run_metadata: 41086
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 41086 | SRR3666782 | SRX1845187 | SRS1504027 | 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 rep2 | GSM2199907 | tissue:melanoma|strain:Tgmitfa:BRAFV600E; p53zdf1; Tgmitfa:EGFP; albb4|age:adult|cell type:melanoma | ZF melanoma rep2 | 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 | GSM2199907 | GSM2199907: ZF melanoma rep2; Danio rerio; RNA Seq | GSM2199907 | 1 | RNA was harvested from cells using Trizol reagent. Illumina TruSeq | GEO Accession:GSM2199907 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP076552 | Melanoma_2_R1.fastq.gz Melanoma_2_R2.fastq.gz | fastq fastq | 5820855420.0 | 57067210.0 | GSM2199907 r1 | 0:51 1:51 | A:1608054488;C:1286088047;G:1295801092;T:1626675668;N:4236125 | 51 | 51 | 1608054488 | 1286088047 | 1295801092 | 1626675668 | 4236125 | SRX1845187 | SRS1504027 | SRA433946 | GEO | PMM Bioinformatics Core, Program in Molecular Medicine, University of Massachusetts | 2 | 0.9408 | 0.88645 | 0.14414 | 0.13333 | 0.76441 | 0.77291 | 0.53482 | 0.53362 | 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 |