run_metadata: 56573
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 56573 | SRR10990708 | SRX7652110 | SRS6081581 | 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 Rep5 | GSM4290793 | source name:Tumour|strain:tp53m214K/m214k; mitfa / ; nras G12D|tissue:Melanoma|genotype:Tgmitfa:dgat1a | Tgmitfa:dgat1a Rep5 | 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 | GSM4290793 | GSM4290793: Tgmitfa:dgat1a Rep5; Danio rerio; RNA Seq | GSM4290793 | 1 | Tumours were removed and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols | GEO Accession:GSM4290793 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP246169 | DWDGAT5_S72_R2_001.fastq.gz DWDGAT5_S72_R1_001.fastq.gz | fastq fastq | 4651371627.0 | 30842966.0 | GSM4290793 r1 | 0:75.44 1:75.36 | A:1179690324;C:1135674487;G:1124761084;T:1209401950;N:1843782 | 75 | 75 | 1179690324 | 1135674487 | 1124761084 | 1209401950 | 1843782 | SRX7652110 | SRS6081581 | SRA1034701 | GEO | University of Manchester | 2 | 0.93624 | 0.93698 | 0.08047 | 0.07907 | 0.69765 | 0.70061 | 0.50191 | 0.50441 | 74 | 75 | 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 |