NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE23762 Query DataSets for GSE23762
Status Public on Aug 25, 2010
Title Off-Target Analysis of Zinc Finger Nucleases
Organism Danio rerio
Experiment type Other
Genome binding/occupancy profiling by high throughput sequencing
Summary Zinc Finger Nucleases (ZFNs) facilitate precise editing of DNA enabling targeted genomic modifications in vivo. ZFNs have been employed to obtain genetically modified plants and animals, and cell-based therapies utilizing ZFNs are undergoing clinical trials. However, many ZFNs display dose-dependent toxicity presumably due to the generation of undesired double stranded breaks at off-target sites within the genome. To evaluate the parameters influencing the functional specificity of ZFNs, we compared the in vivo activity of ZFN variants targeting the zebrafish kdrl locus, which display both high on-target activity and dose-dependent toxicity. We evaluated their functional specificity by assessing lesion frequency at 141 potential off-target sites within the zebrafish genome using Illumina sequencing. Only a minority of these off-target sites displayed significant lesion frequency with kdrl ZFNs. Furthermore, we find that active off-target sites appear to be defined by the thermodynamics of zinc finger-DNA recognition. Surprisingly, we observed that the zinc finger protein specificity and the choice of the engineered dimerization domain of the FokI nuclease could independently influence the fidelity of these ZFNs. The results of this study have implications for the assessment of likely off-target sites within a genome and point to both ZFP-dependent and –independent mechanisms of potential improvement for engineering ZFNs with higher levels of precision.
 
Overall design Examined lesions at 141 off-target sites for various treatments of ZFNs and compare to the untreated sample
stage 1: raw read but missing quality values
stage 2: fastq files available from SRA
 
Contributor(s) Gupta A, Wolfe S
Citation(s) 20843781
Submission date Aug 23, 2010
Last update date May 15, 2019
Contact name Scot Wolfe
E-mail(s) scot.wolfe@umassmed.edu
Organization name UMass Medical School
Department MCCB
Street address 364 Plantation Street, LRB 619
City Worcester
State/province MA
ZIP/Postal code 01605
Country USA
 
Platforms (1)
GPL10164 Illumina Genome Analyzer (Danio rerio)
Samples (21)
GSM586305 Original ZFNs DD/RR 20pg monster stage_1_off_target_seq_barcode_AT
GSM586306 original ZFNs DD/RR 10pg monster stage_1_off_target_seq_barcode_CG
GSM586307 New ZFNs DD/RR 20pg monster stage_1_off_target_seq_barcode_CT
Relations
SRA SRP003361
BioProject PRJNA130845

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
GSE23762_RAW.tar 43.9 Mb (http)(custom) TAR (of TXT)
GSE23762_off_target_sites.txt.gz 27.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap