Case Study Datasets
Three case studies below gives you a taste of different capabilities of our Annotation workflow. The datasets you will be exploring are:
PBMC 10K Multiome from 10X
Raw data can be directly downloaded from 10X webpage: https://support.10xgenomics.com/single-cell-multiome-atac-gex/datasets/1.0.0/pbmc_granulocyte_sorted_10k
scATAC of Triple Negative Breast Cancer (TNBC)
Citation: Zhang, Yuanyuan, Hongyan Chen, Hongnan Mo, Xueda Hu, Ranran Gao, Yahui Zhao, Baolin Liu, et al. 2021. “Single-Cell Analyses Reveal Key Immune Cell Subsets Associated with Response to PD-L1 Blockade in Triple-Negative Breast Cancer.” Cancer Cell 39 (12): 1578–93.e8.
We selected one scATAC sample (9,935 cells) collected from TNBC patients and applied the TIL reference atlas to annotate TIL cells from the TNBC query data
scATAC of two hold-out Basal cell carcinoma samples
Citation: Satpathy, Ansuman T et al. “Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion.” Nature biotechnology (2019)
We selected two BCC samples held out from the BCC TIL reference building as query data. One sample is pre-treatment and the other is post-treatment by immunotherapy. The original information of BCC cells is shown below:
