run_metadata: 41993

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
41993	SRR5366718	SRX2661986	SRS2063952	SRP102311	PRJNA380129	H3K27me3 deposition over sarcomeric and cytoskeletal promoters is required for cardiomyocyte cytokinesis and wound invasion during zebrafish heart regeneration [RNA seq]	GSE96929	Transcriptome Analysis	We identify the global transcriptional changes that occur between homeostatic and proliferative cardiomyocytes in the zebrafish heart and uncover an essential role for H3K27me3 deposition in facilitating successful myocardial regeneration. Specifically we learned that cardiomyocyte proliferation is accompanied by downregulation of sarcomeric and cytoskeletal components and upregulation of the polycomb methylase Ezh2. Using ChIPseq we demonstrate that this transcriptional repression is associated with deposition of new H3K27me3 modifications over the promoters. Using new genetic zebrafish lines that allow for inducible and cardiomyocyte specific expression of a mutant form of histone 3 that is unable to be tri methylated on lysine 27 H3.3K27M we discovered that addition of H3K27me3 marks is essential for cardiac regeneration in vivo. Earlier in the regenerative window we found that H3.3K27M–expressing wound edge cardiomyocytes aberrantly maintain homeostatic levels of sarcomeric and actomyosin gene expression and show significant retention of sarcomere structure. While DNA replication occurs normally in these H3.3K27M cardiomyocytes we observed significant increases in cardiomyocyte nucleation a phenotype indicative of cytokinesis failures. In addition nuclear density at the wound edge increases as new cardiomyocytes fail to colonize the injured area. Together our study reveals that production of new cardiomyocytes and their infiltration into the injured region relies on H3K27me3 mediated sarcomeric and actomyosin cytoskeletal gene repression. Overall design: Transcriptional profiling RNA seq of regenerting versus uninjured FACS purified cardiomyocytes from zebrafish ventricle apexes in triplicates	parent bioproject:PRJNA380125	pubmed:31427288		Uninjured cardiomyocytes rep1	GSM2546208		source name:Cardiac ventricle tissue\|tissue:Cardiac ventricle apex\|strain:Gata4:GFP\|batch:uninjured	Uninjured cardiomyocytes rep1	Reads from three replicates of uninjured “uninjured” and 5 xxx post injury “5 dpa” heart samples were aligned against the GRCz10 genome assembly of the Zebrafish ENSEMBL 89 annotation using STAR v. 2.5.3a in paired end mode with parameters runThreadN 16 runMode alignReads outFilterType BySJout outFilterMultimapNmax 20 alignSJoverhangMin 8 alignSJDBoverhangMin 1 outFilterMismatchNmax 999 alignIntronMin 10 alignIntronMax 1000000 alignMatesGapMax 1000000 outSAMtype BAM SortedByCoordinate quantMode TranscriptomeSAM . The resulting Aligned.toTranscriptome.out.bam files were postprocessed using RSEM v. 1.3.0 using following flags paired end calc ci alignments p 8 forward prob 0. Posterior mean estimates of counts RPKM and TPM were retrieved for each gene in each sample. Differential expression analysis between uninjured and 5 dpa samples was performed using DESeq2 in the R statistical environment v. 3.3.3 on protein coding genes according to ENSEMBL’s biotype assignments. Supplementary files format and content csv files are a DEseq2 estimations of changes in read density of protein coding genes according to ENSEMBL release 89’s biotype assignments between experimental groups. Supplementary files format and content: IGVtools utility 'count' was used on aligned bam files to compute the average alignment over 164 base windows across the genome and generate binary tiled data .tdf files Thorvaldsdottir et al. 2013.	Cardiac ventricle tissue		Ventricle apexes were removed and cleared of injury tissue then dissociated using the Miltenyi neonate heart dissociation kit pelleted and resuspended in PBS/serum. Cell suspensions were strained on a 50 micron nylon mesh and immediately FACS sorted directly into RLT lysis buffer RNeasy micro prep RNA extraction kit Qiagen. RNA integrity and concentration were checked on a Fragment Analyzer Advanced Analytical. cDNA samples were generated using the Ovation low input v2 kit Nugen according to the manufacturer’s. The resulting cDNA samples were then end repaired and adaptor ligated using the SPRI works Fragment Library System I Beckman Coulter Genomics and indexed during amplification. Libraries were quantified using the Fragment Analyzer Advanced Analytical and qPCR before being loaded for paired end sequencing 2X40 nt using the Illumina HiSeq 2000.		tissue:Cardiac ventricle apex\|strain:Gata4:GFP\|batch:uninjured	GSM2546208	GSM2546208: Uninjured cardiomyocytes rep1; Danio rerio; RNA Seq	GSM2546208		1	Ventricle apexes were removed and cleared of injury tissue then dissociated using the Miltenyi neonate heart dissociation kit pelleted and resuspended in PBS/serum. Cell suspensions were strained on a 50 micron nylon mesh and immediately FACS sorted directly into RLT lysis buffer RNeasy micro prep RNA extraction kit Qiagen. RNA samples were prepared according to Qiagen protocol cDNA libraries were generated and sequenced on an Illumina HiSeq 2000 RNA libraries were prepared for sequencing using standard Illumina protocols.	GEO Accession:GSM2546208	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP102311			Gata4u1_end1.fq.gz Gata4u1_end2.fq.gz	fastq fastq	2243134682.0	27355301.0	GSM2546208 r1	0:41 1:41	A:637700051;C:456179088;G:471197897;T:672624830;N:5432816	41	41			637700051	456179088	471197897	672624830	5432816	SRX2661986	SRS2063952	SRA548505	GEO	Caroline Burns, CVRC, MGH	2	0.83024	0.86786	0.17153	0.17971	0.82741	0.82345	0.80221	0.79802	41	41	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown		United States	2017-03-22	Undetermined	Undetermined	Heart	Cardiovascular System