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The Molecular Biology Team hosts the Botnar Sequencing Small Research Facility, which provides Next Generation Sequencing via an Illumina NextSeq 500. Complementing this, the group has expertise in library preparation for RNAseq, ChIPseq and ATACseq, as well as bespoke assay development, for batch sizes up to 96 samples.

Molecular biology oppermann group

In close cooperation with the Computational Biology Team, these techniques have been used to explore many of the group’s research interests, including iPSC and mesenchymal stem cell differentiation, somatic cell reprogramming, pathomechanisms of uterine fibroids, drug response of bone and mesenchymal cancers and the epigenetics of inflammatory diseases.

 

Single cell sequencing has become a focus of the group, with cell sorting capabilities provided by a Sony SH800 FACS and single cell encapsulation for Drop-seq using the Nadia Innovate System.  Using this powerful technique the group has been able to identify distinct cellular subtypes within populations previously thought of as homogeneous and monitor changes to lymphocyte populations following drug exposure.

 

The group makes extensive use of various knockdown technologies including siRNAs, LNAs, lentiviral shRNAs and lentiviral CRISPRi/a and maintains a comprehensive collection of small molecule inhibitors targeting proteins involved in epigenetic processes.  Custom pooled lentiviral shRNA or CRISPR libraries targeting >400 epigenetic targets in combination with NGS allows the rapid identification of key epigenetic processes.

 

Plasmid cloning supports many of the projects within the group as well as the activities of the Structural Biology Team.  The group also heavily utilises immunohistochemistry, particularly for the validation of putative targets identified by systems biology approaches.

 

The Oppermann Molecular Biology Group collaborates widely within the Department, across the University of Oxford, nationally and internationally to provide access to the groups capabilities.

Molecular Biology Team

Key Technologies

Next Generation Sequencing 

RNAseq

ChIPseq

ATACseq

Single cell sequencing 

Drop-seq 

Lentiviral CRISPR and  shRNAs