CRISPR design statistics

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CRISPR design specifications


Unique identifier OMICS_06185
Name CRISPR design
Interface Web user interface
Restrictions to use None
Input data Target region seq (single and batched)
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Feng Zhang

Publication for CRISPR design

CRISPR design citations


Chromatin accessibility is associated with CRISPR Cas9 efficiency in the zebrafish (Danio rerio)

PLoS One
PMCID: 5912780
PMID: 29684067
DOI: 10.1371/journal.pone.0196238

[…] Target sequences () for sgRNA design were chosen using the online based CRISPR design tool (, ChopChop.V1 or V2 [,] or CRISPRscan []. Target site uniqueness was verified with the NCBI BLAST analysis against the zebrafish genome (GRCz10). sgRNAs were […]


Genome editing applications of CRISPR–Cas9 to promote in vitro studies of Alzheimer’s disease

PMCID: 5808714
PMID: 29445268
DOI: 10.2147/CIA.S155145

[…] can lead to disease, researchers need to perform experiments in cells that carry these exact mutations. shows the general workflow of CRISPR– Cas9-mediated gene knock-ins in cultured cells including CRISPR design (, sgRNA design (, cloning, delivery of the genomic alteration, validation of regeneration, s […]


Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein

PLoS Pathog
PMCID: 5738113
PMID: 29261807
DOI: 10.1371/journal.ppat.1006758

[…] CRISPR-Cas9 single guide RNAs (sgRNAs) for selected target genes were designed using the CRISPR Design Tool [], sgRNA Designer [] and E-CRISPR v4.2 [] online tools based on the target genome sequences obtained from Ensembl genome browser or merged Ensembl/Havana transcripts. Complementary […]


Structural basis for genome wide recognition of 5 bp GC motifs by SMAD transcription factors

Nat Commun
PMCID: 5727232
PMID: 29234012
DOI: 10.1038/s41467-017-02054-6
call_split See protocol

[…] sgRNAs targeting genomic regions of interest were designed using CRISPR Design Tool ( and synthesized by IDT, Inc. Single cells were sorted onto irradiated MEF feeder for increased viability through FACS 72 h post transfection. Mutant clones […]


Multimode drug inducible CRISPR/Cas9 devices for transcriptional activation and genome editing

Nucleic Acids Res
PMCID: 5861443
PMID: 29237052
DOI: 10.1093/nar/gkx1222

[…] d on prediction of high efficiency and low off-target effect by the computational analyses using the GPP web portal ( (,) and the CRISPR DESIGN web portal ( (). They are cloned into an optimized single chimeric guide RNA scaffold (A-U flip extension) () and experimentally examined for their potency using t […]


SNAIL1 mediated downregulation of FOXA proteins facilitates the inactivation of transcriptional enhancer elements at key epithelial genes in colorectal cancer cells

PLoS Genet
PMCID: 5714381
PMID: 29155818
DOI: 10.1371/journal.pgen.1007109

[…] Design of the gRNAs targeting different transcription factor binding sites in the EPHB3 enhancer and for the FOXA1 knockout was done with the CRISPR design tool developed by the Zhang lab ( []. The sequences of the different gRNAs targeting the EPHB3 enhancer are the following: FOX binding sites 5’-CTGGCTGGCTGTGTTTGTCC […]


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CRISPR design institution(s)
Broad Institute of MIT and Harvard, Cambridge, MA, USA; McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA

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