run_metadata: 57261

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
57261	SRR11294126	SRX7899685	SRS6307735	SRP252540	PRJNA612190	Tp53 suppression promotes cardiomyocyte proliferation during zebrafish heart regeneration	GSE146859	Transcriptome Analysis	Transcriptome sequencing of uninjured and regenerating 7dpi tp53M214K and tp53WT ventricles. Overall design: 4 experimental groups were analyzed in triplicates: 1 uninjured ventricle of tp53 mutant fish; 2 injured ventricle of tp53 mutant fish; 3 uninjured ventricle of tp53 wild type fish; 4 injured ventricle of tp53 wild type fish.		pubmed:32877671		Ventricles uninj p53 pos.rep1	GSM4407930		source name:Ventricles of uninjured TgtpWT zebrafish\|genotype:Tgtp53WT\|strain:EK /AB strain\|treatment: 17 hours treatment with 0.5 μM tamoxifen\|tissue:Ventricles	Ventricles uninj p53 pos.rep1	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest	Ventricles of uninjured TgtpWT zebrafish	Fish were treated 17 hours with 0.5 μM tamoxifen to ablate cardiomyocytes. Control fish were equally treated.	Zebrafish ventricles were collected and placed in cold PBS while still pumping to help decrease intra ventricular blood. Atrium and outflow tract were removed and ventricles 5 per sample were homogenized in Trizol using a Tissue Lyser II QIAGEN. RNA was extracted using the standard Trizol protocol genomic DNA removed using RNA clean and Concentrator Kit Zymo Research and processed for libraries preparation. Libraries were constructed by single end 50 bp sequencing with 30 M reads/sample was performed at BGI. RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. DESeq2 v 1.26.0 was employed for differential expression analysis.	Fish were grown at 28 degrees. Male and female animals between 6 month and 12 month and of 2 cm in length were used.	genotype:Tgtp53WT\|strain:EK /AB strain\|treatment: 17 hours treatment with 0.5 μM tamoxifen\|tissue:Ventricles	GSM4407930	GSM4407930: Ventricles uninj p53 pos.rep1; Danio rerio; RNA Seq	GSM4407930		1	Zebrafish ventricles were collected and placed in cold PBS while still pumping to help decrease intra ventricular blood. Atrium and outflow tract were removed and ventricles 5 per sample were homogenized in Trizol using a Tissue Lyser II QIAGEN. RNA was extracted using the standard Trizol protocol genomic DNA removed using RNA clean and Concentrator Kit Zymo Research and processed for libraries preparation. Libraries were constructed by single end 50 bp sequencing with 30 M reads/sample was performed at BGI. RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. DESeq2 v 1.26.0 was employed for differential expression analysis.	GEO Accession:GSM4407930	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500		SRP252540			CL100137114_L1_HK500ZEBortRAABRAAPEI-510_1.fq.gz	fastq	1834689950.0	36693799.0	GSM4407930 r1	0:50	A:504160420;C:403583740;G:412496526;T:514449264;N:0	50				504160420	403583740	412496526	514449264	0	SRX7899685	SRS6307735	SRA1054226	GEO	Poss, Cell Biology, Duke University	1	0.93629		0.08291		0.77356		0.49244		50		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown		United States	2020-03-12	Adult	Adult	Heart	Cardiovascular System