Developments taking place in the CGEBM
Single cell sequencing with 10x Genomics and CGEBM
Wednesday 27th March, IMS Level 7 conference room from 14:00 – 16:00
Come and learn about this exciting new technology and how it can add real impact to your research at a free series of short seminars by 10x Genomics and by the research team we have been collaborating with during development.
Chromium single cell gene expression technology allows a comprehensive, scalable solution for characterisation of cells, including in complex heterogeneous populations, and gene expression profiling of hundreds to tens of thousands of cells.
CGEBM now have the capability to carry out single cell expression projects utilising the latest 10x Genomics Chromium technology. After a successful trial period in collaboration with research groups at the IMS, this capability as well as dedicated bioinformatics analysis, is now being rolled out to the University research community.
Dr Micheal Day – 10x Genomics: Single cell gene expression profiling, Immune profiling, CNV detection and ATAC-seq for epigenomics (Chromatin accessibility at single cell resolution)
Dr Fraser Collins – University of Aberdeen: Stem cell profiling in Mice
The meeting is free but registration is required HERE.
The CGEBM Bioinformatics team are now offering support for analysis of proteomics data sets. Raw data sets are processed and proteins quantified using the MaxQuant software. Differential protein abundance can then be statistically computed to identify both individual proteins, and functional pathways, of interest. Analysis pipelines are comparable to those used for RNA sequencing analysis, allowing for easier correlation between the two data types if collected within the same experiment. The CGEBM team, with the HPC IT team, have established the tools to carry out this analysis using the UoA High Performance Compute Cluster, Maxwell, allowing for much faster analysis times compared to analysis on a standard PC.
Oxford Nanopore Technology - MinIon
Long read sequencing using Oxford Nanopore MinIon is now established in CGEBM. Ultra-long read lengths are possible (hundreds of kb) with over 10 Gb DNA sequence data generated on each flowcell.
CGEBM have expertise in preparing samples and analysing MinIon data and have used this technology to improve genome assemblies, including closing bacterial genomes and eukaryotic chromosomes with a number of research groups at UoA. Additional applications for this technology include detection of structural variation, fusion transcripts, haplotype phasing, direct DNA/ RNA sequencing. Our bioinformatics team have dedicated workflows to analyse your generated data and CGEBM have recently added a MinIT dedicated GPU for added speed and efficiency of base-calling and data handling for ONT data.