This is a project which is currently making use of HPC facilities at Newcastle University. It is active.
For further information about this project, please contact:
Investigating the possibility utilising inherent mitochondrial DNA mutations for therapeutic targeting in colorectal cancer through a multi-omics approach.
Conduct transcriptomic and proteomic characterisation of novel colorectal cancer cell lines to investigate for any mtDNA mutation related metabolic rewiring and identify potential therapeutic targets. Unbiased metabolomics will be performed to investigate the different molecular outputs of glucose metabolism within the cell lines and identify potential therapeutic targets.
At a more basal level, investigate how metabolism is affected within my cell lines when grown in physiologicaly relevant conditions as opposed to traditional cell culture conditions through a multi-omic approach.
Linux based bioinformatics toolkits:
SAMtools - .bam file handing, viewing and interrogation of key aligned sequence file benchmarks.
BCFtools - .vcf file handling, normalisation and viewing of variant calls.
GATK mutect2 - variant calling, used for indel calls as part of my pipeline.
Mutserve - mitochondrial DNA specific variant caller, used for SNV calls as part of my pipeline.
Haplocheck - mitochondrial DNA sample contamination checker