metadata: run_metadata: 1 row where technology = "icell8" and tissue_curation

1 row where technology = "icell8" and tissue_curation_coarse = "Cardiovascular System"

descending

Link	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
75393	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		Zebrafish heart 105275	GSM7311139		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		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× PBS solution containing 200 µg/ml of Liberase DL Roche for 20 min at 33ºC 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 µm nylon mesh by centrifugation into Falcon round bottom polystyrene test tube Corning Inc. at 300 g for 4 min at 4ºC. 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× 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/µl 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.		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× PBS solution containing 200 µg/ml of Liberase DL Roche for 20 min at 33ºC 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 µm nylon mesh by centrifugation into Falcon round bottom polystyrene test tube Corning Inc. at 300 g for 4 min at 4ºC. 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× 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/µl 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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP436667		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				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		0.15933		0.86425		0.67371		79		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	icell8		Germany	2023-05-09	Undetermined	Adult	Heart	Cardiovascular System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;