Project Planning

The overall goal of the GPP is to accelerate the field of functional genomics, the toolkit of experimental approaches for understanding gene function. To fulfill this mission, we partner with scientists in the Broad community and beyond on their biological question of interest, engaging in the project from conception to analysis to publication.

Our expertise includes inherent challenges, pitfalls, and optimization guidelines that are not always obvious - this technical information, and years of experience seeing common challenges across projects, often makes the difference between a good idea and a successful experiment. Continued engagement will also ensure that a project has access to cutting-edge tools and methodologies we develop far in advance of publication.

A typical collaboration using a pooled screening approach looks like this:

collaboration-flow

Reviewing our GPP Collaboration Guide and scheduling an introductory meeting with one or more GPP screening scientists is a good place to start. To aid in conceptualizing a screen, here we provide an overview of our most commonly-used reagents, but this is not an exhaustive list and further discussion is often helpful.

Inventoried Reagents

GPP maintains a collection of pooled CRISPR libraries across modalities - knockout, activation, and inhibition - as well as a human open reading frame (ORF) library:

Selecting a Genome-Wide Library
Guidance on genome-wide libraries and considerations across the numerous CRISPR modalities
Druggable CRISPR Libraries
Additional details for a suite of libraries targeting genes annotated as druggable from the Pharos project

A full list of existing pooled libraries: Browse existing libraries

Instructions for acquiring these reagents can be found here: Ordering Pooled Libraries

GPP also maintains individual (arrayed) reagents that can be provided as bacterial streaks and/or plasmid DNA and/or lentivirus:

sgRNAs
Largely for CRISPR knockout
shRNAs
Our collection of RNAi reagents
ORFs
Human Open Reading Frames

Customized Reagents

GPP can also generate customized libraries, and then clone those libraries into a wide variety of existing vectors, which can be browsed using dimgarF, or a new vector can be designed using Fragmid:

Designing a Pooled Library with CRISPick
Supports multiple Cas enzymes and modalities.
Designing a Multi-Guide Cas12a Library
For a combinatorial library, that is, perturbing two genes at the same time in the same cell, we recommend Cas12a.
Designing a Base Editor Library with Beagle
For studying genes of interest at near-amino-acid-level resolution via base editor-directed endogenous mutagenesis.
Screening with Deep Mutational Scanning
Deep Mutational Scanning (DMS) technology enables high resolution interrogation of a protein of interest by probing every possible amino acid substitution at every position. In a DMS screen, a library of cDNAs encoding the protein variants is synthesized, incorporated into an expression cassette, and ectopically expressed.

Additional information on ordering a customized library is found here: Order custom sgRNA pooled libraries.

Custom cloning of individual (arrayed) reagents in 96-well plate format is also available.