run_metadata: 48430
This data as json
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| 48430 | SRR7266721 | SRX4170560 | SRS3382369 | SRP149832 | PRJNA474730 | Transcriptome analysis of wt1b:eGFP positive macrophages in the regenerating zebrafish heart | GSE115381 | Transcriptome Analysis | Little is known about zebrafish macrophage subtypes and their contribution to organ regeneration. Using the transgenic line wt1b:eGFP we identified a subtype of macrophages in the regenerating heart that is transcriptionally different from the rest of macrophages. Overall design: Hearts from Tgwt1b:eGFP; mpeg1:mCherry zebrafish were cryoinjured and at 4 dpi mCherry and GFP/mCherry cells were FAC sorted. RNA was extracted from 4 pools of GFP/mCherry and 4 pools of mCherry single positive cells and RNAseq was performed. | parent bioproject:PRJNA485878 | pubmed:31365871 | MR 4 | GSM3177083 | tissue:mpeg1:mCherry cells from 4dpi hearts|phenotype:mpeg1:mCherry|library batch:2 | MR 4 | 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 v1.2.3. Genome build: Ensembl genebuild 75 Danio rerio assembly Zv9. Supplementary files format and content: matrix table.xls file contains ENSEMBL gene Ids and TMM normalized batch corrected counts per million for each sample. | mpeg1:mCherry cells from 4dpi hearts | Four biological replicates consisting of FAC sorted cells coming from five to seven pooled hearts were used per phenotype. | RNA was extracted with PicoPure™ RNA Isolation Kit Index tagged cDNA libraries were constructed in two batches from total RNA 1 ng with the TruSeq RNA sample preparation v2 kit Illumina post amplification with the NuGen OvationSC RNA Seq System. Quality quantity and size distribution of the Illumina libraries were determined using the DNA 1000 kit Agilent Bioanalyzer. RNASeq. Libraries were sequenced single end mode and length of 60 61 bp on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5. | All experiments were conducted with adult zebrafish between 6 month and 9 month of age raised at a density of 3 fish/l. | phenotype:mpeg1:mCherry|library batch:2 | GSM3177083 | GSM3177083: MR 4; Danio rerio; RNA Seq | GSM3177083 | 1 | RNA was extracted with PicoPure™ RNA Isolation Kit Index tagged cDNA libraries were constructed in two batches from total RNA 1 ng with the TruSeq RNA sample preparation v2 kit Illumina post amplification with the NuGen OvationSC RNA Seq System. Quality quantity and size distribution of the Illumina libraries were determined using the DNA 1000 kit Agilent Bioanalyzer. RNASeq. Libraries were sequenced single end mode and length of 60 61 bp on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5. | GEO Accession:GSM3177083 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP149832 | MR4__AnaBelenGarcia_RNA_Seq_OvationSC_AAGAGG_L002_R1_001.fastq.gz | fastq | 1031492188.0 | 16909708.0 | GSM3177083 r1 | 0:61 1:0 | A:275201446;C:215010611;G:277227531;T:263995484;N:57116 | 61 | 0 | 275201446 | 215010611 | 277227531 | 263995484 | 57116 | SRX4170560 | SRS3382369 | SRA715602 | GEO | Bioinformatics Unit, CNIC | 1 | 0.8243 | 0.31617 | 0.83883 | 0.54481 | 61 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | sc_generic | single_cell_generic | generic-scrnaseq-only | Spain | 2018-06-05 | Adult | Adult | Heart | Cardiovascular System |