Please find our protocols on protocols.io:
Please request our plasmids through the Kampmann Lab page on Addgene.
- MAGeCK-iNC, a pipeline for the analysis of pooled genetic screens.
Ruilin Tian, Kampmann Lab (2019)
- 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
- 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.
- iNeuron-RNA-Seq, visualization of gene expression during Ngn2-driven neuronal differentiation from human iPSCs
Connor Ludwig, Kampmann Lab (2017).
- NCBI GEO gene expression data sets related to our publications:
- Tian el al (2019) Neuron: GSE124703
- Datasets related to next-generation shRNA libraries described in Kampmann et al (2015) PNAS
(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):