{"database": "metadata", "table": "run_metadata", "rows": [[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"]], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": ["rowid"], "primary_key_values": ["57291"], "units": {}, "query_ms": 11.193451995495707}