run_metadata: 56579
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 56579 | SRR10990702 | SRX7652104 | SRS6081565 | SRP246169 | PRJNA604017 | DGAT1 is a bona fide oncogene stimulating cell growth and suppressing oxidative stress while enabling fatty acid accumulation | GSE144555 | Transcriptome Analysis | Forced over expression of dgat1a using the minicoopR system increased the rate of tumour formation in tp53m214K/m214k; mitfa / ; nras G12D. This was through increased TOR signalling and alterations in key metabolic pathways. Overall design: Examination of the effect of dgat1a overexpression in NRAS driven Zebrafish Melanoma using the miniCoopR system. | Tgmitfa:egfp Rep2 | GSM4290787 | source name:Tumour|strain:tp53m214K/m214k; mitfa / ; nras G12D|tissue:Melanoma|genotype:Tgmitfa:egfp | Tgmitfa:egfp Rep2 | Adapters were trimmed from raw sequencing reads using Trimmomatics v0.32 Trimmed reads were aligned to the zebrafish genome Ensembl GRCz11 using STAR v2.5.3 Reads that mapped to chromosomes 1 25 were retained Gene counts were determined using featureCounts v1.6.2 and differential expression analysis was performed using DESeq2 v1.14.1 using a adjusted p value cut off of <0.05 DESeq2 was used to generate log2 normalised variance stabilising transformed VST counts Genome build: Ensembl GRCz11 Supplementary files format and content: fpm DGAT1 RNAseq GEO Supplementary files format and content: GFP DGAT1 allresults GEO Supplementary files format and content: VST DGAT1 RNAseq GEO | Tumour | Tumours were removed and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols | Age matched tumours were harvested at 10 12 weeks | strain:tp53m214K/m214k; mitfa / ; nras G12D|tissue:Melanoma|genotype:Tgmitfa:egfp | GSM4290787 | GSM4290787: Tgmitfa:egfp Rep2; Danio rerio; RNA Seq | GSM4290787 | 1 | Tumours were removed and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols | GEO Accession:GSM4290787 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP246169 | DWGFP2_S64_R2_001.fastq.gz DWGFP2_S64_R1_001.fastq.gz | fastq fastq | 4667263195.0 | 30934249.0 | GSM4290787 r1 | 0:75.48 1:75.40 | A:1182060905;C:1141466935;G:1126881818;T:1215329644;N:1523893 | 75 | 75 | 1182060905 | 1141466935 | 1126881818 | 1215329644 | 1523893 | SRX7652104 | SRS6081565 | SRA1034701 | GEO | University of Manchester | 2 | 0.93907 | 0.93804 | 0.09417 | 0.09165 | 0.7167 | 0.7189 | 0.49426 | 0.50125 | 75 | 74 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2020-01-30 | Juvenile | Juvenile | Cancer or Tumor | Cancer or Tumor |