run_metadata: 59994

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
59994	SRR12083050	SRX8610201	SRS6899879	SRP268691	PRJNA641676	Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration	GSE153170	Transcriptome Analysis	Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms such as zebrafish cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b / n=20 ventricles. All cells were sent for single cell RNA sequencing.		pubmed:34486669		HUB DB 010	GSM4635176		tissue:Epicardial cells of the Zebrafish heart ventricle\|line:Tgtcf21:mCherry\|genotype/variation:WT\|treatment:Cryoinjured heart\|Stage:7dpi\|cell type:Epicardial cells of adult heart ventricle	HUB DB 010	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. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following order: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv". Read 1 was not used for quantification. Read 2 containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values	Epicardial cells of the Zebrafish heart ventricle	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates each well containing 1 cell.	Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for library prep Hashimony et al. 2016.		line:Tgtcf21:mCherry\|genotype/variation:WT\|treatment:Cryoinjured heart\|Stage:7dpi\|cell type:Epicardial cells of adult heart ventricle	GSM4635176	GSM4635176: HUB DB 010; Danio rerio; RNA Seq	GSM4635176		1	Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for library prep Hashimony et al. 2016.	GEO Accession:GSM4635176	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP268691			HUB-DB-010_H3HCLBGXC_S2_L002_R1_001.fastq.gz HUB-DB-010_H3HCLBGXC_S2_L002_R2_001.fastq.gz	fastq fastq	642282486.0	7468401.0	GSM4635176 r2	0:26 1:60	A:156140841;C:120979080;G:123582811;T:241577191;N:2563	26	60			156140841	120979080	123582811	241577191	2563	SRX8610201	SRS6899879	SRA1090808	GEO	Hubrecht	2	0.10877	0.86702	0.10115	0.2848	0.98961	0.84122	0.5621	0.48392	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	trueseq	sc	single_cell_plate	celseq		Netherlands	2020-06-24	Adult	Adult	Heart	Cardiovascular System