See wermelinglab.com/green-listed for more information.


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Videos How to use How to cite

To get you started you can try the following two demo alternatives:

Using the included GeCKOv2 Reference Library:

  1. Choose a GeCKOv2 library, for example the human A+B library.
  2. Copy the content of the demo_input_example.txt file (found here) and paste it in the input box. Alternatively input a number of genes of your interest. Make sure to press enter between each gene.
  3. Press the run button.

Using another Reference Library:

  1. Download the sample Reference Library demo_source_list.txt here.
  2. Upload the demo_source_list.txt under “Upload a Reference Library”.
  3. Set the Gene ID Column to 1 (as the first column of this reference library contains the Gene IDs).
  4. Set the gRNA Column to 2 (as the second column of this reference library contains the gRNA sequences).
  5. Download an example of a typical input query demo_input_example.txt here.
  6. Copy the content of the demo_input_example.txt file and paste it in the input box.
  7. Press the run button

Note:The sample Reference Library (demo_source_list.txt) file contains only a few genes and cannot be used to designing a functional library as the gRNA sequences and scores are random.

Reference Library


Detailed Information

Doench JG*, Fusi N*, Sullender M, Hegde M, Vaimberg EW, Donovan KF, Smith I, Tothova Z, Wilen C, Orchard R, Virgin HW, Listgarten J*, Root DE*. (Corresponding authors *)
Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9.
Nat Biotechnol. 2016 Feb;34(2):184-91. doi:10.1038/nbt.3437. Epub 2016 Jan 18.
Link


Upload a Reference Library | info

Format: Tab Delimited Text File.


Gene ID Column
gRNA Column
Rank Column (optional) Use Ranking
Input

Enter the genes to query. Press Enter after each one.

Allow for partial matches

Row count: 0

Options
Ranking Order:
Interval:
Limit to top:
5'
3'
5' Bases
3' Bases

Syntax: {Name}:{Sequence}

Example:

BsaI:ggtctc

BsmBI:cgtctc

Columns to use for the compact output:
Output file name:

This project was financially supported by the Swedish Research Council, the Swedish Foundation for Strategic Research, the Wenner-Gren Foundations, the Jeanssons Foundations, BILS (National Bioinformatics Infrastructure for Life Sciences), and the Karolinska Institutet.

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