run_metadata: 42898

This data as json

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42898	SRR5818011	SRX2996261	SRS2347493	SRP111553	PRJNA393878	Comparison of the expression profile of GFP positive cells from Tg 6.8wt1a:EGFP with the rest of the cells in adult zebrafish cardiac ventricles	GSE101204	Transcriptome Analysis	wt1a:GFP labels a population of subepicardial cells in the uninjured ventricle. Here we compare the expression profile of wt1a:GFP positive cells to the rest of the cells of the ventricle. Overall design: Four paired biological replicates of wt1a:GFP positive and wt1a:GFP negative cells obtained from pools of 3 5 zebrafish heart ventricles.		pubmed:29610343		wt1aGFP 2 pos	GSM2700329		tissue:Heart\|cell type:wt1a+\|pool:2	wt1aGFP 2 pos	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 counts.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	No treatment was applied.	Whole zebrafish heart ventricles 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.	cell type:wt1a+\|pool:2	GSM2700329	GSM2700329: wt1aGFP 2 pos; Danio rerio; RNA Seq	GSM2700329		1	Whole zebrafish heart ventricles 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:GSM2700329	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP111553			wt1aV_32_pos__HS_RNA_Seq_OvationSC_GCACTA_L002_R1_001.fastq.gz	fastq	768777327.0	12602907.0	GSM2700329 r2	0:61	A:216934227;C:147173989;G:191157153;T:213483110;N:28848	61				216934227	147173989	191157153	213483110	28848	SRX2996261	SRS2347493	SRA585736	GEO	Bioinformatics Unit, CNIC	1	0.82552		0.31671		0.79088		0.50918		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