HEAP
HEAP stands for Halo-enhanced Ago2 pull down and was developed as a collaboration with Christina Leslie’s group. Thanks to a novel genetically engineered mouse model harboring a conditionally tagged Ago2 allele, it simplifies and streamlines the identification of Ago2/miRNA binding sites in cells and tissues. More details are available in the Molecular Cell paper.
All datasets generated as part of this work are available at GEO (GSE139349) following this link.
The open CLIPAnalyzer software developed by Yuri Prytikin in the Leslie lab is also available for download from bitbucket.
Detailed protocols and computational pipelines are available here.
GuideScan 1.0
GuideScan is a software to design single and paired gRNA CRISPR libraries we have developed in collaboration with Christina Leslie’s group, here at MSKCC. It is fully customizable and opensource. A companion website with precompiled SpCas9 and Cpf1 gRNA databases for the most commonly used organisms is also available.
More details are available in this Nature Biotechnology paper.
Psicoligomaker 3.0
This is a simple mac application we wrote that takes care of designing optimized shRNAs to be cloned in pSico and its derivatives. The user can modify the oligo design so that the shRNA can be cloned in any other expression plasmid as long as they are driven by a polIII promoter. While we and many other labs have found this software useful keep in mind that YMMW.
You can download pSicoligomaker 3.0 by clicking here, while pSico and its derivatives are available from Addgene . Source code for pSicoligomaker3 (entirely written in Swift) is available as a a git repository As it will be obvious to anyone reading the code, its author (Andrea), is NOT a professional programmer, so feel free to improve it and send us your feedback.
How to use pSicoligomaker3
The program is pretty intuitive to use. You can paste a sequence, load it from a disk (best if in fasta format), or directly import it from the Ensembl database. Once the sequence is loaded, click on the magnifying lens to identify the optimal target sites. Each site has a score from 1 to 10, with 10 being the best (you can filter the target site based on a minimum score using the popover button in the lower right corner). Select the target sequence(s) for which you want to design the oligos and click on “Design Oligos”. A new window will appear with the oligo pairs for each target sequence ready to be ordered from your favorite vendor (we use IDT). To change the loop sequence and the overhangs in the shRNAs click on “Oligo Settings” or go to “Preferences -> Oligo design Settings”.
Good luck with your experiments!
The Ventura Lab 