run_metadata: 56961

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
56961	SRR11186427	SRX7806761	SRS6219796	SRP250826	PRJNA608913	Single cell analysis of non myocytes during heart regeneration reveals sequential coordinated responses from distinct cell populations [bulk RNA seq]	GSE145979	Transcriptome Analysis	Cardiac regeneration occurs primarily through proliferation of existing cardiomyocytes yet the regenerative response also involves complex interactions between distinct cardiac cell types including not only cardiomyocytes but also non cardiomyocytes nonCMs. However the molecular features and cellular functions of the highly heterogeneous populations of nonCMs and how these populations cooperate to regenerate the injured heart remain largely unexplored. Using the newly developed LIGER algorithm that allows flexible modeling across highly diverse single cell datasets we analyzed the transcriptome dynamics of 61 977 individual nonCMs isolated at multiple time points during zebrafish heart regeneration. Combining single cell analysis and in situ hybridization we identified major nonCM cell types including multiple novel subpopulations with unique tempo spatial distributions and highly cooperative interactions in the regenerating heart. Interestingly genetic perturbation of macrophage function by kit knockout led to accumulation of fibrotic deposits and severely compromised cardiomyocyte proliferation and myocardium regeneration. Our single cell transcriptomic analysis of nonCMs during cardiac regeneration provides a blueprint for interrogating the molecular and cellular basis of cardiac regeneration. Overall design: To assess the proliferation defect of kit aka c kit mutant CMs we conducted transcriptome wide bulk RNA seq of control and mutant cardiomyocytes	parent bioproject:PRJNA608906	pubmed:34523214		zCM kit 14dpi2	GSM4340636		source name:zCM kit 4dpi\|genotype/variation:kit mutant; kitaw34b2;kitbsa15356\|treatment/timepoint:14 xxx post injury\|age:4 month 6 month\|tissue:heart\|cell type:cardiomyocytes	zCM kit 14dpi2	Qualities of de barcoded raw sequence reads were checked by fastqc. The alignment was performed using BBMap/38.1213 against the reference zebrafish genome UCSC DanRer10 Gene counts were obtained using featureCounts. The raw counts were normalized to sequencing depth using counts per million CPM. Genome build: UCSC DanRer10 Supplementary files format and content: tab delimited text files containing CPM values for each sample	zCM kit 4dpi	Zebrafish were anesthetized by immersion with 0.04% tricaine and immobilized in a dampened foam with ventral side up. A small incision was made between the gills to expose the ventricle. About 20% of ventricular apex was resected using iridectomy scissors. post apex resection fish were returned to a recovery tank with fresh system water.	Total RNAs of isolated adult zebrafish cardiomyocytes from eight pooled ventricles were extracted using QIAGEN RNeasy Micro kit. Illumina libraries were prepared using TrueSeq Standard mRNA Sample Preparation Kit.	Zebrafish were raised and maintained under standard laboratory conditions.	genotype/variation:kit mutant; kitaw34b2;kitbsa15356\|treatment/timepoint:14 xxx post injury\|age:4 month 6 month\|tissue:heart\|cell type:cardiomyocytes	GSM4340636	GSM4340636: zCM kit 14dpi2; Danio rerio; RNA Seq	GSM4340636		1	Total RNAs of isolated adult zebrafish cardiomyocytes from eight pooled ventricles were extracted using QIAGEN RNeasy Micro kit. Illumina libraries were prepared using TrueSeq Standard mRNA Sample Preparation Kit.	GEO Accession:GSM4340636	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP250826			Z14DPI-2-z14dpi-2_GTGAAA_S35_L008_R1_001.fastq.gz Z14DPI-2-z14dpi-2_GTGAAA_S35_L008_R2_001.fastq.gz	fastq fastq	4085937600.0	40859376.0	GSM4340636 r1	0:50 1:50	A:1106357295;C:903286911;G:928696833;T:1146285046;N:1311515	50	50			1106357295	903286911	928696833	1146285046	1311515	SRX7806761	SRS6219796	SRA1048426	GEO	University of North Carolina at Chapel Hill	2	0.93972	0.94157	0.07791	0.07653	0.77331	0.77784	0.65617	0.66424	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk		United States	2020-02-26	Adult	Adult	Heart	Cardiovascular System