run_metadata: 34062

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
34062	SRR31040094	SRX26425365	SRS22944830	SRP539398	PRJNA1174770	cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [Bulk RNA seq]	GSE279843	Transcriptome Analysis	Cardiac regeneration involves interplay of complex interactions between many different cell types including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response myofibril assembly proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this we determined that cited4a a p300/CBP transcriptional co activator is xxx post injury in mature cardiomyocyte population. Moreover loss of cited4a mutants showed increased dedifferentiation proliferation and accelerated heart regeneration. Thus suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa. Total RNA was extracted from ventricles was used for RNA seq experiments.		pubmed:39713454		cited4a 5 S10	GSM8581867		source name:heart ventricle\|tissue:heart ventricle\|genotype:cited4a pt38a/pt38a\|treatment:3 dpa\|geo loc name:missing\|collection date:missing	cited4a 5 S10	fastq files were processed with Cutadapt to remove adaptors Trimmed seq files were mapped to the zebrafish geneome using HiSat2 Mapped files were processed within featureCount for gene expression counts featureCount reads were imported into R package DeSeq2 for gene expression analysis. WT3 and cited4a 3 samples were omitted from the DeSeq2 analysis due to poor mapping. Normalized counts were calculated and log2 fold change and padj values were calculated using DeSeq2. Assembly: Danio rerio GRC.z11 Supplementary files format and content: RFR WTvsCited4aDeSeq2.xlsx Supplementary files format and content: .csv files are raw counts from featureCount processing post HiSat2 mapping.	heart ventricle		Adutls hearts were injured through ventricular resection and allowed to recover until 3 dy post amputation. Ventricles were removed flash frozen on dry ice and RNA was harvested using Trizol reagent and Quiagen RNeasy micro kit Cat# 74004.	Zebrafish adult at 6 month 1year of age	tissue:heart ventricle\|genotype:cited4a pt38a/pt38a\|treatment:3 dpa	GSM8581867	GSM8581867: cited4a 5 S10; Danio rerio; RNA Seq	GSM8581867 r1	GSM8581867	1	Adutls hearts were injured through ventricular resection and allowed to recover until 3 dy post amputation. Ventricles were removed flash frozen on dry ice and RNA was harvested using Trizol reagent and Quiagen RNeasy micro kit Cat# 74004.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP539398			cited4a_5_S10_R1_001.fastq.gz cited4a_5_S10_R2_001.fastq.gz	fastq fastq	9406981002.0	47541872.0	GSM8581867 r1	0:98.92 1:98.95	A:2544850290;C:2146373234;G:2187647121;T:2515525772;N:12584585	98	98			2544850290	2146373234	2187647121	2515525772	12584585	SRX26425365	SRS22944830	SRA1993635	Cell Biology, University of Pittsburgh	Cell Biology, University of Pittsburgh												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	bulk	bulk		United States	2024-10-18	Adult	Adult	Heart	Cardiovascular System