We used CRISPETa to design knockout libraries for a variety of genomic element classes in human and other genomes. These are principally composed of elements that cannot be targeted by traditional RNAi, either because their function is not thought to depend on RNA production (eg ultraconserved elements [UCEs]), or because their RNA product is too short (eg microRNAs). We also created a collection of random intergenic target regions in human as a reference and for use as negative controls in screening projects. This designs are made for DECKO (where at least one sgRNA must commence with "G") and non-DECKO requirements. All target sets and mask files were prepared and obtained in April 2016:
- Coding genes were obtained from the Gencode v19 annotation, filtered for the "protein_coding" biotype (Ref).
- CTCF binding sites for GM12878 cells were downloaded from ENCODE data hosted in the UCSC Browser (Ref)
- Enhancers were obtained from Vista (Ref).
- Pre-miRNAs were obtained from miRBASE (Ref).
- Disease-associated SNPs were obtained from the GWAS database (Ref).
- Ultraconserved regions were obtained from UCNEbase (Ref).
- To generate random intergenic locations, the entire span of all Gencode v19 genes (both coding and noncoding, introns and exons), in addition to 100 kb up- and downstream, were subtracted. Random locations were selected within the remaining regions.
Below you can look up some precomputed sets. For more information see CRISPETa publication (soon).
- DECKO design:
- General design:
- miRNA genes across species: