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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
69918 SRR19176077 SRX15241414 SRS12974373 SRP374910 PRJNA837476 An injury associated transient progenitor state in the epicardium mediates heart regeneration GSE202836 Transcriptome Analysis Adult zebrafish regenerate heart muscle post severe cardiac damage without xxx scarring. The epicardium a mesothelial cell sheet covering the vetebrate heart is activated by injury and supports muscle regeneration through paracrine effects and as a source of multipotent cells. The understudied cellular heterogeneity of the adult epicardium during heart regeneration has constrained the effort in mobilizing the epicardium for heart repair. To dissect epicardial cell states and the underlying mechanisms that lead to successful heart regeneration in zebrafish we performed single cell RNA sequencing of isolated epicardial cells from the regenerating adult heart and revealed their dynamic cellular heterogeneity. We defined the epithelial and mesenchymal layers of the epicardium and identified a transiently activated epicardial progenitor cell aEPC subpopulation that expresses aldh1a2 ptx3a col12a1b and marcksb. Upon heart amputation injury aEPCs emerge from the existing epicardial cells migrate to enclose the wound and disappear as regeneration progresses. Genetic lineage tracing combined with modified RNA labelling confirmed an epithelial mesenchymal transition EMT process of aEPCs and their differentiations to pdgfrb+ mural cells and pdgfra+hapln1a+ mesenchymal fibroblast like cells that support heart regeneration. Genetic ablation of aEPCs blocked wound closure of the injured ventricle suppressed cardiomyocyte proliferation and disrupted heart regeneration. Our findings define a transient progenitor state of the adult epicardium that is an indispensable driver of zebrafish heart regeneration and identified ptx3a as a regeneration specific non ontogenetic regulator of the epicardium. Overall design: Single cell RNA sequencing of isolated epicardial cells from uninjured zebrafish hearts and hearts post amputation injury   pubmed:36513650   7 dy post amputation epicardial cells scRNA seq GSM6133972   source name:heart ventricle|cell type:epicardial cells|tissue:heart ventricle|strain:EK tcf21:nucEGFP|age:6 month|treatment:partial ventricular amputation 7 dy post amputation epicardial cells scRNA seq Demultiplexing barcoded processing gene counting and aggregation done with Cell Ranger software v3.0.2 Sample integration batch correction expression value normalization clustering cell type annotation and so on were done with SCTransform scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/Cao Epicardium Assembly: GRCz10 Supplementary files format and content: Cell Ranger output files barcodes.tsv features.tsv matrix.mtx heart ventricle Heart amputation injury Hearts were dissociated into single cells and the epicardial cells were isolated by FACS as described previously PMID 26657776. Library prep was performed according to the manufacturer’s instructions single cell three prime v3 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with amplified by PCR and the appropriate sized fragments were selected for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added. Single Cell three prime GEM Gel Bead Kit v3 Chromium Single Cell B Chip Kit Standard zebrafish breeding conditions cell type:epicardial cells|tissue:heart ventricle|strain:EK tcf21:nucEGFP|age:6 month|treatment:partial ventricular amputation GSM6133972 GSM6133972: 7 dy post amputation epicardial cells scRNA seq; Danio rerio; RNA Seq GSM6133972 r1 GSM6133972 1 Hearts were dissociated into single cells and the epicardial cells were isolated by FACS as described previously PMID 26657776. Library prep was performed according to the manufacturer's instructions single cell three prime v3 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with amplified by PCR and the appropriate sized fragments were selected for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added. Single Cell three prime GEM Gel Bead Kit v3 Chromium Single Cell B Chip Kit   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP374910   loader:fastq load.py Sample_7dpa-epi_S6_L004_I1_001.fastq.gz Sample_7dpa-epi_S6_L004_R1_001.fastq.gz Sample_7dpa-epi_S6_L004_R2_001.fastq.gz fastq fastq fastq 5305140534.0 39590601.0 GSM6133972 r2 0:8 1:28 2:98 A:1130899517;C:825440203;G:874010632;T:1048032074;N:1496472 8 28 98   1130899517 825440203 874010632 1048032074 1496472 SRX15241414 SRS12974373 SRA1419237 Applied Bioinformatics Core, Physiology & Biophysics, Weill Cornell Medicine Applied Bioinformatics Core, Physiology & Biophysics, Weill Cornell Medicine 1 0.89954   0.16556   0.84299   0.5185   98   B   usable mapping rate illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   United States 2022-05-12 Adult Adult Heart Cardiovascular System