{"database": "metadata", "table": "run_metadata", "rows": [[68656, "SRR18097957", "SRX14248907", "SRS12068875", "SRP360907", "PRJNA809307", "Generation of specialized blood vessels via lymphatic transdifferentiation", "GSE197161", "Transcriptome Analysis", "The lineage and developmental trajectory of a cell are key determinant s of cellular identity. In the  vascular system  endothelial cells ECs of blood and lymphatic vessels LVs differentiate and diversify  to cater the different physiological demands of each organ . While LVs are known to originate from  multiple origins   lymphatic ECs LECs themselves are not known to generate other cell   types . Here  we  u s e recurrent imaging and lineage   tracing of ECs in zebrafish anal fins AF from early development  through maturity   to uncover an unexpected mechanism of specialized blood vessel formation  through transdifferentiation of LECs . Moreover  we demonstrate distinct functional implications for  deriving AF vessels from either LECs or blood ECs  uncovering a link between cell ontogeny and  functionality. We further use scRNA   seq to characterize the different cellular populations and transition  states involved in the transdifferentiation process . Finally  we show that akin to its normal  development  the vasculature is re   derived from lymphatics during AF regeneration   demonstr ating that LECs in adult fish retain both potency and plasticity for generating blood ECs .  Overall  our work highlights a new innate mechanism of blood vess el formation through LEC  trans differentiation  and provides in vivo evidence for a link between cell ontogeny and functionality in  ECs Overall design: 80 anal fins from immature zebrafish were digested. Sorting and RNA extraction was performed on fli1a:dsRed positive cells", null, "pubmed:35614218", null, "Immature fin ECs plate3", "GSM5910460", null, "source name:fli1a:dsRed positive cells|tissue:Anal fin|cell type:endothelial cells|Stage:II III", "Immature fin ECs plate3", "GRCz10 genome mapping was done using Bowtie2 with default parameters Demultiplexing and UMI count matrixes were based on 4bp pool barcodes in Read1 for each sample. 8bp of UMI with 7bp of cell barcodes in Read2  and performed as described in Jaitin et al. 2014 Genome build: GRCz10 Supplementary files format and content: AB006.txt  AB007.txt  AB008.txt: expression dataset  txt files containing UMI counts table per plate. Single cell metadata p1.xslx: xslx file  sheet1  pool barcode of plate1  sheet2  cell barcodes and coordinates  required for MARS seq pipeline Jaitin et al.  2014  sheet3  plate1 analyzed cell names. Single cell metadata p2.xslx: xslx file  sheet1  pool barcode of plate2  sheet2  cell barcodes and coordinates required for MARS seq pipeline Jaitin et al.  2014  sheet3  plate2 analyzed cell names. Single cell metadata p3.xslx: xslx file  sheet1  pool barcode of plate3  sheet2  cell barcodes and coordinates required for MARS seq pipeline Jaitin et al.  2014  sheet3  plate3 analyzed cell names", "fli1a:dsRed positive cells", null, "80 anal fins were dissected  manually chopped with a sterile razor and enzymatically digested using Liberase I  Trypsin B and DNaseI. Single cells were sorted into 384 well plates containing lysis solution UPW  8nM poly dT barcodes  0.1%triton and RNAse inhibitor MARS seq libraries were prepared as described Jaitin et al Science 2014", null, "tissue:Anal fin|cell type:endothelial cells|Stage:II III", "GSM5910460", "GSM5910460: Immature fin ECs plate3; Danio rerio; RNA Seq", "GSM5910460 r1", "GSM5910460", "1", "80 anal fins were dissected  manually chopped with a sterile razor and enzymatically digested using Liberase I  Trypsin B and DNaseI. Single cells were sorted into 384 well plates containing lysis solution UPW  8nM poly dT barcodes  0.1%triton and RNAse inhibitor MARS seq libraries were prepared as described Jaitin et al Science 2014", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP360907", null, null, "BC3_S0_R1_001.fastq.gz BC3_S0_R2_001.fastq.gz", "fastq fastq", 5000226570.0, 55558073.0, "GSM5910460 r1", "0:75 1:15", "A:1398279779;C:1105834990;G:1278168650;T:1217071842;N:871309", 75, 15, null, null, 1398279779, 1105834990, 1278168650, 1217071842, 871309, "SRX14248907", "SRS12068875", "SRA1376737", "Weizmann Institute of Science", "Department of Biological Regulation, Weizmann Institute of Science", 2, 0.75587, 0.0, 0.22384, 0.0, 0.87665, 1.0, 0.59533, null, 75, 15, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2022-02-22", "Undetermined", "Adult", "Fin", "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": ["68656"], "units": {}, "query_ms": 8.249245001934469}