Genome Imaging & Editing

Multicolor CRISPR (Ma et al., PNAS 2015), CRISPR-Broccoli (Ma et al., J Cell Biol 2016), CRISPRainbow (Ma et al., Nat Biotechnol 2016), CRISPR-Sirius (Ma et al., Nat Methods 2018) and many other CRISPR image system require high-copy target loci. However, there are very few high-copy chromosome-specific loci in the human genome. This tool, CRISPRbar, is what we design to find the loci.
The UCSC Genome Browser is an on-line, and downloadable, genome browser hosted by the University of California, Santa Cruz (UCSC).[2][3][4] It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations.

PrimeDesign is a flexible and comprehensive design tool for prime editing. PrimeDesign can be utilized for the installation of substitution, insertion, and deletion edits, and is generalizable for both single and combinatorial edits. Given an edit of interest, PrimeDesign identifies all possible prime editing guide RNAs (pegRNAs) and nicking guide RNAs (ngRNAs) within a specified parameter range for the optimization of prime editing.

Juicebox.js allows users to zoom in and out of such datasets using an interface similar to Google Earth. Juicebox.js also has many features designed to facilitate data reproducibility and sharing. Furthermore, Juicebox.js encodes the exact state of the browser in a shareable URL. Creating a public browser for a new Hi-C dataset does not require coding and can be accomplished in under a minute. The web app also makes it possible to create interactive figures online that can complement or replace ordinary journal figures.

FISH Probes Design

Bioinformatically designed complex oligonucleotide probe sets for FISH. If you want to find probe forme Oligopaints database, you'd better read this.

Other Useful Tools

NCBI gene downloader:  When we are doing Genome editing or FISH probes designing, we need to download a specific region of genes from the NCBI or other database. However, it will waste your time to calculate the upstream position or the downstream position, especially you need to edit a lot of genes. With this script, you just input the location of desire gene and the base numbers of the up or downstream, then you will get the GeneBank file form NCBI. 

Read About It


CRISPRainbow and Genome Visualization
Visualizing Genomic Loci with CRISPR-Sirius
屏幕截图 2021-02-18 104305
A rapid sgRNA cloning protocol for CRISPRainbow