About Us

CRISPR-Cas9 gene editing has provided enormous opportunities for functional genomics studies. Investigators can either carry our functional studies for given genes or perform genome-wide screening on specific phenotypes. This can be achieved in even single laboratories owing to the simplicity of the technique and publicly available resources.

The first step of CRISPR-Cas9 gene editing is designing efficient single guide RNAs (sgRNAs). There are already multiple commercial or academic websites offering tools to enable and populate the applications of CRISPR-Cas9 gene editing. In this website, we provide an online tool to design sgRNAs focusing on a specific subsets of genes that encode cell surface proteins. This tool can facilitate understanding of the interactions between cells and macromolecules (e.g. viruses, exosomes, proteins and nucleic acids) and discovery of novel drug targets (e.g. for infectious diseases and cancers) via a loss-of-function approach.

The current database options for “Search” function includes the information of the first-generation CRISPR surfaceome library (V1) [1] which defines cell surface proteins based on mass spectrometry information [2]. This library has been validated in a previous study that discovered a novel host factors of rhinoviruses [1]. The database options will continuously grow to include other versions of libraries (e.g. mouse cell surface proteins).

This website is constructed to facilitate both basic and translational research and it will be available, without any limitation, to the research community in a FREE mode FOR EVER. You can submit queries for specific genes via the website or download the whole datasets. Here are several notes for the sgRNA design:

1. The sgRNAs in human V1 library are designed to target protein-coding regions (NCBI CCDS data, released on 8-Sep-2016) [3].

2. Off-target scores are calculated according to an established algorithm developed by Feng Zhang’s laboratory [4].

3. On-target scores are calculated using Rule Set 2 [5] developed by Professor David Root’s group. Whenever possible, top 12 gRNAs are selected for each gene .

The CRISPR library and this website are designed, constructed and maintained by Dr. Jia Liu, Dr. Hong Mei in Dr. Jia Liu’s Laboratory of Macromolecule Drug Delivery and by Dr. Wei Wang and Dr. Lichun Jiang in the Biomedical Big Data platform at SIAIS.

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Enjoy gene editing with cell surface proteins!