التفاصيل البيبلوغرافية
| العنوان: |
GiRAFR improves gRNA detection and annotation in single-cell CRISPR screens. |
| المؤلفون: |
Yu, Qian, Van Minsel, Paulien, Galle, Eva, Thienpont, Bernard |
| المصدر: |
Communications Biology; 9/23/2023, Vol. 6 Issue 1, p1-10, 10p |
| مصطلحات موضوعية: |
CRISPRS, ANNOTATIONS, RNA sequencing, TRANSCRIPTOMES, HIGH throughput screening (Drug development) |
| مستخلص: |
Novel methods that combine single cell RNA-seq with CRISPR screens enable high-throughput characterization of transcriptional changes caused by genetic perturbations. Dedicated software is however lacking to annotate CRISPR guide RNA (gRNA) libraries and associate them with single cell transcriptomes. Here, we describe a CRISPR droplet sequencing (CROP-seq) dataset. During analysis, we observed that the most commonly used method fails to detect mutant gRNAs. We therefore developed a python tool to identify and characterize intact and mutant gRNAs, called GiRAFR. We show that mutant gRNAs are dysfunctional, and failure to detect and annotate them leads to an inflated estimate of the number of untransformed cells, attenuated downregulation of target genes, as well as an underestimated multiplet frequency. These findings are mirrored in publicly available datasets, where we find that up to 35% of cells are transduced with a mutant gRNA. Applying GiRAFR hence stands to improve the annotation and quality of single cell CRISPR screens. GiRAFR is a python tool that tackles especially the difficult detection of mutant gRNAs, improving annotation and quality of single-cell CRISPR screening. [ABSTRACT FROM AUTHOR] |
|
Copyright of Communications Biology is the property of Springer Nature and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.) |
| قاعدة البيانات: |
Complementary Index |
Full Text Finder