ProjecTILs case studies
We will be posting here interesting/instructive case studies of single-cell data analysis using ProjecTILs. Read the notebooks linked below, or get the source code to run it on your machine from the GitHub repository
1. MC38 TILs with clonotype analysis
In this case study, we build an integrated scRNA-seq analysis workflow to interpret the transcriptional (scRNA-seq) and clonal structure (scTCR-seq) of tumor-infiltrating T cells in MC38 colon adenocarcinoma.
2. Project human data on mouse TIL atlas
Exploiting the ortholog mapping functionality of ProjecTILs, we project scRNA-seq from melanoma patients (Sade-Feldman, 2018) onto a mouse reference atlas, to interpret T cell phenotype differences between responders and non-responders to checkpoint blockade therapy.
3. T cell diversity across multiple tissues
Apply ProjecTILs to investigate transcriptional profiles of CD8 T cells in chronic infection from six different tissues.
4. Exhausted CD8 T cells are associated with ICB responsiveness in breast cancer
Re-analysis of the dataset by Bassez et al. Nat Med (2020) of breast cancer patients treated with anti-PD-1 therapy
5. Memory phenotypes of CD4+ T cells after acute infection
A case study of projection of virus-specific CD4+ T cells in late acute infection.
6. Detecting novel/unrepresented cell states
Projection of tumor-specific T cells on a viral reference, illustrating how one can interpret subtypes not represented in the reference.
7. Effect of anti-PD-L1 therapy on CD4+ T cells
Analysing the transcriptional phenotype of CD4+ T cells in chronic infection after treatment with an anti-PD-L1 antibody.
8. Exploring dendritic cell diversity in human spleen
Projection of human DCs from spleen from the study of Brown et al. Cell (2019)