run_metadata: 29201

This data as json

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
29201	SRR27319715	SRX22996941	SRS19961590	SRP479504	PRJNA1055557	Border zone cardiomyocytes and macrophages contribute to remodeling of the extracellular matrix to promote cardiomyocyte invasion during zebrafish cardiac regeneration	GSE251856	Other	Despite numerous advances in our understanding of zebrafish cardiac regeneration an aspect that remains less studied is how newly proliferated cardiomyocytes invade and eventually replace the collagen containing fibrotic tissue following injury. Here we provide an in depth analysis of the process of cardiomyocyte invasion and migration using live imaging and histological approaches. We observed a close interaction between protruding cardiomyocytes and macrophages at the wound border zone and irf8 mutant zebrafish which largely lack macrophages exhibited defects in extracellular matrix ECM remodeling and cardiomyocyte protrusion into the injured area. Using a resident macrophage ablation model we show that defects in ECM remodeling at the border zone and subsequent cardiomyocyte protrusion can be partly attributed to a population of resident macrophages. Single cell RNA sequencing analysis of cells at the wound border revealed a population of cardiomyocytes and macrophages with fibroblast like gene expression signatures including the expression of genes encoding ECM structural proteins and ECM remodeling proteins. The expression of mmp14b which encodes a membrane anchored matrix metalloproteinase was restricted to cells in the border zone and genetic deletion of mmp14b led to a decrease in 1 collagen degradation at the border zone 2 macrophage recruitment to the border zone and 3 subsequent cardiomyocyte invasion. Furthermore cardiomyocyte specific overexpression of mmp14b was sufficient to enhance cardiomyocyte invasion both into the injured area and along the apical surface of the wound. Altogether our data shed important insights into the process of cardiomyocyte invasion of the collagen containing injured tissue during cardiac regeneration. They further suggest that cardiomyocytes and resident macrophages contribute to ECM remodeling at the border zone to promote cardiomyocyte replenishment of the fibrotic injured tissue. Overall design: The border zone of regenerating wild type zebrafish hearts at 7 dpci was microdissected and subjected to scRNA seq		pubmed:39962064;pubmed:40268967		scRNA seq of wild type border z1 cells of regenerating hearts at 7 dpci	GSM7989198		source name:Heart\|tissue:Heart\|genotype:Wild type\|treatment:Hearts were cryoinjured and border z1 cells were microdissected at 7 dpci and pooled for scRNA seq\|geo loc name:missing\|collection date:missing	scRNA seq of wild type border z1 cells of regenerating hearts at 7 dpci	Reads were aligned against the zebrafish genome DanRer11 and counted by StarSolo. Preprocessed counts were further analysed using Scanpy. Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed 23 cells in total that did not express more than 300 genes or had a mitochondrial content greater than 40%. Furthermore we filtered 9874 genes if they were detected in less than 30 cells <0.01%. Raw counts per cell were normalised to the median count over all cells and transformed into log space to stabilise variance. We initially reduced dimensionality of the dataset using PCA retaining 50 principal components. Subsequent steps like low dimensional UMAP embedding and cell clustering via community detection were based on the initial PCA. Final data visualization was done by scanpy and cellxgene packages. Assembly: danRer11 Supplementary files format and content: starsolo outputs	Heart	Zebrafish hearts were cryoinjured and extracted at 7 dpci.	Border zone cells from 8 hearts were pooled and tissue dissociation was performed using the Pierce Primary Cardiomyocyte Isolation kit according to manufacturer's instructions. Cells were resuspended in DMEM with 10% FBS and 1x glutamate. The cell suspensions were depleted for dead cells using LeviCell 1.0 device Levitas Bio counted with MOX Z cell counter and diluted according to manufacturer’s protocol to obtain 10.000 single cell data points per sample. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 10xGenomics. Single cell RNAseq library preparation was done using standard protocol.		tissue:Heart\|genotype:Wild type\|treatment:Hearts were cryoinjured and border z1 cells were microdissected at 7 dpci and pooled for scRNA seq	GSM7989198	GSM7989198: scRNA seq of wild type border z1 cells of regenerating hearts at 7 dpci; Danio rerio; RNA Seq	GSM7989198 r1	GSM7989198	1	Border zone cells from 8 hearts were pooled and tissue dissociation was performed using the Pierce Primary Cardiomyocyte Isolation kit according to manufacturer's instructions. Cells were resuspended in DMEM with 10% FBS and 1x glutamate. The cell suspensions were depleted for dead cells using LeviCell 1.0 device Levitas Bio counted with MOX Z cell counter and diluted according to manufacturer's protocol to obtain 10.000 single cell data points per sample. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 10xGenomics. Single cell RNAseq library preparation was done using standard protocol.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 2000		SRP479504			Arica_10x_Zebrafish_Borderzone_Lib_R2.fastq.gz Arica_10x_Zebrafish_Borderzone_Lib_R1.fastq.gz	fastq fastq	35579193737.0	447572139.0	GSM7989198 r1	0:28 1:51.49	A:9662436792;C:7884457111;G:8055970010;T:9787114480;N:189215344	28	51			9662436792	7884457111	8055970010	9787114480	189215344	SRX22996941	SRS19961590	SRA1774131	MPI for heart and lung research	MPI for heart and lung research	2	0.00237	0.94011	0.00086	0.09945	0.99571	0.81907	0.32746	0.60892	28	51	T	B	sc-like readlen	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		Germany	2023-12-21	Undetermined	Undetermined	Heart	Cardiovascular System