Bioinformatics Seminar
Time:
Venue: Na
5 November 2019
NaSingle-cell transcriptome and V(D)J analysis for mammary carcinoma treated with different radiotherapy regimens
Yang LiaoWEHI Bioinformatics
Radiotherapy is one of the first-line treatments for cancer. Radiotherapy can be carried out in different regimens. However ; the molecular mechanisms underlying the difference in treatment effect from different regimens are poorly understood. In this study ; we used a mouse mammary carcinoma model to investigate the transcriptome changes ; cell population changes and clonotype changes with different regiments at the single-cell level. We had four mice treated with different regimens of irradiation ; including 20 Grays for once and 4 Grays in three continuous days. There were four other mice treated in the same way but without the irradiation as the control. We performed single-cell RNA sequencing and T-cell Receptor V(D)J sequencing by using the 10x Chromium platform on the cells from the tumour tissues of the mice.
In this talk ; I will present the design of our experiment ; and introduce the pipelines used for the analysis. I will talk about the dimensional reduction algorithm and the cell classification algorithm for cell clustering and annotation ; and the interactive program for manually marking the clusters on the tSNE plot. A few tSNE plots will be presented to show the clusters of the cells ; and the cell composition of each cluster will be revealed by overlaying the cell classification results with the tSNE plots. The two biological replicates of sample types will be compared to show their consistency in terms of cell compositions ; and the abundances of different cell types will be compared between regimens. I will lastly present the V(D)J clonotype analysis results ; and link the clonotype annotations with the scRNA-seq data ; revealing the enrichment of clonotypes in the clusters.