run_metadata: 56576
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 56576 | SRR10990705 | SRX7652107 | SRS6081571 | 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:dgat1a Rep2 | GSM4290790 | source name:Tumour|strain:tp53m214K/m214k; mitfa / ; nras G12D|tissue:Melanoma|genotype:Tgmitfa:dgat1a | Tgmitfa:dgat1a 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:dgat1a | GSM4290790 | GSM4290790: Tgmitfa:dgat1a Rep2; Danio rerio; RNA Seq | GSM4290790 | 1 | Tumours were removed and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols | GEO Accession:GSM4290790 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP246169 | DWDGAT2_S68_R2_001.fastq.gz DWDGAT2_S68_R1_001.fastq.gz | fastq fastq | 4733397495.0 | 31387433.0 | GSM4290790 r1 | 0:75.44 1:75.36 | A:1191292169;C:1166880803;G:1148695321;T:1223832965;N:2696237 | 75 | 75 | 1191292169 | 1166880803 | 1148695321 | 1223832965 | 2696237 | SRX7652107 | SRS6081571 | SRA1034701 | GEO | University of Manchester | 2 | 0.94258 | 0.94221 | 0.07204 | 0.06973 | 0.71719 | 0.71995 | 0.49403 | 0.50374 | 76 | 76 | 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 |