run_metadata: 65014
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 65014 | SRR14902692 | SRX11217414 | SRS9271513 | SRP325444 | PRJNA741108 | Transcriptional Profile in Zebrafish Melanocytes and Melanoma Tumors [RNA seq] | GSE178801 | Transcriptome Analysis | With high genetic heterogeneity in melanoma understanding epigenetic and transcriptional differences between melanocytes and melanoma cells will enable further understanding of the genes pathways and epigenetic regions influencing melanoma development. We performed RNA seq and ATAC seq on fluorescently isolated melanocytes and melanoma cells from a zebrafish melanoma model. Overall design: RNA seq profiles of FACS isolated mitfa:mCherry reporter positive melanocytes and crestin:GFP positive melanoma cells from adult zebrafish D. rerio. | parent bioproject:PRJNA741103 | pubmed:34791221 | MA3B RNAseq | GSM5397959 | source name:Sorted melanoma tumor|genotype:BRAFV600E/p53lf/lf/crestin:EGFP|tissue:Melanoma | MA3B RNAseq | Assess read quality with FastQC Align to GRCz11/danRer11 using STAR Quantify transcriptome using RSEM Normalize reads with DESeq2 Genome build: danRer11 Supplementary files format and content: tab delimited text files with CPM values for each sample Supplementary files format and content: tab delimited text files with RPKM values for each sample Supplementary files format and content: Excel spreadsheet summarizing log2FC values between melanocytes and melanoma cells as well as | Sorted melanoma tumor | FACS for fluorescent tag: mCherry for melanocytes MC and GFP for melanoma cells MA then use Machery Nagel kit to extract total RNA cDNA generated using Clontech SMARTer cDNA amplification kit | genotype:BRAFV600E/p53lf/lf/crestin:EGFP|tissue:Melanoma|run #:1 | GSM5397959 | GSM5397959: MA3B RNAseq; Danio rerio; RNA Seq | GSM5397959 | 1 | FACS for fluorescent tag: mCherry for melanocytes MC and GFP for melanoma cells MA then use Machery Nagel kit to extract total RNA cDNA generated using Clontech SMARTer cDNA amplification kit | GEO Accession:GSM5397959 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP325444 | MA3B.fq.gz | fastq | 1437189100.0 | 28743782.0 | GSM5397959 r1 | 0:50 1:0 | A:398259972;C:317724608;G:311519412;T:408662664;N:1022444 | 50 | 0 | 398259972 | 317724608 | 311519412 | 408662664 | 1022444 | SRX11217414 | SRS9271513 | SRA1250059 | GEO | Kaufman, Oncology, Washington University in St. Louis | 1 | 0.89689 | 0.14892 | 0.73959 | 0.52927 | 50 | B | usable mapping rate | illumina | hiseq_era | full_length | cdna_unspecified | smarter | bulk | unknown | unknown | United States | 2021-06-24 | Undetermined | Adult | Cancer or Tumor | Cancer or Tumor |