run_metadata: 41085
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 41085 | SRR3666783 | SRX1845188 | SRS1504029 | SRP076552 | PRJNA325656 | Differential gene expression of zebrafish melanocytes and melanomas [RNA seq] | GSE83343 | Transcriptome Analysis | We report the gene expression comparison of zebrafish melanocytes and melanomas. These comparisons were used for integrative genomic studies that identified the BMP factor GDF6 as a new oncogene that is specifically expressed in melanomas. Overall design: Examination of gene expression in two different cell types | parent bioproject:PRJNA325808 | pubmed:29202482 | ZF melanoma rep3 | GSM2199908 | tissue:melanoma|strain:Tgmitfa:BRAFV600E; p53zdf1; Tgmitfa:EGFP; albb4|age:adult|cell type:melanoma | ZF melanoma rep3 | Star v2.3 was used to align the reads htseq count was used to count mappped reads DESeq2 was used to perform differential gene expression analysis Genome build: Zebrafish Zv9 Supplementary files format and content: tab delimited txt file includes FPKM values for all samples | melanoma | RNA was harvested from cells using Trizol reagent. Illumina TruSeq | Unpigmented EGFP positive melanocytes and melanoma cells were isolated by FACS | strain:Tgmitfa:BRAFV600E;p53zdf1;Tgmitfa:EGFP;albb4|age:adult|cell type:melanoma | GSM2199908 | GSM2199908: ZF melanoma rep3; Danio rerio; RNA Seq | GSM2199908 | 1 | RNA was harvested from cells using Trizol reagent. Illumina TruSeq | GEO Accession:GSM2199908 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP076552 | Melanoma_3_R1.fastq.gz Melanoma_3_R2.fastq.gz | fastq fastq | 6025625112.0 | 59074756.0 | GSM2199908 r1 | 0:51 1:51 | A:1664666728;C:1334918212;G:1342599896;T:1679035262;N:4405014 | 51 | 51 | 1664666728 | 1334918212 | 1342599896 | 1679035262 | 4405014 | SRX1845188 | SRS1504029 | SRA433946 | GEO | PMM Bioinformatics Core, Program in Molecular Medicine, University of Massachusetts | 2 | 0.93254 | 0.8901 | 0.13621 | 0.13127 | 0.75858 | 0.76562 | 0.52486 | 0.51808 | 51 | 51 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | United States | 2016-06-14 | Adult | Adult | Cancer or Tumor | Cancer or Tumor |