- GImap, a suite of bioinformatics tools for the analysis of pooled genetic screens and the construction of genetic interaction maps.
Based on the quantitative framework we developed: Kampmann M, Bassik MC and Weissman JS (2013) Integrated platform for genome-wide screening and construction of high-density genetic interaction maps in mammalian cells.Proceedings of the National Academy of Sciences 110(25): E2317-26. PMC3690882.
- CRISPRiaDesign, tools for CRISPRi and CRISPRa sgRNA prediction and machine learning.
Described in Horlbeck MA, Gilbert LA, Villalta JE, Adamson B, Pak RA, Chen Y, Fields AP, Park CY, Corn JE, Kampmann M, Weissman JS (2016) Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation. Elife. e19760
- CRISPulator, a discrete simulation tool for pooled genetic screens.
Described in Nagy T and Kampmann M (2017) CRISPulator: a discrete simulation tool for pooled genetic screens. BMC Bioinformatics 18:347
(replace extension with .stl after download)
Gel combs for size fractionation of genomic DNA from pooled screens
- Gel comb A (1 ladder well, 2 wide wells with narrow separator):
- Gel comb B (1 ladder well, 2 wide wells with wide separator):
- Gel comb C (1 ladder well, 3 wide wells with wide separators):
Fluorescent reporters for mammalian cells (lentiviral)
- pMK1163: Integrated stress response (ATF4-5'UTR-Venus-IRES-BFP)
shRNA expression plasmids (lentiviral)
- pMK1320: library expression, EF1A promoter, tagBFP
- pMK1209: library expression, SFFV promoter, tagBFP
- pMH19: library expression, EF1A promoter, mCherry (thanks to Max Horlbeck)
- pMH20: library expression, SFFV promoter, mCherry (thanks to Max Horlbeck)
- pMK1200: Double-shRNA vector, EF1A promoter, mCherry
- pMK1221: Double-shRNA vector, SFFV promoter, mCherry
- pMK1224: Double-shRNA vector, SFFV promoter, tagBFP
- pMK1201: Inducible shRNA expression vector (based on pInducer10, thanks to Steve Elledge)
CRISPRi/a plasmids (lentiviral)
- pMK1315: TRE3G promoter, KRAB-dCas9-P2A-neoR
- pMK1316: UBC promoter, KRAB-dCas9-P2A-mCherry
- pMK1321: UBC promoter, dCas9-BFP-KRAB
See also: Weissman lab CRISPRi/a plasmids.