run_metadata: 66208

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
66208	SRR16098000	SRX12384067	SRS10354361	SRP339110	PRJNA767032	Amino acid primed mTOR activity is essential for heart regeneration [scRNA seq]	GSE184914	Transcriptome Analysis	Heart disease is the leading cause of death as there is no current method to repair damaged myocardium due to the limited proliferative capacity of adult cardiomyocytes. Curiously mouse neonates and zebrafish larvae or adult are able to regenerate their hearts via cardiomyocyte de differentiation and proliferation. However a molecular mechanism of why these cardiomyocytes can re enter cell cycle is poorly understood. Here we identify a unique metabolic state that primes adult zebrafish and neonatal mouse ventricular cardiomyocytes to proliferate. Zebrafish and neonatal mouse hearts display elevated glutamine levels predisposing them to amino acid driven activation of TOR. We show that this TOR activation is required for zebrafish cardiomyocyte regeneration in vivo. post injury we observe pS6 in both the epicardium and ventricular cardiomyocytes suggesting these are amino acid primed cells necessary for regeneration. Through single cell and system wide RNA sequencing LQC proteomics and microscopy we identify dramatic metabolic and mitochondrial changes during the first week of regeneration. These data suggest that regeneration of zebrafish myocardium is driven by metabolic remodeling and reveals a unique metabolic regulator TOR primed state in which zebrafish and mammalian cardiomyocytes are regeneration competent. Overall design: We performed single cell RNA seq of zebrafish heart pre injury and 3 7 xxx post injury	parent bioproject:PRJNA778001	pubmed:34988408		zebrafish day 3	GSM5600323		source name:Zebrafish heart\|tissue:heart\|strain:AB\|time:xxx post injury	zebrafish day 3	Raw reads were processed using the CellRanger software from 10X genomics using recommended default settings. Monocle version 3 alpha was used for single cell RNA seq data analysis and visualization. We kept cells with at least 200 expressed genes and 1000 Unique Molecular Identifiers UMIs and less than 40% reads mapped to mitochondrial transcripts. Genome build: GRCz10 Supplementary files format and content: tab delimited file of normalized gene level read counts for each cell	Zebrafish heart	All chemical ventricular cardiomyocyte VCM ablation were conducted on adult Zebrafish 5 mpf 12 mpf. For chemical mediated VCM ablation fish were treated with 5 mM Metronidiazole MTZ; Sigma containing 0.1% dimethyl sulfoxide DMSO or vehicle control 0.1% DMSO for 48 hours protected from light and refreshed every 24 hours. For Wnt and DKK heat shock heterozygous animals 7.5 mM MTZ was used. Following chemical treatment fish were placed back in original aquaria and hearts were collected at 0 prior to MTZ 3 7 12 and 30 xxx post injury dpi. Larval hearts 72 hpf were isolated and pooled as previously described [68 69]. 6 hearts 3 males and 3 females were isolated from Adult UI 3 dpi and 7 dpi zebrafish. Each group had 2 sets of samples of 3 hearts each for the digestion process. Each set of 3 hearts were single celled as previously described [79]. All cells per group were then pooled and sent for sequencing.	Cells were resuspended in PBS containing 0.04% BSA at a concentration of 2600 cells/ 33.8 μL solution. In total 2600 cells per sample were loaded into each well of a 10X Chromium single cell capture chip with a recovery of 272 cells for uninjured heart 141 cells for 3 xxx post injury and 368 cells for 7 xxx post injury sample. The captured cells then underwent lysis reverse transcription cDNA amplification and library preparation with indexing per the manufacturer’s protocol 10X Genomics. The libraries were sequenced together on an Illumina HiSeq 4000 Illumina Inc. San Diego CA using a high output 150 cycle kit with read lengths recommended by 10X Genomics.	Wild type AB; Zebrafish International Resource Center Eugene OR USA hsWnt8:GFP [Tghsp70l:Wnt8a GFPw34] and hsDKK1:GFP [Tghsp70l:DKK1b GFPw32] [19] and vmhc:mCherry NTR [Tgvmhc:mCherry Eco.NfsB] [5] were used and maintained using standard procedures [67] in accordance with the Institutional Animal Care and Use Committee approved protocols IACUC 2057 01 & 4364 02. Reverse osmosis system water is used and the water chemistry was adjusted to a temperature of 27.5°C pH of 7.5 conductivity of 800 µS hardness of 140 ppm alkalinity of 35 ppm dissolved oxygen content of 7.8 mg/L and a total gas pressure of 101%. The average nitrate level is 55 ppm the average nitrite level is 0.05 ppm and the average ammonium level is 0.01 ppm. Larval feed starting at 5 dpf dpf is a rotifer polyculture supplemented with the Zeigler larval diet at 12 dpf live artemia is added to the diet and at 60 dpf 90 dpf the fish are started on the Zeigler adult diet supplemented with live artemia once per day. The health status of the colony showed low presence of pseudoloma neurophilia and an extremely low presence of mycobacterium spp. with no major clinical or subclinical findings of significance.	tissue:heart\|strain:AB\|time:xxx post injury	GSM5600323	GSM5600323: zebrafish day 3; Danio rerio; RNA Seq	GSM5600323 r1	GSM5600323	1	Cells were resuspended in PBS containing 0.04% BSA at a concentration of 2600 cells/ 33.8 μL solution. In total 2600 cells per sample were loaded into each well of a 10X Chromium single cell capture chip with a recovery of 272 cells for uninjured heart 141 cells for 3 xxx post injury and 368 cells for 7 xxx post injury sample. The captured cells then underwent lysis reverse transcription cDNA amplification and library preparation with indexing per the manufacturer's protocol 10X Genomics. The libraries were sequenced together on an Illumina HiSeq 4000 Illumina Inc. San Diego CA using a high output 150 cycle kit with read lengths recommended by 10X Genomics.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP339110		assembly:GRCz10\|intentional duplicate	zf_3db_possorted_genome_bam.bam	10X Genomics bam file	35567557578.0	362934261.0	GSM5600323 r1	0:98	A:11273935957;C:7072680901;G:7397087735;T:9812130858;N:11722127	98				11273935957	7072680901	7397087735	9812130858	11722127	SRX12384067	SRS10354361	SRA1301815	Institute for Stem Cell and Regenerative Medicine	Institute for Stem Cell and Regenerative Medicine	1	0.91795		0.07118		0.87418		0.58423		98		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		United States	2021-09-28	Multi-stage	Multi-stage	Heart	Cardiovascular System