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Series GSE130621 Query DataSets for GSE130621
Status Public on May 13, 2019
Title Mapping of microhomologies at CRISPR/Cas9 deletions
Organism Mus musculus
Experiment type Other
Summary The CRISPR system is widely used in genome editing for biomedical research. Here, using either dual paired Cas9D10A nickases or paired Cas9 nuclease we characterise unintended larger deletions at on-target sites that frequently evade common genotyping practices. We found that unintended larger deletions are prevalent at multiple distinct loci on different chromosomes, in cultured cells and mouse embryos alike. We observed a high frequency of microhomologies at larger deletion breakpoint junctions, suggesting the involvement of microhomology-mediated end joining in their generation. In populations of edited cells, the distribution of larger deletion sizes is dependent on proximity to sgRNAs and cannot be predicted by microhomology sequences alone.
 
Overall design Targeted amplicon sequencing at two sites targeted using CRISPR/Cas9
 
Contributor(s) Owens DD, de Bruijn M
Citation(s) 31127293
Submission date May 02, 2019
Last update date Jun 07, 2019
Contact name Dominic Owens
E-mail(s) dominic.owens@utoronto.ca
Organization name University of Oxford
Department MRC WIMM
Street address John Radcliffe Hospital
City Oxford
ZIP/Postal code OX3 9DS
Country United Kingdom
 
Platforms (1)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (4)
GSM3744938 E14 mESCs CRISPR/Cas9 Site 7 replicate 1
GSM3744939 E14 mESCs CRISPR/Cas9 Site 7 replicate 2
GSM3744940 E14 mESCs CRISPR/Cas9 Site 9 replicate 1
Relations
BioProject PRJNA540816
SRA SRP194544

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

Supplementary file Size Download File type/resource
GSE130621_RAW.tar 1000.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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