run_metadata: 49231
This data as json
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| 49231 | SRR7813752 | SRX4665318 | SRS3760346 | SRP160900 | PRJNA490132 | Morphogenesis and differentiation of embryonic vascular smooth muscle cells in zebrafish | GSE119718 | Transcriptome Analysis | Molecular and cellular analysis of mural cell development during zebrafish embryonic development Overall design: RNAseq was performed on mural or endothelial cells isolated from transgenic zebrafish embryos | pubmed:31199900 | kdrl negative rep1 | GSM3381535 | source name:non endothelial cells|tissue:embryonic vascular smooth muscle cells|cell population:non endothelial cells|Stage:5 dpf isolated cells | kdrl negative rep1 | For mural cellls raw NextSeq500 reads were processed and demultiplexed using bcl2fastq 2.14 Illumina to generate fastq files for each sample. For kdrl cells raw HiSeq2000 data files were processed with CASAVA 1.8.2 Illumina to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples if index sequences were non redundant we allowed for 1 mismatch or N in the index. Paired end reads were aligned to 26 chromosomes and 967 primary assembly scaffolds of the zebrafish genome GRCz11 with star 2.5.3a Dobin et al. 2013. Aligned exon fragments with mapping quality higher than 20 were counted toward gene expression with featureCounts 1.5.2 Liao Smyth & Shi 2014. Normalization and differential expression DE analysis was performed with DESeq2 1.20.0 Love Huber & Anders 2014. For DE analysis the original DESeq2 shrinkage estimator was used to estimate log2 fold change LFC for each comparison. Genome build: GRCz11 Refseq GCF 000002035.6 Supplementary files format and content: comma separated text file | non endothelial cells | embryos were dissociated and single cell suspensions were fixed acccording to the MARIS protocol; transgene expressing cells were isolated by fluorescence activated cell sorting. | total RNA was isolated using TRIzol oligo dT primed libraries were constructed using the TotalScript kit Epicentre | zebrafish embryos were grown to 4 or 5 dpf | tissue:embryonic vascular smooth muscle cells|cell population:non endothelial cells|Stage:5 dpf isolated cells | GSM3381535 | GSM3381535: kdrl negative rep1; Danio rerio; RNA Seq | GSM3381535 | 1 | total RNA was isolated using TRIzol oligo dT primed libraries were constructed using the TotalScript kit Epicentre | GEO Accession:GSM3381535 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP160900 | 08_WT_negative-27726816_R2.fastq.gz 08_WT_negative-27726816_R1.fastq.gz | fastq fastq | 6768499011.0 | 47415000.0 | GSM3381535 r1 | 0:71.36 1:71.39 | A:2052636566;C:1320197120;G:1348340134;T:2032751679;N:14573512 | 71 | 71 | 2052636566 | 1320197120 | 1348340134 | 2032751679 | 14573512 | SRX4665318 | SRS3760346 | SRA770492 | GEO | Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School | 2 | 0.88397 | 0.88537 | 0.50832 | 0.50894 | 0.68509 | 0.69528 | 0.52501 | 0.52779 | 74 | 75 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | United States | 2018-09-10 | Larval | Larval | Muscle | Muscular System |