|
| Status |
Public on Jan 30, 2023 |
| Title |
Tg(mitfa:dgat1a) Rep5 |
| Sample type |
SRA |
| |
|
| Source name |
Tumour
|
| Organism |
Danio rerio |
| Characteristics |
strain: tp53m214K/m214k; mitfa-/-; nras G12D
tissue: Melanoma
genotype: Tg(mitfa:dgat1a)
|
| Growth protocol |
Age matched tumours were harvested at 10-12 weeks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tumours were removed and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
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
|
| |
|
| Submission date |
Jan 30, 2020 |
| Last update date |
Jan 30, 2023 |
| Contact name |
Adam Hurlstone |
| E-mail(s) |
adam.hurlstone@manchester.ac.uk
|
| Organization name |
University of Manchester
|
| Street address |
Michael Smith Building
|
| City |
Manchester |
| ZIP/Postal code |
M13 9PT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21741 |
| Series (1) |
| GSE144555 |
DGAT1 is a bona fide oncogene stimulating cell growth and suppressing oxidative stress while enabling fatty acid accumulation |
|
| Relations |
| BioSample |
SAMN13947597 |
| SRA |
SRX7652110 |
