Datasets

miR-17~92 expression profiles

Description: To understand the regulatory potential of individual miRNA families encoded by the miR-17~92 cluster we have generated a set of mouse models carrying targeted deletions of one or multiple components of the miR-17~92 polycistronic gene. The phenotypic characterization of these animals is described in our 2015 Nat. Genetics paper, and the expression profiles microdissected tissues from mid-gestation (E9.5) embryos (3 tissues; 8 mouse strains; 3 biological replicates) can be found at Gene Expression Omnibus (GEO).

Reference: Han, Vidigal, Mu et al, Nat. Genetics 2015

GEO Accession number: GSE63813

Plasmids

Cloning of paired gRNA libraries

Description: We have developed an experimental approach that allows the cloning of CRISPR libraries carrying pairs of gRNAs starting from short oligonucleotides. This protocol requires Donor plasmids that we have made freely available through Addgene and that carry one of 3 versions of the U6 promoter.

Reference: Vidigal et al, Nat. Comm 2015

Addgene numbers:  #69351 (pDonor_sU6), #69312 (pDonor_hU6), #69350 (pDonor_mU6)

Software

Guidescan CRISPR software

Description: We have developed fully customizable software for CRISPR database construction and batch design of single or paired gRNA libraries. Guidescan employs a Trie data structure to accurately enumerate potential off-target sites for gRNAs in the database. Our work shows that this approach is significantly superior to the short-read aligners used by competitor tools, which consistently fail to identify all mismatch neighbors and as a consequence yield highly promiscuous gRNAs.

Reference: Perez, Pritykin, Vidigal, et al, Nat Biotech 2017

website: http://guidescan.com/

source code: go to our bitbucket page.