My second research project done as part of my master degree was completed within the Robinson Lab under the supervision of Anthony Sonrel and Prof. Mark D. Robinson. During this project, we gathered data from five different publications that used CITE-seq technology and tried to define the best pipeline to analyse such data. This novel technology first described in 2017 represents a huge improvement in the field of single-cell sequencing, itself nominated as “Breakthrough of the Year” in 2018 by Science. The information collected during CITE-seq is twofold: the single-cell RNA sequencing (scRNA-seq) part tell us about the transcriptomics (i.e. which genes are actually expressed) and the antibody-derived tags (ADTs) tell us about the proteomics (i.e. which proteins are actually present) in the cell. We were particularly interested in the later. We investigated the potential and limitations of the ADTs and looked at some methods designed to analyse cells based simultaneously on their scRNA-seq and ADTs profile. Moreover, we designed a novel evaluation metrics which would help determining which normalization method worked best, based on ADTs with particular properties.
You can find more information and some illustrations in my report.
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