{"database": "metadata", "table": "run_metadata", "rows": [[26490, "SRR26034374", "SRX21751583", "SRS18859090", "SRP459779", "PRJNA1015242", "Gene expression data from zebrafish SHH medulloblastoma brains and normal brains.", "GSE242897", "Transcriptome Analysis", "Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals  3 individual tp53 mutant and ptch1 crispant animals  and 3 individual tp53 heterozygous and ptch1 crispant animals.", null, "pubmed:39078737", null, "19521X3 tp53mut tumor", "GSM7774459", null, "source name:brain|tissue:brain|tumor status:tumor|age:4 wpf|genotype:tp53 mutant|geo loc name:missing|collection date:missing", "19521X3 tp53mut tumor", "The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id  log2FC  padj  and raw counts.", "brain", "Brains were frozen at  80C in RNA stabilization solution QIAGEN.", "Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.", "Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.", "tissue:brain|tumor status:tumor|age:4 wpf|genotype:tp53 mutant", "GSM7774459", "GSM7774459: 19521X3 tp53mut tumor; Danio rerio; RNA Seq", "GSM7774459 r1", "GSM7774459", "1", "Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. 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