run_metadata: 42914

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
42914	SRR5820058	SRX2997959	SRS2349067	SRP111705	PRJNA393987	postnb lineage traced cells at 7 and 60 days post cryoinjury dpi during adult zebrafish cardiac ventricle regeneration	GSE101199	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the ventricular apex. Regeneration is preceeded by a transient fibrotic response. Here we compare the expression profile of fibroblast like cells at 7 different time points of fibrosis resolution. Using a postnb:CreERT2; ubb:loxP GFP loxP mCherrycz1701 double transgenic line we permanently label cells that expressed postnb at 3 and 4 xxx post injury dpi with mCherry by administration of 4 OHT. We sequenced mCherry labelled cells obtained from the ventricular apex at 7 and 60 dpi. Overall design: postnb derived cells were FAC sorted from a pool of three to five biological samples. Four pools were collected at 7 dpi and three at 60 dpi. RNA was extracted from those pools and further processed for transcriptome analysis.		pubmed:29610343		postnbCreERT2 7dpi 3	GSM2700296		tissue:Heart\|treatment:7 dpi	postnbCreERT2 7dpi 3	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	postnb:CreERT2;ubb:loxP GFP loxP mCherry fish were treated over night with 4 OHT 10 µM at 3 and 4 dpi. Fish were dissected at 7 or 60 dpi.	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and 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. 3 5 pooled hearts were used per sample. 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.	treatment:7 dpi	GSM2700296	GSM2700296: postnbCreERT2 7dpi 3; Danio rerio; RNA Seq	GSM2700296		1	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and 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. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700296	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP111705			pstnC7dpi_23__HS_RNA_Seq_OvationSC_AGCATG_L002_R1_001.fastq.gz	fastq	742926320.0	12179120.0	GSM2700296 r2	0:61	A:205824167;C:142245364;G:193518156;T:201311005;N:27628	61				205824167	142245364	193518156	201311005	27628	SRX2997959	SRS2349067	SRA586092	GEO	Bioinformatics Unit, CNIC	1	0.83963		0.28878		0.78577		0.57339		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