|
Status |
Public on Jan 30, 2023 |
Title |
Tg(mitfa:dgat1a) Rep3 |
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 |
SAMN13947600 |
SRA |
SRX7652108 |