This repo provides code for the analysis of MINECRAFT-seq data corresponding to Baglaenko, et al, biorxiv, 2024.
Contact: Yuriy Baglaenko [email protected], Michelle Curtis [email protected]
Contained in this repo are figures/analysis notebooks or scripts for each of the following experiments.
| Experiment | Figure # | Notebooks/Scripts | Notes |
|---|---|---|---|
| PTEN | Figure 1 | PTEN Notebook.ipynb | Joint Notebook with DQB1/FBXO11. No CRISPR editing |
| FBXO11 | Figure 2 | FBXO11_Run 1 Notebook.ipynb FBXO11_Run 2 - Joint Analysis.ipynb |
Run 1 and Run 2 merged and analyzed together. Alternative splicing to induce a knockout with CRISPR |
| DQB1 | Figure 2 | DQB1_Notebook.ipynb DQB1_Heatmap.ipynb |
CRISPR-Cas cutting and HDR in HLA-DQB1. |
| PTPRC | Figure 3 | PTPRC_Notebook.ipynb GSEA_PTPRC_IL2RA.ipynb Bootstrapping CD45 Data.ipynb |
Induction of ESC with CRISPR base editors |
| RPL8 | Figure 4 | RPL8_Notebook.ipynb | RPL8 eQTL CRISPR base editing |
| IL2RA | Figure 4 | IL2RA_Run 1.ipynb IL2RA_Run 2.ipynb IL2RA_Joint Analysis Notebook 2.ipynb GSEA_PTPRC_IL2RA.ipynb |
CRISPR editing of IL2RA variant in Th1 and Treg polarized naive CD4 T cells |
| PAX5 | Figure 5 | PAX5_genotype_analysis.R PAX5_RNA_analysis.R PAX5_RNA_glmNB.R PAX5_ADT_glmNB.R PAX5_genotyping.ipynb |
PAX5 multiplexed editing with CRIPSR base editors |
| Misc | Mixscape_Comparison_Latest.ipynb TotalAlignmentStats_Latest.ipynb Example Flow Cytometry Analysis.ipynb |
Extras | |
| Supplemental Note | Supplemental Note and Genotype Calling.ipynb | Fully replicatable genotyping analysis. Key files deposited in folder |
Sample data for the PTEN, FBXO11, and DQB1 experiments is located on Zenodo. GEO records are being generated to deposit count matrices with trimmed meta data.
File: DNA Filtering Functions has updated function on allele calling and genotyping of single cell along with extra utility functions.