This repo provides code for the analysis of CRAFT-seq data corresponding to Baglaenko, et al, biorxiv, 2024.
Contact: Yuriy Baglaenko [email protected], Phoenix Mu [email protected]
Contained in this repo are notebooks or scripts for the analyses and figures included in the manuscript. We have also provided a tutorial notebook for the entire pipeline of analyzing data produced by CRAFT-Seq. This notebook utilizes data produced from the PTPRC experiment.
| 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 |
File: DNA Filtering Functions has updated function on allele calling and genotyping of single cell along with extra utility functions.
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, and dbGAP records will be made available for raw sequencing data. QCed data from the PTPRC experiment is also available on Zenodo and utilized in our tutorial notebook.