CRISPR References and Information
Addgene CRISPR Resources
- CRISPR Plasmids
- Addgene's collection of CRISPR plasmids.
- CRISPR Guide
- Addgene's guide to using CRISPR plasmids in your lab, from knockouts to pooled library screening.
- CRISPR eBook
- Addgene's downloadable eBook about all things CRISPR.
- Addgene CRISPR blogs
- CRISPR tips, FAQs, and news published on the Addgene blog.
- CRISPR Pooled Libraries
- Addgene's collection of CRISPR pooled libraries for large-scale functional screens. Available for knockout, activation, inhibition, and barcoding.
- CRISPR Kits
- Addgene's collection of CRISPR plasmid kits.
CRISPR Software
Sanger Indel Analysis
- ICE (Inference of CRISPR Edits)
- This open access tool from Synthego allows you to determine rates of CRISPR editing at a given locus. To use the tool, you'll need Sanger sequencing reads from PCR amplicons that cover your locus of interest and correspond to edited and non-edited cell populations. For more information, see the Hsiau et al. (2019) (Link opens in a new window).
Deep Sequencing Data Analysis
- CRISPResso
- CRISPResso2 is a robust and easy-to-use computational pipeline for the analysis of genome editing experiments. It enables rapid and intuitive interpretation of results produced by amplicon sequencing. The updated CRISPresso2 can analyze outcomes from cleaving nucleases (e.g. Cas9, Cas12a) and noncleaving nucleases (e.g. base editing). Developed by the Luca Pinello Lab (Link opens in a new window). For more details, see Clement et al. (2019) (Link opens in a new window).
- MAGeCK
- Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout (MAGeCK). This tool can identify positively or negatively selected sgRNAs, genes, or pathways. For use with genome-scale CRISPR-Cas9 knockout screens (or GeCKO) technology. Developed by the Xiaole Shirley Liu Lab. For more information, see Li et al. (2014) (Link opens in a new window).
- protoSpaceJAM
- protoSpaceJAM is an all-around platform for CRISPR knock-in design at scale. It uses an open-source algorithm to automate and optimize gRNA and HDR donor design. The current version supports SpCas9, SpCas9-VQR, and enAsCas12a Cas enzymes. Developed by the Manuel Leonetti Lab. For more information, see Peng et al. (2024) (Link opens in a new window).
gRNA Design
- DeepSpCas9(Link opens in a new window)
- A webtool that uses deep learning models for SpCas9 gRNA design and efficiency prediction. Developed by the Hyongbum Kim Lab.
- DeepBE(Link opens in a new window)
- A webtool that uses deep learning models for base editor gRNA design and efficiency prediction. Developed by the Hyongbum Kim Lab.
- DeepPrime(Link opens in a new window)
- A webtool that uses deep learning models for prime editor pegRNA design and efficiency prediction. Developed by the Hyongbum Kim Lab.
- GenET (Genome Editing Toolkit) (Link opens in a new window)
- A library of various python functions for the purpose of designing and evaluating experiments. Developed by the Hyongbum Kim Lab.
- Green Listed - a CRISPR Screen Tool (Link opens in a new window)
- Design gRNAs for custom CRISPR screens targeting a long or short list of genes provided by the user. Developed by the Fredrik Wermeling Lab. Read more about it on the Addgene blog.
- CRISPOR (Link opens in a new window)
- This tool helps design (10 different prediction scores), clone (primer design), and evaluate gRNAs, as well as predict off-targets, for CRISPR in 180+ genomes. Developed by the Jean-Paul Concordet Lab. For more information, see Haeussler et al. (2016) (Link opens in a new window). Also try CRISPOR batch(Link opens in a new window) for lentiviral screens.
- sgRNA Scorer 2.0 (Link opens in a new window)
- A tool that identifies putative target sites for S. pyogenes Cas9, S. aureus Cas9, S. thermophilus Cas9, N. meningitidis Cas9, or Cas12a from your input sequence or list of sequences. Developed by the George Church Lab and maintained by the Frederick National Laboratory at the National Cancer Institute.
- Cas-OFFinder (Link opens in a new window)
- Identifies gRNA target sequences from an input sequence and checks for off-target binding. Supports a range of Cas enzymes (Cas9 and Cas12) and organisms. Developed by the Jin-Soo Kim Lab.
- Cas-Designer (Link opens in a new window)
- Searches for targets that maximize knockout efficiency while having a a low probability of off-target effects. Cas-Designer integrates information from Cas-OFFinder and Microhomology predictor. Developed by the Jin-Soo Kim Lab.
- CRISPR-ERA: CRISPR-mediated editing, repression, and activation (Link opens in a new window)
- A sgRNA design tool for genome editing, as well as gene regulation (repression and activation). Genome support for bacteria (E. coli, B. subtilis), yeast (S. cerevisiae), worm (C. elegans), fruit fly, zebrafish, mouse, rat, and human. Developed by the Stanley Qi Lab.
- CCTop - CRISPR/Cas9 target online predictor (Link opens in a new window)
- Identifies candidate sgRNA target sites by off-target quality. Validated for gene inactivation, NHEJ, and HDR. Includes a wide range of reference genomes, including animals, plants, bacteria, fungi, protists, and viruses. Developed by the Joachim Wittbrodt and Juan L. Mateo (Link opens in a new window) Labs.
- ACEofBASEs (Link opens in a new window)
- Identification of sgRNA target sites and off-target evaluation for base edits using adenine (ABE) and cytosine (CBE) base editors. Includes a wide range of reference genomes, including animals, plants, bacteria, fungi, protists, and viruses. Developed by the Joachim Wittbrodt and Juan L. Mateo (Link opens in a new window) Labs.
- Off-Spotter: tool for CRISPR/Cas design (Link opens in a new window)
- Program for designing optimal gRNAs. Provides feedback on number of potential off-targets, target's genomic location, and genome annotation. Available genomes are human (hg19 & hg38), mouse (mm10), and yeast (strain w303). Developed by Venetia Pliatsika and Isidore Rigoutsos. See Pliatsika and Rigoutsos (2014) (Link opens in a new window) for more information.
- CRISPR MultiTargeter (Link opens in a new window)
- Can be used to identify novel gRNA target sites in a single gene, as well as a target site common to a set of similar sequences. Organisms include human, mouse, rat, chicken, frog, zebrafish, fly, worm, Japanese rice fish, maize, Arabidopsis, and rice. Proof-of-concept performed in zebrafish. Developed by the Jason Berman Lab.
- CRISPRdirect (Link opens in a new window)
- Identifies candidate gRNA target sequences in an input sequence, which can be an accession number, genomic location, pasted nucleotide sequence, or a sequence text file you upload. Currently supports a wide selection of organisms. From the Database Center for Life Science (DBCLS) in Japan. Developed by the Kumiko Ui-Tei Lab.
- CRISPick (Link opens in a new window)
- Ranks and picks candidate CRISPRko/a/i sgRNA sequences to maximize on-target activity for selected target(s). Uses human, mouse, and rat reference genomes. Hosted by the Broad GPP and developed by the John Doench, David Root, and Hyongbum Kim Labs.
- E-CRISPR (Link opens in a new window)
- Identifies gRNA target sequences from an input sequence and checks for off-target binding. Currently supports a wide range of organims. Developed by the Michael Boutros Lab.
- CasFinder: Flexible algorithm for identifying specific Cas9 targets in genomes (Link opens in a new window)
- A program that identifies gRNA target sequences from an input sequence, checks for off-target binding and can work for S. pyogenes, S. thermophilus, or N. meningitidis Cas9 PAMs. Currently supports: mouse and human. Developed by the George Church Lab.
- CRISPR Optimal Target Finder (Link opens in a new window)
- Identification of gRNA target sequences from an input sequence and checks for off-target binding. Currently supports over 20 model and non-model invertebrate species. Developed by the Kate O'Connor-Giles Lab.
General Resources
- CasPEDIA(Link opens in a new window)
- An encyclopedia of Class 2 CRISPR systems with wiki entries describing enzyme activity, experimental considerations, and more. CasPEDIA is a community resource created and maintained by the Jennifer Doudna Lab. Read more about it on the Addgene blog.
- CRISPRflydesign(Link opens in a new window)
- A collection of protocols, materials, and publications by members of the Division of Signaling and Functional Genomics at the German Cancer Research Center (DKFZ) in Heidelberg.
- CRISPR FAQ forum(Link opens in a new window)
- A Google groups forum started by the Feng Zhang Lab.
Protocols
| Lab(s) | Description | Plasmids in protocol | Download protocol |
|---|---|---|---|
| Addgene | CRISPR pooled library amplification | CRISPR pooled libraries | Protocol at Addgene |
| Church | gRNA design and cloning | gRNA cloning vector | PDF, 118 KB |
| Church | gRNA design and cloning for Cas9 orthologs | Cas9 plasmids | PDF, 107 KB |
| Chen and Wente | Zebrafish: gRNA cloning, in vitro transcription, injection | gRNA core; Cas9; optimized Cas9 | PDF, 66.8 KB |
| Fujii | gRNA design and cloning |
gRNA cloning vector
Retroviral vectors: neomycin (pSIR-neo), GFP (pSIR-GFP), DsRed (pSIR-DsRed-Express2), human CD2 (pSIR-hCD2) |
PDF, 108 KB |
| Fujii | iChIP/enChIP to purify genomic DNA | FLAG tagged dCas9 | PDF, 110 KB |
| Goldstein | Nematode: gRNA design and cloning | Cas9-sgRNA construct | PDF, 364 KB |
| Goldstein | Nematode: Injection and selection for Cas9-triggered homologous recombination | Cas9-sgRNA target construct; pMA122 (negative selection marker); pGH8 (neuronal co-injection marker); pCFJ104 (body wall muscle co-injection marker); pCFJ90 (pharyngeal co-injection marker); pDD104 (Cre recombinase) | PDF, 105 KB |
| Jaenisch | CRISPR plasmid summary for transcriptional activation |
dCas9 activators sgRNA dual expression:
pAC2,
pAC152,
pAC153,
pAC154;
pmax dCas9 activator expression: pAC91, pAC92, pAC93, pAC94, pAC95; dCas9 activator gateway donors: pAC84, pAC1, pAC147, pAC148, pAC149; Gateway destination: pAC90 |
PDF, 1.1 MB |
| Katic | Nematode: Cas9 and gRNA use | Cas9 (pIK86); gRNA empty backbone (pDR274) | PDF, 89 KB |
| Liu | Fly: gRNA cloning | pAc-sgRNA-Cas9 | PDF, 169 KB |
| Marraffini | Bacteria: pCas9 new spacer cloning | pCas9 | PDF, 129 KB |
| Marraffini | Bacteria: pCRISPR new spacer cloning | pCRISPR | PDF, 109 KB |
| Mendenhall and Myers | Mammalian: FLAG tagging endogenous proteins | pFETCh_Donor; additional HDR & gRNA plasmids are available for CREB1, ATF1, GABPA, and RAD21 | PDF, 138 KB |
| Musunuru | CRISPRs in human pluripotent stem cells | pCas9_GFP; gRNA empty vector | Protocol at StemBook |
| O'Connor-Giles | Fly: gRNA and ssODNs design and cloning; injection protocol | pU6-BbsI-chiRNA; phsp70-Cas9 | PDF, 109 KB |
| Orkin and Bauer | Protocol for Genomic Deletions in Mammalian Cell Lines | pSpCas9(BB) (pX330) | Protocol at Addgene |
| Parrott | NEBuilder Assembly of CRISPR vectors using ssDNA oligos | p201G Cas9; p201B Cas9; p201H Cas9; p201N Cas9; pUC gRNA Shuttle | PDF, 500 KB |
| Sabatini and Lander | gRNA cloning into pLX-sgRNA | pLX-sgRNA | PDF, 129 KB |
| Sontheimer | gRNA design and cloning | All-in-one plasmid containing expression cassette for NmCas9 and BsmBI site for cloning in gRNA: pSimpleII-U6-tracr-U6-BsmBI-NLS-NmCas9-HA-NLS(s) | PDF, 49 KB |
| Vosshall and Matthews(Link opens in a new window) | CRISPR/Cas9 reagent generation; gRNA design; HDR design; Deep sequencing |
Cas9:
pMLM3613
dsDNA donor plasmid backbones pSL1180-HR-PUbECFP & pSL1180polyUBdsRED |
PDF, 597 KB |
| Zhang | gRNA cloning |
CRISPR RNA array:
Cas9 (pX260) or Cas9 D10A (pX334);
tracrRNA: Cas9 (pX330) or Cas9 D10A (pX335) |
PDF, 255 KB |
| Zhang | sgRNA cloning |
lentiCRISPR v2
packaging plasmids: pVSVg, psPAX2; positive control: CMV-EGFP |
PDF, 2.4 MB |
| Zhang | GeCKO pooled library amplification |
1 vector system:
lentiCRISPR v2
2 vector system: lentiCas9-Blast and lentiGuide-Puro packaging plasmids: pVSVg, psPAX2 positive control: CMV-EGFP Pooled libraries are also available for human and mice |
PDF, 276 KB |
Content last reviewed on 9 June 2025.