{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_source = \"TRANSCRIPTOMIC SINGLE CELL\", technology = \"icell8\" and tissue_curation_coarse = \"Cardiovascular System\"", "rows": [[75393, "SRR24480612", "SRX20266197", "SRS17594880", "SRP436667", "PRJNA970725", "Endocardial cells function as antigen presenting cells to promote zebrafish heart regeneration [dst93 scrnaseq]", "GSE232060", "Other", "In contrast to adult mammals  adult zebrafish are able to fully regenerate injured cardiac tissue  and this regeneration process requires an adequate and tightly controlled immune response.  However  which immune aspects drive particular aspects of the regenerative response are unclear.  Here  we report the participation and requirement of the antigen presentation adaptive immunity axis during zebrafish cardiac regeneration.  We found that  in addition to immune cells  endocardial cells start expressing antigen presentation genes following the initial innate immune response.  Consistent with this finding  we observed that helper T cells  a.k.a. Cd4+ T cells  are closely associated with phosphoERK+ pERK+ i.e.  activated endocardial cells at these stages.  We inactivated major histocompatibility complex MHC class II antigen presentation by generating cd74a; cd74b double mutants  which display a defective immune response.  In these mutants  both Cd4+ T cells and pERK+ endocardial cells fail to efficiently infiltrate the injured tissue.  Notably  this model of compromised antigen presentation exhibits additional defects in cardiac regeneration including reduced cardiomyocyte dedifferentiation and proliferation.  Altogether  these findings reveal a necessary role for antigen presentation during zebrafish cardiac regeneration and point to an immune crosstalk between T cells and endocardial cells  thereby further establishing a link between the adaptive immune response and tissue regeneration. Overall design: scRNA Seq of FACS sorted zebrafish Tgmhc2dab:EGFP+ and/or Tgptprc:DsRed+  immune cells from uninjured ventricles and ventricles at various time points post cryoinjury [i.e.  6  24  72 hours post cryoinjury hpci and 7  14 and 30 days post cryoinjury dpci]. For each time point  three ventricles from 2 females and 1 male  or 1 female and 2 males were pooled.", "parent bioproject:PRJNA970722", "pubmed:38684665", null, "Zebrafish heart 105275", "GSM7311139", null, "source name:heart ventricle|tissue:heart ventricle|cell type:immune cells|time:mixed samples 6  24  72 hours post cryoinjury hpci and 7  14  30 days post cryoinjury dpci|geo loc name:missing|collection date:missing", "Zebrafish heart 105275", "Raw reads were aligned against the zebrafish genome DanRer11 and counted by StarSolo. Secondary analysis was performed in Annotated Data Format. post preprocessing  cells were analyzed via the Scanpy framework. Preprocessed counts were used to calculate quality metrics in order to estimate cell quality regarding ribosomal content  mitochondrial content  number of genes and total read count. Doublets were removed by Scrublet. Raw counts per cell were normalized to the median count over all cells and transformed into log space to stabilize variance. Assembly: DanRer11 Supplementary files format and content: Tab separated files of barcodes  basic observations  variable annotations and gene counts.", "heart ventricle", null, "To isolate immune cells  pools of three whole ventricles from Tgmhc2dab:EGFP; Tgptprc:DsRed zebrafish containing at least one female and one male were used.  Ventricles were cut into small pieces and dissociated in a 1\u00d7 PBS solution containing 200 \u00b5g/ml of Liberase DL Roche for 20 min at 33\u00baC with constant agitation.  The solution was gently pipetted up and down every 3 min to promote tissue disaggregation.  The cell suspensions were passed through a 35 \u00b5m nylon mesh by centrifugation into Falcon round bottom polystyrene test tube Corning Inc. at 300 g for 4 min at 4\u00baC. EGFP+ and/or DsRed+ cells were sorted using a FACSAria III BD sorter  following exclusion of dead cells using DAPI staining.  Cells were sorted into a 20% FBS solution in 1\u00d7 PBS and subsequently used for scRNA Seq analysis. Single cell RNAseq was performed on ICELL8 platform Takara Bio using the V2 protocol with in chip preamplifcation. Samples were pre sorted into HBSS Gibco in a concentration of 20 cells/\u00b5l and stained with Hoechst dye Invitrogen for 5min at RT prior loading to MSND dispenser. For each sample 1 dispense in 630 wells were made on one 5184 well chip resulting in 1479 wells containing a single cell post selection in CellSelect software Takara Bio. Selected wells were processed for RT  in chip preamplification and cDNA was pooled for final library preparation using standard Nextera protocol Illumina. Library was checked in Labchip Gx touch 24 Perkin Elmer and sequenced on Nextseq500 Illumina using V2 chemistry and paired end setup 11bp Read1  80bp Read2. A total of 656M reads were obtained.", null, "tissue:heart ventricle|cell type:immune cells|time:mixed samples 6  24  72 hours post cryoinjury hpci and 7  14  30 days post cryoinjury dpci", "GSM7311139", "GSM7311139: Zebrafish heart 105275; Danio rerio; RNA Seq", "GSM7311139 r1", "GSM7311139", "1", "To isolate immune cells  pools of three whole ventricles from Tgmhc2dab:EGFP; Tgptprc:DsRed zebrafish containing at least one female and one male were used.  Ventricles were cut into small pieces and dissociated in a 1\u00d7 PBS solution containing 200 \u00b5g/ml of Liberase DL Roche for 20 min at 33\u00baC with constant agitation.  The solution was gently pipetted up and down every 3 min to promote tissue disaggregation.  The cell suspensions were passed through a 35 \u00b5m nylon mesh by centrifugation into Falcon round bottom polystyrene test tube Corning Inc. at 300 g for 4 min at 4\u00baC. EGFP+ and/or DsRed+ cells were sorted using a FACSAria III BD sorter  following exclusion of dead cells using DAPI staining.  Cells were sorted into a 20% FBS solution in 1\u00d7 PBS and subsequently used for scRNA Seq analysis. Single cell RNAseq was performed on ICELL8 platform Takara Bio using the V2 protocol with in chip preamplifcation. Samples were pre sorted into HBSS Gibco in a concentration of 20 cells/\u00b5l and stained with Hoechst dye Invitrogen for 5min at RT prior loading to MSND dispenser. For each sample 1 dispense in 630 wells were made on one 5184 well chip resulting in 1479 wells containing a single cell post selection in CellSelect software Takara Bio. Selected wells were processed for RT  in chip preamplification and cDNA was pooled for final library preparation using standard Nextera protocol Illumina. Library was checked in Labchip Gx touch 24 Perkin Elmer and sequenced on Nextseq500 Illumina using V2 chemistry and paired end setup 11bp Read1  80bp Read2. A total of 656M reads were obtained.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP436667", null, "loader:fastq load.py", "Zebrafish_heart_105275_R2.fastq.gz", "fastq", 52350849282.0, 656847439.0, "GSM7311139 r1", "0:79.70", "A:19403956194;C:9642917615;G:10517986323;T:12777094682;N:8894468", 79, null, null, null, 19403956194, 9642917615, 10517986323, 12777094682, 8894468, "SRX20266197", "SRS17594880", "SRA1647185", "Bioinformatics, Max Planck Institute for Heart and Lung Research", "Bioinformatics, Max Planck Institute for Heart and Lung Research", 1, 0.80027, null, 0.15933, null, 0.86425, null, 0.67371, null, 79, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "icell8", null, "Germany", "2023-05-09", "Undetermined", "Adult", "Heart", "Cardiovascular System"]], "truncated": false, "filtered_table_rows_count": 1, "expanded_columns": [], "expandable_columns": [], "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": [], "units": {}, "query": {"sql": "select 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 from run_metadata where \"experiment.library_source\" = :p0 and \"technology\" = :p1 and \"tissue_curation_coarse\" = :p2 order by rowid limit 101", "params": {"p0": "TRANSCRIPTOMIC SINGLE CELL", "p1": "icell8", "p2": "Cardiovascular System"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&technology=icell8&tissue_curation_coarse=Cardiovascular+System", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 1, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&technology=icell8&tissue_curation_coarse=Cardiovascular+System&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&technology=icell8&tissue_curation_coarse=Cardiovascular+System", "results": [{"value": "TRANSCRIPTOMIC SINGLE CELL", "label": "TRANSCRIPTOMIC SINGLE CELL", "count": 1, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?technology=icell8&tissue_curation_coarse=Cardiovascular+System", "selected": true}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": 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