run_metadata: 42882

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
42882	SRR5817920	SRX2996174	SRS2347409	SRP111552	PRJNA393857	Comparison of the expression profiles of kdrl:mCherry positive cells in injured versus uninjured zebrafish cardiac ventricle and analysis of the expression prolife of postnb:citrin positive cells upon injury compared to the rest of cardiac cells.	GSE101200	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the cardiac ventricular apex. Regeneration is preceed by a fibrotic response. To understand the contribution of different cell sources to zebrafish cardiac fibrosis we performed an RNASeq including endocardial kdrl:mCherry cells from an uninjured heart and activated endocardial kdrl:mCherry cells postnb:citrine fibroblasts and the rest of the cells at 7 xxx post injury. Overall design: Three to six biological replicates consisting of different cell types obtained from the ventricular apex.		pubmed:29610343		kdrl mCherry 7dpi 09	GSM2700307		tissue:Heart\|cell type:kdrl:mCherry+\|treatment:7 xxx post injury\|pool:9	kdrl mCherry 7dpi 09	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	Double transgenic postnb:citrine;kdrl:mCherry were cryoinjured or not as indicated.	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:kdrl:mCherry+\|treatment:7 xxx post injury\|pool:9	GSM2700307	GSM2700307: kdrl mCherry 7dpi 09; Danio rerio; RNA Seq	GSM2700307		1	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700307	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP111552			kdrl_7dpi_09__HS_OvationSC_TGGTGA_L001_R1_001.fastq.gz	fastq	2145360789.0	35169849.0	GSM2700307 r1	0:61	A:559652295;C:434757157;G:629761603;T:521131593;N:58141	61				559652295	434757157	629761603	521131593	58141	SRX2996174	SRS2347409	SRA585701	GEO	Bioinformatics Unit, CNIC	1	0.76139		0.25919		0.80608		0.67486		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only		Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System