run_metadata: 48805
This data as json
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| 48805 | SRR7299174 | SRX4201608 | SRS3411843 | SRP150378 | PRJNA475809 | Transcriptome analysis of zebrafish wildtype adult brain and rb1 embryonal brain tumors by RNA Seq | GSE115719 | Transcriptome Analysis | Zebrafish wildtype adult brain and rb1 embryonal brain tumor transcriptomes were used to identify candidate rb1 interacting chromatin remodelers and epigenetic regulators altered in rb1 transformed brain tumor cells. The data was also used for comparative analysis with zebrafish rb1 / mutant transcriptome to identify molecular pathways that distinguish transformed rb1 tumor cells from non transformed rb1 / mutant cells. Overall design: RNA Seq libraries were prepared from 10 tumor biological replicates and two pools of three normal adult brains ages 6.5 to 10.5 month. | parent bioproject:PRJNA475805 | pubmed:29914980 | Tumor4a | GSM3188290 | source name:Brain tumor tissue|strain/background:WIK|genotype:rb1 TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor | Tumor4a | Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters “ N 1 t 8 B 4 m 5 A sam split output”. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Tumor raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Tumor FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Tumor DGE.txt: Tab delimited text file includes differential gene expression statistics. | Brain tumor tissue | Dissected zebrafish brain tumor tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA. | strain/background:WIK|genotype:rb1 TALEN somatic targeted|age:6.5 month 10 month|tissue:rb1 brain tumor | GSM3188290 | GSM3188290: Tumor4a; Danio rerio; RNA Seq | GSM3188290 | 1 | Dissected zebrafish brain tumor tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA. | GEO Accession:GSM3188290 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP150378 | P1_05_CAGATC_L001_R1_001.fastq.gz | fastq | 769944093.0 | 15096943.0 | GSM3188290 r1 | 0:51 1:0 | A:204951580;C:182730001;G:176358089;T:205858493;N:45930 | 51 | 0 | 204951580 | 182730001 | 176358089 | 205858493 | 45930 | SRX4201608 | SRS3411843 | SRA720941 | GEO | Maura McGrail, GDCB, Iowa State University | 1 | 0.90377 | 0.11833 | 0.69436 | 0.48968 | 51 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | United States | 2018-06-12 | Adult | Adult | Multi-tissue | Multi-system |