run_metadata: 40164

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
40164	SRR2921973	SRX1432516	SRS1163508	SRP066192	PRJNA302179	Genome–wide transcriptional profiling with spatial resolution identifies Bone Morphogenetic Protein signaling as essential regulator of zebrafish cardiomyocyte regeneration.	GSE74652	Transcriptome Analysis	In contrast to mammals zebrafish regenerate heart injuries via proliferation of cardiomyocytes located at the wound border. Here we show that tomo seq can be used to identify whole genome transcriptional profiles of the injury zone the border zone and the healthy myocardium. Interestingly the border zone is characterized by the re expression of embryonic cardiac genes that are also activated post myocardial infarction in mouse and human including targets of Bone Morphogenetic Protein BMP signaling. Endogenous BMP signaling has been reported to be detrimental to mammalian cardiac repair. In contrast we find that genetic or chemical inhibition of BMP signaling in zebrafish reduces cardiomyocyte dedifferentiation and proliferation ultimately compromising myocardial regeneration while bmp2b overexpression is sufficient to enhance it. Our results provide a resource for further studies on the molecular regulation of cardiac regeneration and reveal intriguing differential cellular responses of cardiomyocytes to a conserved signaling pathway in regenerative versus non regenerative hearts. Overall design: To generate spatially resolved RNA seq data for injured zebrafish hearts 3 and 7 xxx post injury we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina NextSeq using 75bp paired end sequencing.		pubmed:26748692		zebrafish heart WT 7dpi #1	GSM1924888		source name:cryoinjured ventricle of the heart\|tissue:adult heart\|sectioning direction:injury area uninjured remote myocardium\|sectioning thickness:12 µm\|embedding strategy:extracted heart at 7 days post cryoinjury	zebrafish heart WT 7dpi #1	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: zv9 with improved three prime annotation see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections	cryoinjured ventricle of the heart	Unfixed ventricle was embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.	RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 see: Junker et al. 2014 Cell		tissue:adult heart\|sectioning direction:injury area uninjured remote myocardium\|sectioning thickness:12 µm\|embedding strategy:extracted heart at 7 days post cryoinjury	GSM1924888	GSM1924888: zebrafish heart WT 7dpi #1; Danio rerio; RNA Seq	GSM1924888		1	RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 see: Junker et al. 2014 Cell	GEO Accession:GSM1924888	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP066192			FKHEART7_R1.fastq.gz FKHEART7_R2.fastq.gz	fastq fastq	3128649900.0	20745605.0	GSM1924888 r1	0:75.43 1:75.38	A:1025473014;C:388501715;G:410501025;T:1304153289;N:20857	75	75			1025473014	388501715	410501025	1304153289	20857	SRX1432516	SRS1163508	SRA311639	GEO	Jeroen Bakkers, Hubrecht Institute	2	0.31194	0.62458	0.26968	0.18109	0.99308	0.89258	0.54708	0.5286	75	76	T	B	mate1 technical by mapping diff	illumina	nextseq	full_length	random_priming	unknown	sc	single_cell_plate	celseq		Netherlands	2015-11-03	Adult	Adult	Heart	Cardiovascular System