NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE149362 Query DataSets for GSE149362
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)
GSM4498613 T-cell_RNA_seq_rep1
GSM4498614 T-cell_RNA_seq_rep2
This SubSeries is part of SuperSeries:
GSE149363 CHANGE-seq reveals the genome-wide activity of CRISPR-Cas9

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE149362_RAW.tar 5.3 Mb (http)(custom) TAR (of TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap