Quick start

This resource provides optimized guide RNAs to target transcripts in the human transcriptome, model organisms and viral RNA genomes.

Here are the steps to use the design tool:

Navigate to the desired species. For human transcript gRNA design, users can (optionally) access a list of all associated Ensembl transcript isoforms for a gene along with expression data for each isoform in different human cell lines by typing the desired gene in the table stored under the Lookup human transcript expression tab.
After finding the Ensembl transcript ID of the desired transcript, either click or type it in the search box on the upper left side.
Upon lookup, you can browse individual guide RNAs and download a graphical representation of guide RNAs or a table with all guide RNAs that target the transcript.

This online resource for the prediction Cas13d guide RNAs for target transcripts integrates guide RNA design rules from the following manuscripts:

Massively parallel Cas13 screens reveal principles for guide RNA design

Hans-Hermann Wessels, Alejandro Méndez-Mancilla, Xinyi Guo, Mateusz Legut, Zharko Daniloski, Neville E. Sanjana

Transcriptome-wide Cas13 guide RNA design for model organisms and viral RNA pathogens

Xinyi Guo, Jahan Rahman, Hans-Hermann Wessels, Alejandro Méndez-Mancilla, Daniel Haro, Xinru Chen, Neville E. Sanjana

* These authors contributed equally

This resource currently features:

Selection of perfect match guides for all human protein coding and non-coding genes, separted by transcript and mRNA sub-annotation categories (5'UTR, CDS, 3'UTR).
Integration of Cancer Cell Line Encyclopedia (CCLE) gene expression data for the selection by cell type specific expression level.
Selection of perfect match guides for protein coding and non-coding genes in the main model organism, separted by transcript and mRNA sub-annotation categories (5'UTR, CDS, 3'UTR).
Perfect match guides for SARS-CoV-2, MERS, H1N1 and HIV1 RNA virus genes

Please retrieve transcript isoform expression information directly from the CCLE repository if you don't find your cell line represented.

Release notes:

11.2020: v1.1 more user-friendly layout+search, interactive plots, multi-sequence/fasta custom grna design, off-target metrics
07.2020: v1.0.1 addition of RNA viruses.
06.2020: v1.0 guide RNA efficacy predictions for mRNA and ncRNA in human and model organisms.
05.2020: v0.3.1 addition of custom guide predictor.
12.2019: v0.3 model update with improved prediction accuracy. The model is now trained on four tiling screen data sets.
09.2019: v0.2 improved data structure to allow real-time start up. Adding improved visualizations and data download.
07.2019: v0.1 goes online

Sanjana Lab

Design custom gRNAs

To accurately predict local target site accessibility use sequences of > 80 nt length.

To limit run time when designing guides on webpage, please use target sequences of < 500 nt length. For greater length requirements, please use the 'upload multiple single-entry fasta files' option.

Please be patient while the gRNAs are being scored. (100nt ~10sec; 500nt ~ 30sec)

Select Input Type:

Paste single target

Upload one single-entry fasta file

Upload multiple single-entry fasta files (results e-mailed)

Enter target RNA sequence

Please note that the provided fasta file should only contain a single-entry. Otherwise, design results will only be provided for the first sequence in the file.

Select FASTA File for Upload.

Browse...

Please note that all provided fasta files should only contain a single-entry. Otherwise, design results will only be provided for the first sequence in each file.

Select FASTA File(s) for Upload. Performing guide design for more than 10 sequences should be done using command-line tool.

Browse...

Provide an e-mail to send results to:

Cas13 guide RNA predictions

Please use the search field for searching or rank the guide RNA predictions column-wise. Download predictions

Sanjana Lab

Lookup human transcript expression

Please use the Search fields to type in a gene symbol or Ensembl gene ID to retrieve its transcript isoforms and their expression in different human cell lines. Transcript expression data is given as transcripts per million (TPM)

Copy the transcript ID and paste it in the submission field in the next Design guide RNAs tab.

Sanjana Lab

Human gRNA design

GENCODE v19 (hg19)

Enter Ensembl transcript ID:

Find your transcript isoform of interest based on CCLE data in the previous tab Lookup transcript.

Cas13 guide RNA predictions along the target transcript

Cas13 guide RNA scores and quartiles are assigned according to the tiling screens used to predict guide efficiency. Download plot

Cas13 guide RNA predictions

Please use the search field for searching or rank the guide RNA predictions column-wise. Download table

Sanjana Lab

Select a model organism

M. musculus

GENCODE M24 (mm10)

Enter Ensembl transcript ID:

Cas13 guide RNA predictions along the target transcript

Cas13 guide RNA scores and quartiles are assigned according to the tiling screens used to predict guide efficiency. Download plot

Cas13 guide RNA predictions

Please use the search field for searching or rank the guide RNA predictions column-wise. Download table

D. rerio

Ensembl v99 (GRCz11)

Enter Ensembl transcript ID:

Cas13 guide RNA predictions along the target transcript

Cas13 guide RNA scores and quartiles are assigned according to the tiling screens used to predict guide efficiency. Download plot

Cas13 guide RNA predictions

Please use the search field for searching or rank the guide RNA predictions column-wise. Download table

D. melanogaster

Ensembl v99 (BDGP6)

Enter Ensembl transcript ID:

Cas13 guide RNA predictions along the target transcript

Cas13 guide RNA scores and quartiles are assigned according to the tiling screens used to predict guide efficiency. Download plot

Cas13 guide RNA predictions

Please use the search field for searching or rank the guide RNA predictions column-wise. Download table

C. elegans

Ensembl v99 (WBcel235)

Enter Ensembl transcript ID:

Cas13 guide RNA predictions along the target transcript

Cas13 guide RNA scores and quartiles are assigned according to the tiling screens used to predict guide efficiency. Download plot

Cas13 guide RNA predictions

Please use the search field for searching or rank the guide RNA predictions column-wise. Download table

A. thaliana

Ensembl Plants v46 (TAIR10)

Enter Ensembl transcript ID:

Cas13 guide RNA predictions along the target transcript

Cas13 guide RNA scores and quartiles are assigned according to the tiling screens used to predict guide efficiency. Download plot

Cas13 guide RNA predictions

Please use the search field for searching or rank the guide RNA predictions column-wise. Download table

Sanjana Lab

Select a virus

SARS-CoV-2

Enter gene name:

Cas13 guide RNA predictions along the target transcript

Cas13 guide RNA scores and quartiles are assigned according to the tiling screens used to predict guide efficiency. Download plot

Cas13 guide RNA predictions

Please use the search field for searching or rank the guide RNA predictions column-wise. Download table

MERS

Enter gene name:

Cas13 guide RNA predictions along the target transcript

Cas13 guide RNA scores and quartiles are assigned according to the tiling screens used to predict guide efficiency. Download plot

Cas13 guide RNA predictions

Please use the search field for searching or rank the guide RNA predictions column-wise. Download table

H1N1

Enter gene name:

Cas13 guide RNA predictions along the target transcript

Cas13 guide RNA scores and quartiles are assigned according to the tiling screens used to predict guide efficiency. Download plot

Cas13 guide RNA predictions

Please use the search field for searching or rank the guide RNA predictions column-wise. Download table

HIV1

Enter gene name:

Cas13 guide RNA predictions along the target transcript

Cas13 guide RNA scores and quartiles are assigned according to the tiling screens used to predict guide efficiency. Download plot

Cas13 guide RNA predictions

Please use the search field for searching or rank the guide RNA predictions column-wise. Download table

Sanjana Lab

For large-scale design of Cas13 gRNAs of your own, please refer to our Git archive which contains an installation guide and tutorial for custom reagent design. For supplementary code and analyses of the pre-computed data, please refer to to our other Git archive.

Sanjana Lab

Batch download

Download all designed mRNA/ncRNA guides for single species.

Organisms:

H. sapiens (hg19): mRNA ncRNA

M. musculus (mm10): mRNA ncRNA

D. rerio (GRCz11): mRNA ncRNA

D. melanogaster (BDGP6): mRNA ncRNA

C. elegans (WBcel235): mRNA ncRNA

A. thaliana (TAIR10): mRNA ncRNA

Viruses:

SARS-CoV-2 (NC_045512.2)

MERS (NC_019843.3)

H1N1 (NC_026431.1-NC_026438.1)

HIV1 (NC_001802.1)

Sanjana Lab

Thank you for using the Cas13 Design Resource.

All source code for our work is available on our Git archive. We also welcome feedback or questions: Email us at cas13@sanjanalab.org.

For those interested in designing other types of CRISPR reagents for stand-alone use or multiplexed approaches in conjunction with Cas13, please see some of our other online tools:

Prime Editing Design Tool

GUIDES

Sanjana Lab

Quick start

Here are the steps to use the design tool:

Massively parallel Cas13 screens reveal principles for guide RNA design

Hans-Hermann Wessels*, Alejandro Méndez-Mancilla*, Xinyi Guo, Mateusz Legut, Zharko Daniloski, Neville E. Sanjana

Transcriptome-wide Cas13 guide RNA design for model organisms and viral RNA pathogens

Xinyi Guo, Jahan Rahman, Hans-Hermann Wessels, Alejandro Méndez-Mancilla, Daniel Haro, Xinru Chen, Neville E. Sanjana

This resource currently features:

Please retrieve transcript isoform expression information directly from the CCLE repository if you don't find your cell line represented.

Release notes:

Design custom gRNAs

Please note that the provided fasta file should only contain a single-entry. Otherwise, design results will only be provided for the first sequence in the file.

Please note that all provided fasta files should only contain a single-entry. Otherwise, design results will only be provided for the first sequence in each file.

Cas13 guide RNA predictions

Lookup human transcript expression

Please use the Search fields to type in a gene symbol or Ensembl gene ID to retrieve its transcript isoforms and their expression in different human cell lines. Transcript expression data is given as transcripts per million (TPM)

Copy the transcript ID and paste it in the submission field in the next Design guide RNAs tab.

Human gRNA design

GENCODE v19 (hg19)

Cas13 guide RNA predictions along the target transcript

Cas13 guide RNA predictions

Select a model organism

M. musculus

GENCODE M24 (mm10)

Cas13 guide RNA predictions along the target transcript

Cas13 guide RNA predictions

D. rerio

Ensembl v99 (GRCz11)

Cas13 guide RNA predictions along the target transcript

Cas13 guide RNA predictions

D. melanogaster

Ensembl v99 (BDGP6)

Cas13 guide RNA predictions along the target transcript

Cas13 guide RNA predictions

C. elegans

Ensembl v99 (WBcel235)

Cas13 guide RNA predictions along the target transcript

Cas13 guide RNA predictions

A. thaliana

Ensembl Plants v46 (TAIR10)

Cas13 guide RNA predictions along the target transcript

Cas13 guide RNA predictions

Select a virus

SARS-CoV-2

Cas13 guide RNA predictions along the target transcript

Cas13 guide RNA predictions

MERS

Cas13 guide RNA predictions along the target transcript

Cas13 guide RNA predictions

H1N1

Cas13 guide RNA predictions along the target transcript

Cas13 guide RNA predictions

HIV1

Cas13 guide RNA predictions along the target transcript

Cas13 guide RNA predictions

For large-scale design of Cas13 gRNAs of your own, please refer to our Git archive which contains an installation guide and tutorial for custom reagent design. For supplementary code and analyses of the pre-computed data, please refer to to our other Git archive.

Thank you for using the Cas13 Design Resource.

All source code for our work is available on our Git archive. We also welcome feedback or questions: Email us at cas13@sanjanalab.org.

For those interested in designing other types of CRISPR reagents for stand-alone use or multiplexed approaches in conjunction with Cas13, please see some of our other online tools:

Prime Editing Design Tool

GUIDES

Hans-Hermann Wessels, Alejandro Méndez-Mancilla, Xinyi Guo, Mateusz Legut, Zharko Daniloski, Neville E. Sanjana