410605", "GSM4410605: zebrafish 990s C19; Danio rerio; RNA Seq", "GSM4410605", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410605", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 9180689, 8467349, 8402491, 9325656, 10472, "SRX7908642", "SRS6316215", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96283, null, 0.1015, null, 0.87852, null, 0.47362, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s C18", "GSM4410604", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410604", "GSM4410604: zebrafish 990s C18; Danio rerio; RNA Seq", "GSM4410604", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410604", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 4590943, 4269740, 4239656, 4663920, 5331, "SRX7908641", "SRS6316214", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.9647, null, 0.09031, null, 0.93288, null, 0.48597, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s C17", "GSM4410603", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410603", "GSM4410603: zebrafish 990s C17; Danio rerio; RNA Seq", "GSM4410603", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410603", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 8461669, 7712485, 7651317, 8591564, 9549, "SRX7908640", "SRS6316213", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.9592, null, 0.08874, null, 0.91259, null, 0.49461, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s C16", "GSM4410602", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410602", "GSM4410602: zebrafish 990s C16; Danio rerio; RNA Seq", "GSM4410602", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410602", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 6592405, 6192402, 6144035, 6698710, 7536, "SRX7908639", "SRS6316212", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96488, null, 0.06936, null, 0.90636, null, 0.48394, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s C15", "GSM4410601", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410601", "GSM4410601: zebrafish 990s C15; Danio rerio; RNA Seq", "GSM4410601", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410601", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 6387972, 5887843, 5848486, 6481347, 7246, "SRX7908638", "SRS6316211", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96143, null, 0.11709, null, 0.91139, null, 0.48454, null, 40, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s C14", "GSM4410600", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410600", "GSM4410600: zebrafish 990s C14; Danio rerio; RNA Seq", "GSM4410600", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410600", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 6010197, 5556779, 5513064, 6093732, 6579, "SRX7908637", "SRS6316210", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96353, null, 0.10838, null, 0.91863, null, 0.4849, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s C13", "GSM4410599", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410599", "GSM4410599: zebrafish 990s C13; Danio rerio; RNA Seq", "GSM4410599", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410599", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 7486030, 7009056, 6957087, 7604008, 8443, "SRX7908636", "SRS6316209", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96286, null, 0.10457, null, 0.92805, null, 0.47785, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s C12", "GSM4410598", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410598", "GSM4410598: zebrafish 990s C12; Danio rerio; RNA Seq", "GSM4410598", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410598", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 6234424, 5812036, 5765520, 6319939, 7214, "SRX7908635", "SRS6316208", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96519, null, 0.07726, null, 0.90713, null, 0.4802, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s C11", "GSM4410597", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410597", "GSM4410597: zebrafish 990s C11; Danio rerio; RNA Seq", "GSM4410597", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410597", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 4485023, 3646315, 3622640, 4563901, 4977, "SRX7908634", "SRS6316207", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.94782, null, 0.31171, null, 0.93539, null, 0.48256, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s C10", "GSM4410596", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410596", "GSM4410596: zebrafish 990s C10; Danio rerio; RNA Seq", "GSM4410596", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410596", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 5465149, 5010550, 4980276, 5546702, 6531, "SRX7908633", "SRS6316205", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96405, null, 0.10732, null, 0.92744, null, 0.48269, null, 39, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s C1", "GSM4410595", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410595", "GSM4410595: zebrafish 990s C1; Danio rerio; RNA Seq", "GSM4410595", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410595", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 6970707, 6446413, 6411599, 7064656, 8137, "SRX7908632", "SRS6316206", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.9641, null, 0.09528, null, 0.92346, null, 0.50558, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s B9", "GSM4410594", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410594", "GSM4410594: zebrafish 990s B9; Danio rerio; RNA Seq", "GSM4410594", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410594", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 4080022, 3616468, 3595348, 4130253, 4521, "SRX7908631", "SRS6316202", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.95866, null, 0.18239, null, 0.93306, null, 0.49468, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s B8", "GSM4410593", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410593", "GSM4410593: zebrafish 990s B8; Danio rerio; RNA Seq", "GSM4410593", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410593", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 4198717, 3887458, 3856999, 4261238, 4873, "SRX7908630", "SRS6316204", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.95752, null, 0.11124, null, 0.93876, null, 0.48231, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s B7", "GSM4410592", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410592", "GSM4410592: zebrafish 990s B7; Danio rerio; RNA Seq", "GSM4410592", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410592", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 3407078, 3104309, 3085740, 3452172, 3962, "SRX7908629", "SRS6316200", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.9621, null, 0.14005, null, 0.94339, null, 0.48716, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s B6", "GSM4410591", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410591", "GSM4410591: zebrafish 990s B6; Danio rerio; RNA Seq", "GSM4410591", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410591", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 4811790, 4506958, 4476764, 4887270, 5731, "SRX7908628", "SRS6316203", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96323, null, 0.09461, null, 0.91492, null, 0.4842, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s B5", "GSM4410590", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410590", "GSM4410590: zebrafish 990s B5; Danio rerio; RNA Seq", "GSM4410590", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410590", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 5996295, 5637264, 5603679, 6061625, 7000, "SRX7908627", "SRS6316201", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96423, null, 0.07727, null, 0.91581, null, 0.46864, null, 48, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s B4", "GSM4410589", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410589", "GSM4410589: zebrafish 990s B4; Danio rerio; RNA Seq", "GSM4410589", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410589", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 3685085, 3392571, 3377981, 3738614, 4358, "SRX7908626", "SRS6316197", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96687, null, 0.12743, null, 0.94134, null, 0.50108, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s B3", "GSM4410588", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410588", "GSM4410588: zebrafish 990s B3; Danio rerio; RNA Seq", "GSM4410588", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410588", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 5500444, 5141927, 5111797, 5576378, 6654, "SRX7908625", "SRS6316199", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96416, null, 0.07969, null, 0.90218, null, 0.47964, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s B24", "GSM4410587", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410587", "GSM4410587: zebrafish 990s B24; Danio rerio; RNA Seq", "GSM4410587", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410587", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 3847326, 3570345, 3546698, 3915410, 4395, "SRX7908624", "SRS6316198", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96401, null, 0.10549, null, 0.9389, null, 0.47099, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s B23", "GSM4410586", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410586", "GSM4410586: zebrafish 990s B23; Danio rerio; RNA Seq", "GSM4410586", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410586", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 5617471, 5219687, 5183659, 5700225, 6560, "SRX7908623", "SRS6316195", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96243, null, 0.06801, null, 0.877, null, 0.50398, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s B22", "GSM4410585", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410585", "GSM4410585: zebrafish 990s B22; Danio rerio; RNA Seq", "GSM4410585", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410585", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 3814070, 3570992, 3546502, 3872564, 4332, "SRX7908622", "SRS6316196", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96236, null, 0.09761, null, 0.93908, null, 0.47544, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s B21", "GSM4410584", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410584", "GSM4410584: zebrafish 990s B21; Danio rerio; RNA Seq", "GSM4410584", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410584", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 2049070, 1821395, 1808619, 2075260, 2368, "SRX7908621", "SRS6316192", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96154, null, 0.21386, null, 0.9403, null, 0.52429, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s B20", "GSM4410583", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410583", "GSM4410583: zebrafish 990s B20; Danio rerio; RNA Seq", "GSM4410583", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410583", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 4301130, 4085399, 4056346, 4364188, 5178, "SRX7908620", "SRS6316194", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96716, null, 0.06463, null, 0.91956, null, 0.48441, null, 46, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s B2", "GSM4410582", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410582", "GSM4410582: zebrafish 990s B2; Danio rerio; RNA Seq", "GSM4410582", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410582", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 8194727, 7240383, 7192797, 8307778, 9134, "SRX7908619", "SRS6316193", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.9581, null, 0.11638, null, 0.89824, null, 0.47307, null, 38, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s B19", "GSM4410581", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410581", "GSM4410581: zebrafish 990s B19; Danio rerio; RNA Seq", "GSM4410581", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410581", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 4786927, 4465486, 4440781, 4858904, 5700, "SRX7908618", "SRS6316191", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96412, null, 0.07828, null, 0.92125, null, 0.49448, null, 42, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s B18", "GSM4410580", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410580", "GSM4410580: zebrafish 990s B18; Danio rerio; RNA Seq", "GSM4410580", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410580", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 6035531, 5661140, 5621717, 6125715, 7085, "SRX7908617", "SRS6316189", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.963, null, 0.08656, null, 0.90869, null, 0.49805, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s B17", "GSM4410579", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410579", "GSM4410579: zebrafish 990s B17; Danio rerio; RNA Seq", "GSM4410579", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410579", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 2387290, 2106785, 2089721, 2422047, 2754, "SRX7908616", "SRS6316188", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.95954, null, 0.19762, null, 0.94119, null, 0.5018, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s B16", "GSM4410578", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410578", "GSM4410578: zebrafish 990s B16; Danio rerio; RNA Seq", "GSM4410578", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410578", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 5265904, 4820615, 4787256, 5337241, 6045, "SRX7908615", "SRS6316190", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96128, null, 0.10365, null, 0.9231, null, 0.47581, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s B15", "GSM4410577", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410577", "GSM4410577: zebrafish 990s B15; Danio rerio; RNA Seq", "GSM4410577", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410577", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 4274559, 4055734, 4027475, 4325551, 5219, "SRX7908614", "SRS6316187", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.9665, null, 0.07272, null, 0.92851, null, 0.48099, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s B14", "GSM4410576", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410576", "GSM4410576: zebrafish 990s B14; Danio rerio; RNA Seq", "GSM4410576", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410576", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 2056188, 1739845, 1728535, 2089310, 2357, "SRX7908613", "SRS6316186", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.95879, null, 0.27188, null, 0.9373, null, 0.52528, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s B13", "GSM4410575", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410575", "GSM4410575: zebrafish 990s B13; Danio rerio; RNA Seq", "GSM4410575", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410575", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 4463392, 4164427, 4139877, 4526164, 5226, "SRX7908612", "SRS6316185", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.9635, null, 0.10533, null, 0.92977, null, 0.48953, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s B12", "GSM4410574", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410574", "GSM4410574: zebrafish 990s B12; Danio rerio; RNA Seq", "GSM4410574", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410574", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 6063639, 5645203, 5610466, 6148678, 6970, "SRX7908611", "SRS6316184", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96365, null, 0.08835, null, 0.92092, null, 0.47208, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s B11", "GSM4410573", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410573", "GSM4410573: zebrafish 990s B11; Danio rerio; RNA Seq", "GSM4410573", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410573", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 4146889, 3851858, 3828619, 4203084, 4707, "SRX7908610", "SRS6316183", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96384, null, 0.11699, null, 0.94093, null, 0.47805, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s B10", "GSM4410572", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410572", "GSM4410572: zebrafish 990s B10; Danio rerio; RNA Seq", "GSM4410572", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410572", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 3618868, 3414966, 3392328, 3665996, 4393, "SRX7908609", "SRS6316182", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96294, null, 0.09185, null, 0.94107, null, 0.4874, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s B1", "GSM4410571", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410571", "GSM4410571: zebrafish 990s B1; Danio rerio; RNA Seq", "GSM4410571", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410571", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 3672204, 3242179, 3221658, 3716850, 4089, "SRX7908608", "SRS6316181", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.95833, null, 0.14516, null, 0.93385, null, 0.46308, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s A9", "GSM4410570", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410570", "GSM4410570: zebrafish 990s A9; Danio rerio; RNA Seq", "GSM4410570", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410570", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 4456792, 4055609, 4028161, 4529646, 5289, "SRX7908607", "SRS6316180", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96232, null, 0.1102, null, 0.93671, null, 0.50336, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s A8", "GSM4410569", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410569", "GSM4410569: zebrafish 990s A8; Danio rerio; RNA Seq", "GSM4410569", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410569", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 4372174, 4016139, 3987443, 4429512, 5058, "SRX7908606", "SRS6316179", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96283, null, 0.13767, null, 0.93492, null, 0.47721, null, 45, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s A7", "GSM4410568", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410568", "GSM4410568: zebrafish 990s A7; Danio rerio; RNA Seq", "GSM4410568", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410568", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 6590510, 6081778, 6040538, 6683960, 7696, "SRX7908605", "SRS6316178", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96145, null, 0.09912, null, 0.92198, null, 0.47642, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s A6", "GSM4410567", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410567", "GSM4410567: zebrafish 990s A6; Danio rerio; RNA Seq", "GSM4410567", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410567", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 3452902, 3229647, 3208712, 3506704, 4015, "SRX7908604", "SRS6316177", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.95931, null, 0.09851, null, 0.94111, null, 0.48532, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s A5", "GSM4410566", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410566", "GSM4410566: zebrafish 990s A5; Danio rerio; RNA Seq", "GSM4410566", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410566", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 4661192, 4250348, 4214482, 4728075, 5262, "SRX7908603", "SRS6316176", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96336, null, 0.11509, null, 0.93797, null, 0.46297, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s A4", "GSM4410565", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410565", "GSM4410565: zebrafish 990s A4; Danio rerio; RNA Seq", "GSM4410565", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410565", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 5787211, 5352678, 5313520, 5866507, 6536, "SRX7908602", "SRS6316174", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96139, null, 0.08905, null, 0.91851, null, 0.48896, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s A3", "GSM4410564", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410564", "GSM4410564: zebrafish 990s A3; Danio rerio; RNA Seq", "GSM4410564", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410564", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 5650511, 5205874, 5163998, 5730121, 6421, "SRX7908601", "SRS6316175", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96069, null, 0.09546, null, 0.92811, null, 0.48483, null, 41, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s A24", "GSM4410563", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410563", "GSM4410563: zebrafish 990s A24; Danio rerio; RNA Seq", "GSM4410563", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410563", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 5626608, 5288084, 5247861, 5732839, 6699, "SRX7908600", "SRS6316173", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96433, null, 0.08418, null, 0.92139, null, 0.48143, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s A23", "GSM4410562", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410562", "GSM4410562: zebrafish 990s A23; Danio rerio; RNA Seq", "GSM4410562", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410562", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 6380531, 5798072, 5754658, 6476829, 7168, "SRX7908599", "SRS6316172", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.95974, null, 0.11386, null, 0.93141, null, 0.46622, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s A22", "GSM4410561", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410561", "GSM4410561: zebrafish 990s A22; Danio rerio; RNA Seq", "GSM4410561", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410561", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 6081723, 5713915, 5678807, 6184457, 7097, "SRX7908598", "SRS6316171", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96437, null, 0.08101, null, 0.91526, null, 0.48297, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s A21", "GSM4410560", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410560", "GSM4410560: zebrafish 990s A21; Danio rerio; RNA Seq", "GSM4410560", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410560", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 7894692, 7131349, 7077245, 8007295, 8554, "SRX7908597", "SRS6316170", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.95812, null, 0.07769, null, 0.91865, null, 0.5021, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s A20", "GSM4410559", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410559", "GSM4410559: zebrafish 990s A20; Danio rerio; RNA Seq", "GSM4410559", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410559", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 5841447, 5376978, 5332083, 5921650, 6608, "SRX7908596", "SRS6316169", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.95731, null, 0.08786, null, 0.92445, null, 0.49535, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s A2", "GSM4410558", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410558", "GSM4410558: zebrafish 990s A2; Danio rerio; RNA Seq", "GSM4410558", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410558", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 4957048, 4561438, 4531806, 5032248, 5554, "SRX7908595", "SRS6316168", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96252, null, 0.09612, null, 0.91705, null, 0.48496, null, 44, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s A19", "GSM4410557", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410557", "GSM4410557: zebrafish 990s A19; Danio rerio; RNA Seq", "GSM4410557", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410557", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 2093903, 1958192, 1942450, 2128209, 2236, "SRX7908594", "SRS6316166", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96665, null, 0.12458, null, 0.92912, null, 0.48872, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s A18", "GSM4410556", null, "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", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", null, "tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf", "GSM4410556", "GSM4410556: zebrafish 990s A18; Danio rerio; RNA Seq", "GSM4410556", null, "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\u00b0C RNA libraries were prepared using standard SmartSeq2 protocol", "GEO Accession:GSM4410556", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP252691", null, "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, null, null, null, 6776528, 6135214, 6097496, 6862874, 7561, "SRX7908593", "SRS6316165", "SRA1054549", "GEO", "Betsholtz, ICMC - MedH, Karolinska Institutet", 1, 0.96168, null, 0.1033, null, 0.92206, null, 0.47484, null, 41, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2020-03-13", "Hatching", "Embryo", "Trunk", "Surface Structure"], [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", null, "pubmed:32483144", null, "zebrafish 990s A17", "GSM4410555", null, "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: 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