Green Listed

Green Listed is a tool facilitating the rapid design of custom CRISPR screens. It is used to mine publicly available source lists/reference libraries of gRNAs (see examples below) to design custom libraries targeting genes specified by the user, such as all kinases or all genes up-regulated in an RNAseq experiment.

Green Listed can be accessed through “greenlisted.cmm.ki.se” (here).

The publication: Green Listed – A CRISPR Screen Tool. Sudeepta Kumar Panda, Sanjay V. Boddul, Guillermina Yanek Jiménez-Andrade, Long Jiang, Zsolt Kasza, Luciano Fernandez-Ricaud, Fredrik Wermeling. Bioinformatics, 22 December 2016, doi: 10.1093/bioinformatics/btw739. Link

Green listed is only to be used for projects adhering to consensus ethical guidelines.

Several videos describing different parts of the software can be found through our youtube chanel:

Full genomic reference libraries of gRNAs can be found for example in the following excellent publications. They are (intended to be) sorted in reversed chronological order and contains both regular KO libraries, as well as repression and activation libraries. Please cite publications if you use the library:

  1. Gene Essentiality Profiling Reveals Gene Networks and Synthetic Lethal Interactions with Oncogenic Ras. Wang T et al. Cell. 2017. link
  2. A CRISPR Dropout Screen Identifies Genetic Vulnerabilities and Therapeutic targets in Acute Myeloid Leukemia. Tzelepis et al. Cell Reports 2016. link
  3. Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation. Horlbeck et al. eLife 2016. link
  4. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Doench et al. Nature Biotechnology 2016. link
  5. Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach. Chari et al. Nature Methods 2015. link
  6. High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities. Hart et al. Cell 2015. link
  7. Identification and characterization of essential genes in the human genome. Wang et al. Science 2015. link
  8. A CRISPR-Based Screen Identifies Genes Essential for West-Nile-Virus-Induced Cell Death. Ma et al. Cell Reports 2015. link
  9. Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Konermann et al. Nature 2015. link
  10. Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation. Gilbert et al. Cell 2014. link
  11. Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library. Koike-Yusa et al. Nature Biotechnology 2014. link
  12. Improved vectors and genome-wide libraries for CRISPR screening. Sanjana et al. Nature Methods 2014. link
  13. RNA-Guided Human Genome Engineering via Cas9. Mali et al. Science 2013. link

Several of the libraries can be accessed through addgene (link) by clicking the links to the libraries in the end of page.

Please let me know if there is any missed publication in this list. Note that suggested full genomic gRNA libraries, listed here, should be available thorough the publication. I’m sorry for not finding them earlier.