README.md

RNA-Chip Hybridized Association Mapping Platform (RNA-CHAMP)

This repo stores dataset and code used in the manuscript:

Massively Parallel Profiling of RNA-targeting CRISPR-Cas13d

Hung-Che Kuo, Joshua Prupes, Chia-Wei Chou, Ilya J. Finkelstein doi: https://doi.org/10.1101/2023.03.27.534188

Image analysis pipeline

RNA-CHAMP is a protein-RNA interaction profiling platform based on a previously described CHAMP. Image align pipeline is identical to CHAMP and available at https://github.com/finkelsteinlab/CHAMP.

Fitted data use in the manuscript is available in the cas13d_binding_data directory. Linear model and machine learning model is available in the cas13d_modeling directory.

target # explaination

Target 1 & 2 were used in the PFS library. All PFS library has three randomized nucleotides on both ends of the target. Target 1 & 3 were used to generate partailly matched library (mismatches, insertions, and deletions).