{"database": "metadata", "table": "run_metadata", "rows": [[49235, "SRR7813748", "SRX4665314", "SRS3760342", "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", null, "pubmed:31199900", null, "acta2/foxc1b negative rep2", "GSM3381531", null, "source name:non mural cells|tissue:embryonic vascular smooth muscle cells|cell population:non mural cells|Stage:4 dpf isolated cells", "acta2/foxc1b negative rep2", "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. 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