{"database": "metadata", "table": "run_metadata", "rows": [[70167, "SRR19560562", "SRX15612620", "SRS13313398", "SRP378803", "PRJNA846486", "High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways", "GSE205578", "Transcriptome Analysis", "Investigation of convergence and divergence of different Autism Risk genes at the molecular level  in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.", null, "pubmed:36933215", null, "dyrk1a HOM2", "GSM6215031", null, "source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Homozygous|genotype:dyrk1a HOM", "dyrk1a HOM2", "DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0  https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al.  2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al.  2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05  fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al.  2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample", "Whole Brain", null, "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. 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