run_metadata: 56574
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 56574 | SRR10990707 | SRX7652109 | SRS6081570 | 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 Rep4 | GSM4290792 | source name:Tumour|strain:tp53m214K/m214k; mitfa / ; nras G12D|tissue:Melanoma|genotype:Tgmitfa:dgat1a | Tgmitfa:dgat1a Rep4 | 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 | GSM4290792 | GSM4290792: Tgmitfa:dgat1a Rep4; Danio rerio; RNA Seq | GSM4290792 | 1 | Tumours were removed and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols | GEO Accession:GSM4290792 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP246169 | DWDGAT4_S71_R1_001.fastq.gz DWDGAT4_S71_R2_001.fastq.gz | fastq fastq | 5316793956.0 | 35274411.0 | GSM4290792 r1 | 0:75.40 1:75.32 | A:1349226754;C:1296453723;G:1280760811;T:1386598717;N:3753951 | 75 | 75 | 1349226754 | 1296453723 | 1280760811 | 1386598717 | 3753951 | SRX7652109 | SRS6081570 | SRA1034701 | GEO | University of Manchester | 2 | 0.93236 | 0.9317 | 0.08292 | 0.08087 | 0.70646 | 0.70983 | 0.50314 | 0.51129 | 75 | 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 |