|
Status |
Public on Sep 22, 2020 |
Title |
CHANGE-seq reveals the genome-wide activity of CRISPR-Cas9 [RNA-seq] |
Organism |
Homo sapiens |
Experiment type |
Expression profiling by high throughput sequencing
|
Summary |
We recently developed CHANGE-seq (Circularization for High-throughput Analysis of Nuclease Genome-wide Effects by Sequencing), a fast, streamlined, Tn5 tagmentation-based assay for measuring the genome-wide activity of Cas9 in vitro that is easily scalable to many targets and samples. In this study, we directly compare CIRCLE-seq to CHANGE-seq and systematically evaluate Cas9 genome-wide activity on 110 targets across 13 therapeutically-relevant loci leveraging CHANGE-seq. We validate the sensitivity of CHANGE-seq for identifying sites of bona fide cellular off-target mutations using GUIDE-seq and sensitive targeted tag sequencing. Additionally, we sought to evaluate the impact of chromatin accessibility on cellular off-target activity by comparing CHANGE-seq with matched GUIDE-seq cellular off-target, chromatin, and transcriptional profiles generated from the same human primary T-cells.
|
|
|
Overall design |
T-cell_RNA_seq, two biological replicates
|
|
|
Contributor(s) |
Tsai S, Lazzarotto CR |
Citation(s) |
32541958 |
BioProject |
PRJNA625995 |
|
Submission date |
Apr 26, 2020 |
Last update date |
Sep 22, 2020 |
Contact name |
Shengdar Tsai |
E-mail(s) |
shengdar.tsai@stjude.org
|
Phone |
(901) 595-0407
|
Organization name |
St. Jude Children’s Research Hospital
|
Department |
Department of Hematology
|
Lab |
Shengdar Tsai
|
Street address |
262 Danny Thomas Pl, Memphis, TN
|
City |
Memphis |
State/province |
TN |
ZIP/Postal code |
38105 |
Country |
USA |
|
|
Platforms (1) |
GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
|
Samples (2) |
|
This SubSeries is part of SuperSeries: |
GSE149363 |
CHANGE-seq reveals the genome-wide activity of CRISPR-Cas9 |
|