{"database": "metadata", "table": "run_metadata", "rows": [[53494, "SRR9881611", "SRX6634132", "SRS5205092", "SRP217216", "PRJNA558070", "N Glycome regulation limits the transdifferentiation of endothelial cells into hematopoietic stem cells", "GSE135246", "Transcriptome Analysis", "Hematopoietic stem and progenitor cells HSPCs are required to establish and maintain the adult blood system in vertebrates. During development  HPSCs are generated from hemogenic endothelial cells that undergo an endothelial to hematopoietic transition EHT. Growth factors and epigenetic changes can promote EHT  but these mechanisms do not explain its tight spatiotemporal regulation during development. Here  we show that microRNA miR miR 223 mediated regulation of N glycan biosynthesis intrinsically restrains EHT  representing a new pathway that prevents excessive HSPC production. We find that miR 223 is uniquely expressed in hemogenic endothelial cells undergoing EHT and in nascent HSPCs. Loss of miR 223 promotes the expansion of these cells in the zebrafish and mouse aorta gonad mesonephros AGM  where EHT occurs. miR 223 targets alg2 alpha 1 3/ 1 6 mannosyltransferase in the AGM endothelium to restrict hemogenic and HSPC specification. This enzyme is involved in the attachment of the N glycans   a common co translational modification9 12 that influences several pathophysiological processes  but has not yet been implicated in EHT. Using an N glycosensor  we demonstrate that abundant protein N glycan attachment occurs in vascular cells during EHT  and this process is required for HSPC production. High throughput glycome analysis upon loss of miR 223 revealed that terminal alpha 1 3/6 mannose modifications are increased at the expense of alpha 2 3/6 sialic acid sugars. Importantly  pharmacological manipulation targeting these N glycan types in wild type embryos phenocopies the loss of miR 223 and enhances EHT as well as HSPC production. Thus  the N glycome plays a previously unappreciated role as an intrinsic regulator of EHT  with specific mannose and sialic acid modifications serving as key endothelial determinants to restrict the hematopoietic fate. Overall design: Single cell RNA sequencing for zebrafish Tgkdrl:hras mCherrys896 endothelial cells at 27 hpf for wildtype and miR 223ya303 backgrounds", null, "pubmed:33273096", null, "wildtype 27hpf EC1", "GSM3996906", null, "source name:endothelial cell|tissue:trunk endothelium|cell type:endothelial cell|developmental stage:27 hpf 223:KalTA4ya362; Tg5xUAS:eGFPnkuasgfp1a; Tgkdrl:hras mCherrys896|genotype:wildtype", "wildtype 27hpf EC1", "The reads were demultiplexed using bcl2fastq provided by the 10X genomics.  The demultiplexed reads were aligned to the reference genome Grz11  modified to add mCherry  GAL4  and eGFP to obtain digital gene expression matrix data using cellranger program The output of the cellranger was then processed using Seurat in R. All the cells with less than 200 unique transcripts were eliminared.  All genes which are expressed in less than 3 cells were also eliminated. The data was normalized using sctransform  and then clustered.  The clusters were projected for viualization in R using the PHATE algorithm. Genome build: GRCz11 Supplementary files format and content: Average Gene expression matrix for average gene expression per cluster  per condition.  This is a tab separated values file  where each row represents a gene  and each column represents the cluster  and the condition  and each cell represents normalized expression values across all the cells in that cluster for that condition.", "endothelial cell", null, "Trunk tissue was dissected from 27 hpf zebrafish embryos under  0.1% tricaine anesthesia and then disassociated into a single cell suspension using 0.25 mg/ml liberase for 45 minutes. Tgkdrl:hras mCherrys896 endothelial cells were isolated from the single cell suspension via FACS into 0.04% BSA in PBS and applied to the 10X genomics single cell RNA sequencing platform. 10 X genomics Chromium Next GEM Single Cell 3\u2019 Library Construction Kit v2.1", "Zebrafish were raised and maintained at 28.5\u02daC using standard methods and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2017 11473.", "tissue:trunk endothelium|cell type:endothelial cell|developmental stage:27 hpf 223:KalTA4ya362; Tg5xUAS:eGFPnkuasgfp1a; Tgkdrl:hras mCherrys896|genotype:wildtype", "GSM3996906", "GSM3996906: wildtype 27hpf EC1; Danio rerio; RNA Seq", "GSM3996906", null, "1", "Trunk tissue was dissected from 27 hpf zebrafish embryos under  0.1% tricaine anesthesia and then disassociated into a single cell suspension using 0.25 mg/ml liberase for 45 minutes. Tgkdrl:hras mCherrys896 endothelial cells were isolated from the single cell suspension via FACS into 0.04% BSA in PBS and applied to the 10X genomics single cell RNA sequencing platform. 10 X genomics Chromium Next GEM Single Cell three prime Library Construction Kit v2.1", "GEO Accession:GSM3996906", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP217216", null, null, "WT_pssorted_genome_bam.bam", "10X Genomics bam file", 26866951370.0, 274152565.0, "GSM3996906 r1", "0:98", "A:7373453026;C:6169004304;G:6196779570;T:7121490110;N:6224360", 98, null, null, null, 7373453026, 6169004304, 6196779570, 7121490110, 6224360, "SRX6634132", "SRS5205092", "SRA930499", "GEO", "Internal Medicine, Yale University", 1, 0.93015, null, 0.0602, null, 0.83853, null, 0.4683, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-08-01", "Pharyngula", "Embryo", "Multi-tissue", "Multi-system"]], "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": ["53494"], "units": {}, "query_ms": 9.91863700619433}