Code for generating figures and analyzing amplicon sequencing of human mRNA and reporter mRNA targeted with type III-A CRISPR complex from Streptococcus thermophiles
Authors/Creators
- 1. Montana State University Bozeman
- 2. Montana State University
Description
This dataset contains code for analyzing amplicon sequencing data and generating figures in the manuscript by Anna Nemudraia, Artem Nemudryi, and Blake Wiedenheft (2024), "Repair of CRISPR-guided RNA breaks enables site-specific RNA excision in human cells."
Amplicon sequencing data has been deposited to NCBI Sequence Read Archive (SRA) under BioProject PRJNA1099688. The description of read files deposited to SRA can be found in the spreadsheet ./code_for_sequencing_data_analysis/SRA_read_files_description.xlsx
The code for analyzing amplicon sequencing data can be found in the archive "code_for_sequencing_data_analysis.tar.gz." Output files from this analysis were used to generate figures. Figures were generated using the ggplot2 package in R and finalized in CorelDRAW.
Code for generating figures can be found in the archive "code_for_generating_figures.tar.gz".
Any questions or requests regarding the data or the code should be addressed to Dr. Artem Nemudryi at artem.nemudryi@gmail.com.
Files
dataset_description.txt
Files
(8.2 GB)
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md5:def1b4144470daa9c99a234895ac9693
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Additional details
Funding
- National Institute of Allergy and Infectious Diseases
- CRISPR-based editing of RNA and cellular mechanisms that govern RNA repair 5K99AI171893-02
- National Institute of General Medical Sciences
- Structural and functional understanding of bacterial defense and viral counter defense 5R35GM134867-04
- U.S. National Science Foundation
- CRISPR-based engineering of RNA 2331325