run_metadata: 33947

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
33947	SRR31020098	SRX26407226	SRS22927347	SRP538990	PRJNA1173772	Cardiac Transcriptional Enhancer is Repurposed During Regeneration to Activate an Anti proliferative Program	GSE279653	Transcriptome Analysis	Zebrafish have a high capacity to regenerate their xxx post injury.Several studies have surveyed transcriptional enhancers to understand how the dynamics of gene expression are controlled during heart regeneration. We have identified a cardiac transcriptional enhancer that is activated at the site of injury called the runx1 enhancer or REN since it regulates the expression of nearby gene runx1. REN is usually active in cardiomyocytes CMs and epicardial tissues surrounding the cardiac valves of uninjured zebrafish hearts. However when REN is activated in regenerating CM and epicardial tissues at the injury site it is concurrently downregulated around the distal heart valve. Deletion of REN ?REN results in excess Collagen around uninjured zebrafish cardiac valves. This ?REN Collagen phenotype is rescued with a runx1 deletion ?runx1 suggesting that REN and runx1 function in different genetic pathways in uninjured hearts. A different nearby gene that does change expression around valves in ?REN mutant hearts is adamts1 which encodes a metalloproteinase that degrades Collagen. Taken together this suggests that in uninjured hearts REN regulates adamts1 independently of runx1. However during regeneration CM proliferation at the site of injury is enhanced in both ?REN and ?runx1 mutants suggesting that REN is rewired to runx1 to stimulate its transcription. There are two previous descriptions for how enhancers are activated during regeneration. First cis regulatory sequences are reactivated from embryogenesis and second that active adult enhancers are further invigorated during regeneration. Our data point to a third and previously unappreciated mechanism for gene control during zebrafish heart regeneration. We report that an enhancer is repurposed both from one gene and cardiac domain to activate a different nearby gene in regenerating cardiac tissue. Overall design: Comparitive gene expression analysis of REN mutant and Wildtype hearts under uninjured and regenerating 7dpi conditions using bulk RNA sequencing.		pubmed:39803985		Zebrafish heart REN / regenerating 7dpi replicate 2	GSM8577521		source name:Heart\|tissue:Heart\|genotype:delta REN / \|treatment:Regenerating 7dpi\|geo loc name:missing\|collection date:missing	Zebrafish heart REN / regenerating 7dpi replicate 2	Demultiplexed and quality filtered reads were aligned to the Danio rerio reference genome GRCz10 using Hierarchical Indexing for Spliced Alignment of Transcripts 2 HISAT2 Read counts for each gene were quantified using featureCounts software Assembly: Danio rerio reference genome GRCz10 Supplementary files format and content: tab separated feature counts output text file	Heart		Total RNA was extracted using Trizol method Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification. For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification. The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms according to effective library concentration and data amount. Bulk RNA sequencing	Adults less than 1 year old were used for all the experiments. Males and females were mixed in similar proportions in each of the conditions.	tissue:Heart\|genotype:delta REN / \|treatment:Regenerating 7dpi	GSM8577521	GSM8577521: Zebrafish heart REN / regenerating 7dpi replicate 2; Danio rerio; RNA Seq	GSM8577521 r1	GSM8577521	1	Total RNA was extracted using Trizol method Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification. For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification. The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms according to effective library concentration and data amount. Bulk RNA sequencing		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP538990			RENmut_7dpi_Rep2_1.fq.gz RENmut_7dpi_Rep2_2.fq.gz	fastq fastq	13955721000.0	46519070.0	GSM8577521 r1	0:150 1:150	A:3217814296;C:3758561612;G:3907502717;T:3069654484;N:2187891	150	150			3217814296	3758561612	3907502717	3069654484	2187891	SRX26407226	SRS22927347	SRA1992688	Department of Biomedical Informatics College of Medicine, Ohio State University	Department of Biomedical Informatics College of Medicine, Ohio State University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	bulk	bulk		United States	2024-10-16	Adult	Adult	Heart	Cardiovascular System