run_metadata: 73908

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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
73908	SRR23290112	SRX19233403	SRS16637862	SRP420294	PRJNA929922	Cloche is a pro regenerative platelet factor during zebrafish heart regeneration [10x scRNA seq]	GSE224111	Transcriptome Analysis	Zebrafish heart regeneration is a complex process consisting of tempo spatial coordination of cardiomyocyte CM and endothelial cell EC regeneration fibrosis and inflammation. While myocardial endocardial and epicardial signaling have been reported to modulate this process little is known about how leukocyte especially platelet signaling is involved in this regenerative process. Here we report that cloche/npas4l neuronal PAS domain protein 4 like is a pro regenerative platelet factor for adult zebrafish heart regeneration. We found that injury triggered npas4l expression as early as 1 h post ventricular amputation and haploinsufficiency of npas4l disrupted CM and EC proliferation and heart regeneration in clofv087b/+ and clom39/+ mutants post ventricular resection or nitroreductase NTR mediated CM ablation. By constructing a single cell transcriptomic atlas we discovered that npas4l was dynamically expressed in platelets in response to heart injury with robust platelet CM or EC interactions via ligand receptor activity analysis. Decreasing platelets in NTR mediated depletion or mpl mutants impaired CM and EC proliferation and over expression of npas4l in platelets sufficiently made uninjured and injured CM reentry into the cell cycle and rescued CM and EC proliferation in clofv087b/+ mutants. Furthermore Npas4l positively regulated Bmp6 expression in platelets and either BMP6 inhibitors or siRNAs decreased CM proliferation and heart regeneration. This work demonstrates for the first time that injury induced platelets are essential for zebrafish heart regeneration and Npas4l is a core platelet transcription factor for fine tuning heart regeneration partially via Bmp6 signaling. Overall design: Wild type and clofv087b/+ adult zebrafish hearts injured or uninjured were dissected and cardiac cells were disassociation at 4?. Fluorescence activated cell sorting FACS was used to remove cell debris and sort for single cell according to hochest signal intensity. Sorted cell concentration and vaibility were determined on a Countstar Rigel system. 12 000 cells with more than 85% cell vaibility were loaded into 10x Genomics Chromium chip and proceeded to single cell RNA library construction and sequencing.	parent bioproject:PRJNA929937			clofv087b/+ 3dpa	GSM7012025		source name:heart\|tissue:heart\|cell line:isolated primary cells\|cell type:cardiac cells\|genotype:clofv087b/+\|treatment:3 dy post heart amputation\|geo loc name:missing\|collection date:missing	clofv087b/+ 3dpa	Illumina Casava2.1.7 software used for basecalling. Cell Ranger v3.0.2 pipeline 10x Genomics was utilized to demultiplex the cellular barcodes and align reads to the GRCz11 zebrafish reference genome. The output filtered gene expression matrices were loaded and analyzed using the Seurat package v3.1.4 Potential doublet cells were detected and filtered using the R package DoubletFinder v2.0.2 Low quality cells were removed from the datasets based on the following criteria: 1 the number of detected genes <=200 or >=4 000 the percentage of mitochondrial genes >=25 for non cardiomyocytes; 2 the number of detected genes <=200 or >=4 000 for CMs the mitochondrial content was not filtered due to the nature of CMs containing high mitochondrial density Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	heart		For each sample 15 adult ventricles were collected and placed in ice cold perfusion buffer 130 mM NaCl 5 mM KCl 0.5 mM NaH2PO4 10 mM HEPES 10 mM Glucose 10 mM 2 3 butanedionemonoxime 10 mM taurine 5 mM MgCl2 adjusting pH to 7.8 with NaOH. The ventricles were gently torn up transferred and digested in the digestion buffer 10 mg/ml protease 30 μg/ml DNase I in perfusion buffer for 3 h at 4℃ with constant gentle agitation by using a rotator. The digestion was then neutralized with 10% FBS fetal bone serum and the disassociated cells were filtered through a 100 μm strainer to remove large clumps and pelleted at 500 x g for 10 min at 4℃. The pellet was re suspended in Hank’s balance salt solution HBSS. The disassociated cells were stained with Hochest 33342 1:300 diluted in HBSS gone through a 70 μm strainer and loaded on a Beckman Coulter MoFlo XDP system to remove cell debris and sort for single cells. The sorted single cells were pelleted at 1000 x g for 5 min at 4℃. The pellet was resuspended in HBSS. Cell viability and concentration were measured on a Countstar Rigel system ALIT Life Science. Samples with more than 85% cell viability were qualified for single cell loading. Around 12 000 cells per sample were loaded into 10x Genomics Chromium chip. Single cell RNA seq libraries were generated using Chromium Next GEM Single Cell 3’ Kit v3.1 10x Genomics 1000269 according to the manufacturer’s instructions.		tissue:heart\|cell line:isolated primary cells\|cell type:cardiac cells\|genotype:clofv087b/+\|treatment:3 dy post heart amputation	GSM7012025	GSM7012025: clofv087b/+ 3dpa; Danio rerio; RNA Seq	GSM7012025 r1	GSM7012025	1	For each sample 15 adult ventricles were collected and placed in ice cold perfusion buffer 130 mM NaCl 5 mM KCl 0.5 mM NaH2PO4 10 mM HEPES 10 mM Glucose 10 mM 2 3 butanedionemonoxime 10 mM taurine 5 mM MgCl2 adjusting pH to 7.8 with NaOH. The ventricles were gently torn up transferred and digested in the digestion buffer 10 mg/ml protease 30 μg/ml DNase I in perfusion buffer for 3 h at 4℃ with constant gentle agitation by using a rotator. The digestion was then neutralized with 10% FBS fetal bone serum and the disassociated cells were filtered through a 100 μm strainer to remove large clumps and pelleted at 500 x g for 10 min at 4℃. The pellet was re suspended in Hank's balance salt solution HBSS. The disassociated cells were stained with Hochest 33342 1:300 diluted in HBSS gone through a 70 μm strainer and loaded on a Beckman Coulter MoFlo XDP system to remove cell debris and sort for single cells. The sorted single cells were pelleted at 1000 x g for 5 min at 4℃. The pellet was resuspended in HBSS. Cell viability and concentration were measured on a Countstar Rigel system ALIT Life Science. Samples with more than 85% cell viability were qualified for single cell loading. Around 12 000 cells per sample were loaded into 10x Genomics Chromium chip. Single cell RNA seq libraries were generated using Chromium Next GEM Single Cell three prime Kit v3.1 10x Genomics 1000269 according to the manufacturer's instructions.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP420294			het_3dpa_S1_L001_R1_001.fastq.gz het_3dpa_S1_L001_R2_001.fastq.gz	fastq fastq	247976078400.0	826586928.0	GSM7012025 r1												SRX19233403	SRS16637862	SRA1583282	Tsinghua University	Tsinghua University	2	0.60298	0.79816	0.11346	0.10384	0.97772	0.83662	0.60163	0.66023	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		China	2023-01-31	Adult	Adult	Heart	Cardiovascular System