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Pooled Libraries

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In addition to the 151,291 plasmids in Addgene's repository, depositors have shared 351 pooled libraries. To help you find what you're looking for, we've gathered our pooled plasmid libraries on one page.

A pooled library is a set of plasmids all built with the same backbone and only differing in a small region. Pooled libraries are normally supplied as a single tube with all the plasmids in the library mixed together. The number of unique plasmids in a pooled library can range from a few hundred to millions. There are several different types of pooled libraries, including cDNA, shRNA, barcoding, phage display, and gRNA libraries.

Read our Pooled Library Guide for more information about:

  • Library amplification
  • Types of pooled library screens
  • Next-generation sequencing (NGS)

Barcoding Libraries

Barcoded libraries contain very large numbers of unique barcodes used to mark individual cells. These barcodes will then be inherited by any daughter cells, making barcoded libraries ideal for lineage tracing. These libraries are also commonly used to monitor the dynamics of heterogeneous tumors.

Library ID Lentiviral Generation PI Description
pMuSIC pool v1.0 227193 n/a Birtwistle Fluorescent barcoding library with 153 unique fluorescent protein barcodes made from 2-way combinations of 18 individual fluorescent proteins.
LARRY Barcode Library Version 1 140024 3rd Camargo Lentiviral barcoding library for reconstructing transcriptional trajectories in differentiating cell populations.
PolyA Barcode Library 211610 Retroviral Chen Retroviral barcoding library for capturing the transcriptome and cell identities.
SPLINTR Pooled Libraries 179774
179775
179776		 3rd Dawson Lentiviral barcoding libraries for tracing clonal lineages using bulk and single-cell readouts.
Human Genome-wide Intron Tagging Libraries 216133
216134		 3rd Kubicek Library of intron-targeting sgRNAs for pooled tagging of proteins with GFP or other protein tags at their endogenous genomic locus using an intron tagging approach.
macsGESTALT Library 178943 N/A Lengner PiggyBac barcoding library for inducible lineage recording system.
Moffat Lab - Barcode Libraries 179851
179852		 3rd Moffat Lentiviral barcoding library with Puromycin and ZsGreen markers.
CellTag Barcode Library 115643
115644
115645
206045		 3rd Morris Lentiviral barcoding libraries used to combinatorially index cells for single-cell analysis of clonal dynamics.
STICR Library 180483
186334
186335		 3rd Nowakowski Lentiviral barcoding libraries for labeling a starting cell population and for clonal lineage/fate tracing.
Watermelon Library 155257 3rd Regev and Brugge Lentiviral barcoding library for simultaneous tracing of clonal lineages as well as the transcriptional and proliferative state of each cell in the population.
Single-cell quantitative expression reporters (scQers) Libraries 194097
194098
217420
217421
217422
217423
217424
1000000239		 Shendure Libraries for integrating your regulatory elements of interest for single-cell expression reporter assays.
ClonTracer Library 67267 (2.5µg)

69830 (7.5µg)		 3rd Stegmeier Lentiviral library used to conduct positive selection screens for cancer cells resistant to a given treatment. This blog post about the ClonTracer Library describes how the library was used to identify pools cells that were resistant pre-treatment.
Perturb-seq Guide Barcodes (GBC) Library 85968 3rd Weissman Barcode library for cloning gRNA sublibraries for single cell CRISPR analysis.
Target Site Library (PCT48) 170392 3rd Weissman Library backbone contains three Cas9-targetable spacer sequences with a random 14-bp barcode.

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cDNA Libraries

cDNA libraries are created from an organism’s actively transcribed mRNA, as opposed to genomic libraries, which are created from genomic DNA. Since cDNA libraries lack introns and other nontranscribed sequences, they are smaller and easier to use than genomic libraries, but they don’t contain as much regulatory information. To make a cDNA library, cDNA is synthesized, then ligated to adapters, and cloned into a given vector.

Library ID Species PI Description
Monosiga cDNA Library
Discontinued		 25864 Monosiga brevicollis Carroll and King Bacterial expression cDNA library created from the choanoflagellate Monosiga brevicollis.
Proterospongia cDNA library
Discontinued		 25716 Proterospongia King Bacterial expression cDNA library created from Proterospongia, also referred to as Salpingoeca.
S. rosetta Col- cDNA amplified library 62843 Salpingoeca rosetta King Created from the choanoflagellate Salpingoeca rosetta. Col+ refers to DNA isolated from bacteria cultured with the colony-inducing bacteria Algoriphagus machipongonensis.
S. rosetta Col+ cDNA amplified library 62844 Salpingoeca rosetta King Created from the choanoflagellate Salpingoeca rosetta. The Col- library was created from S. rosetta cultured without bacteria.

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CRISPR Libraries

CRISPR knockout libraries are commonly used for loss-of-function screens. In these screens, multiple gRNAs are present for each gene targeted by the library. The effects of CRISPR knockout are not easily reversible, as the targeted gene sequence is mutated by CRISPR. Other CRISPR screens include CRISPR activation (CRISPRa) and inhibition (CRISPRi) screens. These screens use catalytically dead dCas9 to inhibit or activate given genes without direct genomic modification, and the effects are therefore reversible.

When choosing your library, please be aware that some of the library vectors contain Cas9 (1 plasmid system), while others require co-infection with Cas9-expressing virus or use in cells expressing Cas9 (2 plasmid system).

Knockout

CRISPR knockout libraries are designed to create insertions or deletions in targeted genes across the genome, rendering them nonfunctional. Libraries are designed to target throughout the genome unless specified. To limit false positives or false negatives, each library contains multiple gRNAs for each gene targeted by the library. Each library also contains non-targeting control gRNAs.

Library ID Species Lentiviral Generation PI Genes Targeted gRNAs per gene Total gRNAs

Bassik Human CRISPR Knockout Library

This lentiviral genome-scale CRISPR library targets all ~20,500 protein-coding genes in the human genome. The library is divided into 9 sublibraries defined by biological categories of genes, each with their own negative controls.

 101926 — 101934 Human 3rd Bassik Varies (~20,500 in total) ~10 Varies

Bassik Mouse CRISPR Knockout Library

This lentiviral genome-scale CRISPR library targets all ~23,000 protein-coding genes in the mouse genome. The library is divided into 10 sublibraries defined by biological categories, and each of these is then split randomly by gene into two sublibraries (A and B).

 1000000121 — 1000000130 Mouse 3rd Bassik Varies (~23,000 in total) ~10 Varies

Berger Lab Human Paralog Knockout Library (pgPEN)

This lentiviral CRISPR library induces knockouts of paralogous gene pairs. Plasmids express a pair of guide RNAs targeting either individual genes or a pair of paralogs.

 171172 Human 3rd Berger 1,030 gene pairs 8 pgRNA/gene
16 pgRNA/pair		 33,170

Human Epigenetic Knockout Library

This lentiviral CRISPR knockout library targets human epigenetic genes.

162256 Human 3rd Birsoy 2,508 8 20,051

Mouse CRISPR Metabolic Gene Knockout Library

This lentiviral CRISPR library targets mouse metabolic genes and includes most metabolic enzymes and transporters.

160129 Mouse 3rd Birsoy 2,865 8 22,909

Mouse Lipid and Sphingolipid Metabolism Knockout Libraries

These lentiviral CRISPR libraries target mouse lipid and sphingolipid metabolic genes and can be used to find lipid metabolic vulnerabilities in mouse cells.

206248
206249		 Mouse 3rd Birsoy 295
59		 7
10		 2,105
630

Bonifacino Lab Human ubiquitination-related proteins CRISPR KO library

Lentiviral CRISPR library targets human ubiquitation-related proteins and deubiquitinating enzymes.

 174592 Human 3rd Bonifacino 660 6-25 11,108

Borodina Yeast Transporter Libraries

Yeast CRISPR knockout libraries targeting transporter genes. Five sub-pools target different groups of transporters and a sixth library targets all 361 genes.

153101-153106 Yeast N/A Borodina Varies 1 Varies

Bradley Human CRISPR Poison Exon Knockout Library

This lentiviral CRISPR library targets 3' splice sites with paired guide RNAs. It induces skipping of poison cassette exons and corresponding upstream constitutive exons. Directly compare loss of a constitutive coding exon with loss of a poison exon.

 138084 Human 3rd Bradley 963 exons ~9 pairs/exon 9,508

Mouse CRISPR Proximal Poly(A) Site Knockout Library

The mouse pKO library targets proximal poly(A) signal sequences in genes identified to be differentially polyadenylated in the mouse B16-F10 melanoma system.

 190744 Mouse 3rd Bradley 144 proximal poly(A) sites 8-10 pgRNAs 1,718

Mouse Chromatin Regulator Library

CRISPR KO library targeting a comprehensive set of mouse genes with annotated function as chromatin regulators.

 200011 Mouse 3rd

Griffin, Manguso, and Bernstein

 936 6 ~5616

DNA Damage Response MKOv4 Library

Lentiviral CRISPR knockout library targets human DNA damage response and DNA repair genes.

 140219 Human 3rd J. Chen 365 10 4,530

Murine Cell Surface Protein Knockout (McspKO) Library

Lentiviral CRISPR knockout library targets mouse cell surface genes.

 200445 Mouse 3rd J. Chen 1,157 3-4 5,001

Mouse Tumor Suppressor Gene CRISPR Knockout Library

This AAV CRISPR knockout library targets mouse tumor suppressor genes (TSG). Each plasmid carries one TSG-targeting sgRNA in addition to one p53-targeting sgRNA. Because the backbone expresses both luciferase and Cre, the library can be used to interrogate tumorigenesis in vivo using a mouse line expressing Cre-dependent Cas9.

 113584 EFS backbone
113585 TBG backbone		 Mouse N/A S. Chen 56 ~4 286

Mouse Metastasis CRISPR-Cpf1(Cas12a) Double Knockout Library

This lentiviral library is a CRISPR-Cpf1/Cas12a double knockout library. There are 26 genes targeted in the library, chosen from analysis of human metastasis cohorts and a prior mouse metastasis CRISPR screen. It can be used to interrogate the genetic interactions driving metastasis.

 123361 Mouse 3rd S. Chen 26 4 11,934 arrays

Brie mouse genome-wide library

Designed using optimized metrics that are described in Doench et al. (2016), which combined improved on-target activity predictions (Rule Set 2), with an off-target score, the Cutting Frequency Determination (CFD); John Doench’s gRNA design blog post describes how gRNAs were designed for this library.

 73632 (1 plasmid)
73633 (2 plasmid)		 Mouse 3rd Doench and Root 19,674 4 78,637

Brie mouse kinome library

CRISPR knockout pooled library that targets mouse kinome genes

 75317 (1 plasmid)
75316 (2 plasmid)		 Mouse 3rd Doench and Root 713 4 2,852

Brunello human genome-wide library

Designed using optimized metrics that are described in Doench et al. (2016), which combined improved on-target activity predictions (Rule Set 2), with an off-target score, the Cutting Frequency Determination (CFD); John Doench’s gRNA design blog post describes how gRNAs were designed for this library.

 73179 (1 plasmid)
73178 (2 plasmid)		 Human 3rd Doench and Root 19,114 4 76,441

Brunello human kinome library

CRISPR knockout pooled library that targets kinome genes

 75314 (Guides 1-4); 75315 (Guides 5-8)
(1 plasmid)

75312 (Guides 1-4); 75313 (Guides 5-8)
(2 plasmid)

1000000083
Guides 1-4 & 5-8
(1 plasmid)

1000000082
Guides 1-4 & 5-8
(2 plasmid)		 Human 3rd Doench and Root 763 4 3,052

Gattinara human genome-wide library

Designed for assays with limited cell numbers, this can be used with John Doench’s Brunello human genome-wide library.

 136986 Human 3rd Doench 19,993 2 40,964

Gouda mouse genome-wide library

Designed for assays with limited cell numbers, this can be used with John Doench’s Brie mouse genome-wide library.

 136987 Mouse 3rd Doench 21,601 2 44,155

Green monkey (Chlorocebus sabaeus) sgRNA library

Lentiviral CRISPR knockout library targeting green monkey (Chlorocebus sabaeus) genome.

 178284 Green Monkey 3rd Doench and Root 20,991 4 84,963

Humagne Set C and Humagne Set D

The human CRISPR knockout enAsCas12a sgRNA libraries were designed for assays with limited cell numbers.

 172650 (Set C)
172651 (Set D)		 Human 2nd Doench and Root 20,355 2 40,710

Inzolia Human CRISPR/Cas12a Multiplex Knockout

The Inzolia genome-scale human library, with a five-fold reduction in the number of clones required, can be used for assaying genetic interactions.

 209551
209552		 Human 3rd Doench Varies 1, 2, or 4 49,766 arrays

Dow Lab Base Editing Sensor Libraries

Base editor sgRNAs target frequently occurring cancer-associated mutations that can be modeled with cytosine base editing.

 179217-179219 Human, Mouse 3rd Dow 462 ~100 Varies

Mini-human AsCpf1-based Human Genome-wide Knockout Library

Each gene is targeted by an AsCpf1(AsCas12a)-based array containing 3-4 guides concatenated in one vector.

 130630 Human 3rd Draetta 16,977 3-4 17,032 arrays

MYC-CRISPR Library

CRISPR knockout pooled library targets human E-boxes genome-wide.

 173195 Human 3rd Dzikiewicz-Krawczyk 24,981 E-boxes 1-7 per element 46,354

Bison sgRNA Library

Lentiviral CRISPR knockout library targets ubiquitin ligases, deubiquitinases, and control genes.

 169942 Human 3rd Ebert 713 4 2,852

Human Interferon-Stimulated Gene CRISPR Knockout Library

CRISPR knockout pooled library targets a set of human interferon-stimulated genes (ISGs).

 125753 Human 3rd Emerman
OhAinle		 1,902 8 15,416

Human MinLibCas9 Library

Human genome-wide knockout library designed with two sgRNAs per gene.

 164896 Human 3rd Garnett 18,761 2 37,722

KSHV Tiling Library

SgRNA library tiles complete KSHV genome for pooled screening.

 180272 KSHV 3rd Glaunsinger NA NA 24,000

BLaER1 pgRNA Library

Paired guide RNA library targets genes related to B-cell to macrophage transdifferentiation.

 183825 Human 3rd Guigo 1,040 10 11,750

Mouse Metabolism Library

This CRISPR knockout library targets mouse metabolic genes.

163966 Mouse 3rd Kimmelman 2,918 ~6 18,343

Mouse Liver CRISPR Knockout Library

This library can be used for genome-scale screening in the mouse liver.

 192824 Mouse 3rd Knouse 13,189 ~5 71,878

Human Transcription Factor Knockout Library

CRISPR knockout pooled library targets a set of human transcription factors for LOF screening.

 162275 Human 3rd Li 1,639 ~7 11,364

Human UBDUB CRISPR Knockout Library

Human CRISPR Knockout Library targets ubiquitination and de-ubiquitination complex genes.

171531 Human 3rd Li 1500 ~6 9,274

Lin Human miRNA CRISPR Knockout Library

This pooled CRISPR library targets 1,594 primary human miRNA genes. The library contains 4-5 gRNAs per gene and 1,000 non-targeting control gRNAs for a total of 8,382 gRNAs.

 112200 Human 3rd Lin 1,594 ~5 8,382

Oxford Drosophila genome-wide library

This pooled library is designed for genomic targeting and screening in Drosophila cells. To design the gRNAs, the depositing laboratory computed all possible gRNA target sites within the shared exonic regions on either DNA strand of the Drosophila genome.

 64750 D. melanogaster N/A J. Liu 13,501 3 40,279

The Human Druggable CRISPR library

The CRISPR knockout library contains ~10,000 sgRNAs targeting 1,980 human druggable genes (5 sgRNAs per gene and 100 non-targeting control sgRNAs).

 200013 Human 3rd L. Liu 1,980 5 10,000

Human CRISPR Knockout Library

Delivered as two half-libraries h1 and h2. Designed using optimized metrics that are described in Xu et al. (2015), which (1) maximize on-target cleavage effects using the SSC algorithm developed by the Liu Lab ( Xu et al. Genome Research 2015), (2) minimize potential off-target effects, and (3) ensure the fidelity of their sequence with corresponding target loci and avoid regions with possible genomic variations.

 1000000132 Human 3rd X.S. Liu 18,436 10 185,634

Mouse CRISPR Knockout Library in lentiCRISPR v2-Blast

Delivered as two half-libraries M1 and M2, the guide RNAs in this genome-wide CRISPR knockout library are designed to maximize on-target cleavage while minimizing off-target effects.

 1000000173 Mouse 3rd X.S. Liu 18,741 10 185,836

MusCK Library

Delivered as two half-libraries Library A and Library B. The guide RNAs in these CRISPR knockout libraries target mouse genes implicated in tumor initiation, progression, and immune modulation.

 174196 (Library A)
174197 (Library B)
1000000178
(Library A & Library B)		 Mouse 3rd X.S. Liu 4,922 5
5
10		 49,252

Toxoplasma genome-wide library

Used for first apicomplexan parasite knockout screen.

 80636 T. gondii N/A Lourido 8,158 10 80,158

Advanced Catalogue of Epigenetic Regulators (ACER)

The Advanced Catalogue of Epigenetic Regulators (ACER) library consists 748 traditional and newly predicted epigenetic regulators using epigenetic network analyses that integrated publicly available gene codependency (DepMap) and protein-protein interaction data (BioPlex).

 226117 Human 3rd Lu 758 10 8,205

Pan-Druggable Cancer Library

CRISPR knockout library targets cancer-related genes.

 182133 Human 3rd Mali 66 1 74

CHyMErA Knockout Libraries

Two pooled libraries express hybrid Cas9-Cas12a guide RNAs under a single promoter. Used to identify genetic interactions between paralogs and investigate alternative exon function.

 155199
155200		 Human 3rd Moffat and Blencowe 6,333
2,157		 variable 92,746
91,948

Mouse Toronto KnockOut (mTKO) CRISPR Library

Targets mouse protein-coding genes with 4-5 gRNAs/gene. Library includes 418 control gRNAs.

 159392
159393		 Mouse 3rd Moffat 19,463 ~5 94,528

Mouse Validation (mVAL) CRISPR Library

Library targets 182 immune evasion genes allow LOF screening against genes shown to increase sensistivity or resistance of cancer cells to CTRL-mediated toxicity.

 159391 Mouse 3rd Moffat 182 4 1,656

Toronto KnockOut (TKO) genome-wide library - Version 1

Targets nearly all human protein-coding genes. Base library: gRNAs with no predicted off-target sites. Supplemental library: 6 additional gRNAs per gene.

 1000000069 Human 3rd Moffat 17,661 12 176,500

Toronto KnockOut (TKO) genome-wide library - Version 3

The Toronto KnockOut Library v3 (TKOv3) is contains 70,948 gRNAs targeting 18,053 protein coding genes (4 gRNAs/gene) with 142 control gRNAs targeting EGFP, LacZ, and luciferase (71,090 total). It is available in both one- and two-plasmid systems.

The gRNAs are sequence-optimized based on the criteria described in the associated article, and the number of gRNAs per gene is decreased to 4 based on the finding that there are diminishing benefits to more gRNAs per gene beyond four.

 90294 (1 plasmid)
125517 (2 plasmid)		 Human 3rd Moffat 18,053 4 70,948

Human Lipid Droplet and Metabolism Library

CRISPR screen that is useful for the exploration of lipid biology and metabolism.

 191535 Human 3rd Olzmann 1,196 ~10 13,920

Human GlycoGene CRISPR Library

CRISPR knockout library targets human genes involved in cellular glycosylation.

 140961 Human 3rd Neelamegham 347 10 3,637

Human Genome-Wide Reduced Double-gRNA Library

Lentiviral CRISPR knockout library delivers random pairs of optimised gRNAs, reducing screens scale with similar performance to larger libraries.

 137999 Human 3rd Parts 19,657 3 59,576

Drosophila Cell CRISPR Knockout Libraries

Designed for long-term sgRNA delivery in Drosophila cell lines.

 134582
134583
134584		 D. melanogaster 3rd Perrimon 955
2979
9954		 8
6
6		 7,956
17,827
59,406

Mouse Cardiac Transcriptional Regulators CRISPR Knockout Library

AAV CRISPR Library targets transcriptional regulators expressed in cardiomyocytes.

 138015 Mouse N/A Pu 2,444 6 14,671

Pan-cancer CasRx lncRNA Albarossa Library

Genome-scale pan-cancer interrogation of lncRNA dependencies using CasRx.

 212966 Human 3rd Rad 24,171 lncRNAs Varies 156,250

Activity-optimized human genome-wide library

Optimized for cleavage activity in order to maximize the likelihood of gene knockout. Split into three sub-libraries, each containing 10 gRNAs per gene.

 1000000100 Human 3rd Sabatini and Lander 18,663 10 187,535

Activity-optimized human genome-wide library

Discontinued - see #1000000100 for an improved version

 1000000067 Human 3rd Sabatini and Lander 18,166 5 178,896

Human CRISPR Metabolic Gene Knockout Library

 110066 Human 3rd Sabatini 2,981 ~10 30,290

Human mTORC1 Focused Library

Lentiviral CRISPR knockout library targets human genes required for mTORC1 activation and inhibition.

 164084 Human 3rd Sabatini 712 10 7,501

Two plasmid activity-optimized human genome-wide library

Optimized for cleavage activity in order to maximize the likelihood of gene knockout. Split into three sub-libraries, each containing 10 gRNAs per gene.

 1000000095 Human 3rd Sabatini and Lander 18,543 10 187,536

Two plasmid activity-optimized mouse genome-wide library

Optimized for cleavage activity in order to maximize the likelihood of gene knockout. Split into two sub-libraries, each containing 10 gRNAs per gene.

 1000000096 Mouse 3rd Sabatini and Lander 18,986 10 188,509

Focused Ras Synthetic Lethal Human CRISPR Knockout Library

Focused gRNA library that targets synthetic lethal candidate and control genes with oncogenic Ras.
92352 Human 3rd Sabatini and Lander 132 50 6,661

Enriched human sub-pooled libraries

Contains 6 distinct subpools targeting:

  • kinase
  • cell cycle
  • nuclear
  • ribosomal
  • unknown
  • controls
 51043 — 51048 Human 3rd Sabatini and Lander Varies 10 Varies

Human SLC Knockout Library

CRISPR knockout library targeting human SLC proteins.
 132552 Human 3rd Superti-Furga 390 6-7 2,609

Mouse SLC Knockout Library

CRISPR knockout library targeting mouse SLC proteins.
 141436 Mouse 3rd Superti-Furga 378 6-7 2,384

Human Transporter Knockout Libraries

CRISPR knockout library targeting human transmembrane transporters.
 213695
221409
221410		 Human 3rd Superti-Furga 673
653
90		 Varies Varies

Bovine CRISPR Knockout Libraries

Use the genome wide CRISPR knockout libraries to target all the protein coding genes in the cattle genome.

 213927, 213928 Cow 2nd Tan 21,165 4.4 on average 94,000

Yeast Inducible CRISPRi Library – Ampl133

Inducible genome-wide yeast CRISPRi library.

 161829 Yeast N/A Tavazoie 6,685 6-12 51,681

Retroviral Mouse Genome-wide CRISPR Knockout Library

This retroviral CRISPR library contains gRNAs from the Yusa lab Mouse improved genome-wide library v2.

 104861 Mouse N/A Teichmann 18,424 5 90,230

Mouse Cherry Brie Pooled Library

This lentiviral pooled library is a mouse genome-wide CRISPR knockout library. It is identical to the Brie library #73633, replacing Puromycin resistance with mCherry.

 170511 Mouse 3rd Tolar 19,674 ~4 78,637

Human messenger-RBP sgRNA Library

Lentiviral CRISPR knockout library targets human mRNA binding proteins with 10 sgRNAs/gene.

168791 Human 3rd Turner 725 10 8,260

Mouse messenger-RBP sgRNA Library

Retroviral CRISPR knockout library targets mouse mRNA binding proteins with 10 sgRNAs/gene.

169082 Mouse N/A Turner 1,300 10 13,500

Human Kinase Domain-Focused CRISPR Knockout Library

Designed for genomic deletion screening of protein kinases by targeting the kinase domains.

 117725 Human 3rd Vakoc 482 ~6 3,051

Human DNA Binding Domain-Focused CRISPR Knockout Library

Designed for genomic deletion screening of transcription factors by targeting the DNA binding domains.

 123334 Human 3rd Vakoc 1,427 ~6 8,658

sgRNA Pool for Streptococcus pneumoniae

Concise CRISPR pooled library targets the whole genome of S. pneumoniae D39V with one sgRNA per operon or gene.

 170432 S. pneumoniae N/A Veening 2,111 genetic elements 1 1,499

Human paired-guide RNA (pgRNA) Library for long non-coding RNAs (lncRNAs)

Designed for genomic deletion screening of functional lncRNAs (long non-coding RNAs) using lentiviral pgRNAs (paired-guide RNAs).

 89640 Human 3rd Wei 671 lncRNAs Varies 12,472 pairs

Human lncRNA Splicing-targeting CRISPR Library

Designed for genomic deletion screening of functional lncRNAs by targeting their splice sites.

 119977 Human 3rd Wei 10,996 lncRNAs Varies 126,773

Human Whole Genome sgRNA iBAR Library

Enables genome-wide CRISPR screening at high MOI through use of barcoded gRNA plasmids.

 140633 Human 3rd Wei 19,210 3 58,630

BARBEKO sgRNA Library

Uses CRISPR cytosine base editors for genome-scale knockout screens in human cells by perturbing gene start codons, splice sites, or by introducing premature termination codons.

 174163 Human 3rd Wei 17,501 3 53,502

Human genome-wide library v1

Used for genome scale lentiviral CRISPR screening. Target sites were chosen in a region close to the translation initiation site.

 69763 Human 3rd Wu 20,121 4 77,406

Mouse CRISPR/Cas9-assisted Removal of Mitochondrial DNA (CARM) Library

This library is intended to be used as a technical tool for removal of mitochondrial DNA from mouse genomic DNA preparations.

 82480 Mouse N/A Xie gRNAs target every ∼40bp over mitochondrial genome N/A 395

RNA-Binding Protein Pooled CRISPR Knockout Library

This pooled CRISPR knockout library targets RNA-binding proteins with 10 guide RNAs per target.

 141438 Human 3rd Yeo 1,078 10 12,472

Human improved genome-wide library v1

Improved version using new design pipeline and improved gRNA scaffold.

 67989 Human 3rd Yusa 18,010 5 90,709

Mouse genome-wide library

Discontinued 		50947 Mouse 3rd Yusa 19,150 5 87,897

Mouse improved genome-wide library v2

Improved version using new design pipeline and improved gRNA scaffold.

 67988 Mouse 3rd Yusa 18,424 5 90,230

Cas13a/C2c2 Protospacer flanking site (PFS) Library

A library of protospacer flanking sites (PFS) inserted at the 5' end of the β-lactamase gene for screening PFS preference for Cas13a/C2c2.

 79153 Bacterial N/A Zhang 4,096 Protospacer flanking sites N/A N/A

Human GeCKO v2 genome-wide library

Delivered as two half-libraries (A and B) allowing researchers to screen with 3 or 6 gRNAs/gene, respectively.

 1000000048 (1 plasmid)
1000000049 (2 plasmid)		 Human 3rd Zhang 19,052 6 123,411

Mouse GeCKO v2 genome-wide library

Delivered as two half-libraries (A and B) allowing researchers to screen with 3 or 6 gRNAs/gene, respectively.

 1000000052 (1 plasmid)
1000000053 (2 plasmid)		 Mouse 3rd Zhang 20,661 6 130,209

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Activation

CRISPR activation libraries use gRNAs to guide dCas9 bound to a transcriptional activator to target genes and thereby activate their expression. You can learn more CRISPR-based gene regulation on our CRISPR guide page.

Library ID Species Lentiviral Generation PI Genes targeted gRNAs per gene Total gRNAs

Human Metabolic Gene CRISPRa sgRNA Library

Lentiviral CRISPRa library targeting 2,989 human metabolic genes for activation of gene expression.

 187080 Human 3rd Birsoy 2,989 Varies 32,460

Mouse Metabolic Gene CRISPRa sgRNA Library

Lentiviral CRISPRa library targeting 2,989 mouse metabolic genes for activation of gene expression.

 187081 Mouse 3rd Birsoy 2,989 Varies 17,031

FNLCR CRISPRa Cell Surface Libraries

Lentiviral CRISPRa libraries targeting cell surface proteins and soluble factors for activation of gene expression.

 207471
1000000228		 Human 3rd Chari 6,081
7,030		 ~5 30,868
35,517

Calabrese p65-HSF human activation library

CRISPR activation pooled library using p65-HSF

 92379 (Set A); 92379-LV (Lentiviral Prep)

92380 (Set B); 92380-LV (Lentiviral Prep)

1000000111
Set A & Set B		 Human 3rd Doench and Root 18,885 (Set A), 18,843 (Set B) 3-6 56,762 (Set A), 56,476 (Set B)

Caprano p65-HSF mouse activation library

CRISPR activation pooled library using p65-HSF

 92383 (Set A)

92384 (Set B)

1000000113
Set A & Set B		 Mouse 3rd Doench and Root 22,774 (Set A), 22,658 (Set B) 3-6 67,187 (Set A), 66,889 (Set B)

Mouse Transcription Factor Activation Library

Increases transcriptional activation of genes encoding transcription factors in combination with dCas9 activation systems, such as the SunTag and the dCas9-VP64 systems.

 122131 Mouse 3rd Qi 2,428 ~20 51,762

Human SLC Activation Library

CRISPR activation library targeting human SLC proteins.
 132561 Human 3rd Superti-Furga 388 6-7 3,342

CRISPRa-v2 human genome-wide library

Increases transcriptional activation through the dCas9-SunTag-VP64 system, which enables specific recruitment of multiple copies of VP64 to the sgRNA-targeted gene.

 83978
1000000091		 Human 3rd Weissman 18,915 10 104,540
209,080

Subpooled CRISPRa-v2 human libraries

SunTag-VP64 constructs can be used for activation and must be supplied separately.

Subpools include kinases, apoptosis, stress, trafficking, gene expression, membrane proteins, and unknown function.

 83980 — 83986 Human 3rd Weissman Varies 5 Varies

CRISPRa-v2 mouse genome-wide library

Increases transcriptional activation through the dCas9-SunTag-VP64 system, which enables specific recruitment of multiple copies of VP64 to the sgRNA-targeted gene.

 83996
1000000093		 Mouse 3rd Weissman 19,939 10 107,105
214,210

Subpooled CRISPRa-v2 mouse libraries

SunTag-VP64 constructs can be used for activation and must be supplied separately.

Subpools include kinases, apoptosis, stress, trafficking, gene expression, membrane proteins, and unknown function.

 83998 — 84004 Mouse 3rd Weissman Varies 5 Varies

Dual sgRNA CRISPRa Libraries

Ultra-compact, human genome-wide CRISPRa library targeting each gene with a single element encoding a dual sgRNA cassette.

 187249 — 187251
1000000193		 Human 3rd Weissman Varies 6 Varies

CRISPRa genome-wide library
Discontinued

 60956 Human 3rd Weissman 15,977 10 198,810

Human Membrane Protein Activation Library

The Synergistic Activation Mediator (SAM) is an engineered transcriptional activation complex for the transcriptional activation of genes encoding human membrane proteins. Consists of:

  • A nucleolytically inactive Cas9-VP64 fusion
  • sgRNA incorporating two MS2 RNA aptamers at the tetraloop and stem-loop 2
  • MS2-P65-HSF1 plasmid which expresses the activation helper protein
 113345 Human 3rd Wright 6,213 7-14 58,570

Human SAM genome-wide library (2-plasmid system)

The Synergistic Activation Mediator (SAM) is an engineered transcriptional activation complex for the transcriptional activation of endogenous genes. Consists of:

  • A nucleolytically inactive Cas9-VP64 fusion plus sgRNA incorporating two MS2 RNA aptamers at the tetraloop and stem-loop 2
  • MS2-P65-HSF1 plasmid which expresses the activation helper protein
 1000000078 Human 3rd Zhang 23,430 3 70,290

Human SAM genome-wide library (3-plasmid system)

The Synergistic Activation Mediator (SAM) is an engineered transcriptional activation complex for the transcriptional activation of endogenous genes. Consists of:

  • A nucleolytically inactive Cas9-VP64 fusion
  • sgRNA incorporating two MS2 RNA aptamers at the tetraloop and stem-loop 2
  • MS2-P65-HSF1 plasmid which expresses the activation helper protein
 1000000057 (Zeocin)
1000000074 (Puromycin)		 Human 3rd Zhang 23,430 3 70,290

Human SAM lncRNA activation library (3-plasmid system)

The Synergistic Activation Mediator (SAM) is an engineered transcriptional activation complex for the transcriptional activation of lncRNAs. Consists of:

  • A nucleolytically inactive Cas9-VP64 fusion
  • sgRNA incorporating two MS2 RNA aptamers at the tetraloop and stem-loop 2
  • MS2-P65-HSF1 plasmid which expresses the activation helper protein
 1000000106 (Zeocin) Human 3rd Zhang 10,504 10 96,458

Mouse SAM genome-wide library (3-plasmid system)

The Synergistic Activation Mediator (SAM) is an engineered transcriptional activation complex for the transcriptional activation of endogenous genes. Consists of:

  • A nucleolytically inactive Cas9-VP64 fusion
  • sgRNA incorporating two MS2 RNA aptamers at the tetraloop and stem-loop 2
  • MS2-P65-HSF1 plasmid which expresses the activation helper protein
 1000000075 (Puromycin) Mouse 3rd Zhang 23,439 3 69,716

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Inhibition

CRISPR inhibition libraries use gRNAs to guide dCas9 bound to a transcriptional repressor to target genes, block transcription initiation, and thereby repress, or knockdown, their expression. You can learn more CRISPR-based gene regulation on our CRISPR guide page.

Library ID Species Lentiviral Generation PI Genes Targeted gRNAs per gene Total gRNAs

Adamson DNA Repair CRISPRi Libraries

These libraries contain guide RNAs to inhibit human genes involved in DNA repair and an internal edit site on the backbone. They can be used for Repair-seq experiments to map DNA repair processes and identify improved genome editing strategies.

 177663, 177664, 177670 Human 3rd Adamson 118 or 476 ~3 366 or 1,573

Bikard E. coli Genome-wide Inhibition Library v1

This library contains ~93,000 unique guide RNAs targeting random positions along the genome of E. coli MG1655 with a NGG PAM motif. The library contains an average of 19 targets per gene and can be used with SpdCas9 to perform pooled CRISPRi screens.

 115927 E. coli N/A Bikard ~4,500 ~19 92,919

Bikard Lab EcoWG1: E. Coli Genome-wide Inhibition Library v2

This bacterial CRISPR inhibition library targets every small RNA and ORF of the E. coli MG1655 genome. This library has higher inhibition efficiency than the psgRNA library.

 131625 E. coli N/A Bikard 4,444 ~5 21,417

Dolcetto human inhibition library

The fusion protein dCas9-KRAB can be used as the transcriptional repressor and must be supplied separately.

 92385 (Set A)

92386 (Set B)

1000000114
Set A & Set B		 Human 3rd Doench and Root 18,901 (Set A), 18,899 (Set B) 3-6 57,050 (Set A), 57,011 (Set B)

Dolomiti mouse inhibition library

The fusion protein dCas9-KRAB can be used as the transcriptional repressor and must be supplied separately.

 104090 (Set A)

104091 (Set B)

1000000131
Set A & Set B		 Mouse 3rd Doench and Root 22,311 (Set A), 22,247 (Set B) 3-6 67,366 (Set A), 67,194 (Set B)

Ingolia lab S cerevisiae CRISPRi v1 – barcodes 181005

Tet-inducible yeast CRISPR inhibition library targets the genome with barcode linked guide RNAs.

 161769 Yeast NA Ingolia ~6,700 ~6 44,580

Mycobacterium tuberculosis CRISPRi Library (RLC12)

Inducible CRISPR repression library targets open reading frames and non-coding RNAs in M. tuberculosis.

 163954 M. tuberculosis NA Rock 4,052 Varies 96,700

Mycobacterium smegmatis CRISPRi Library (RLC11)

Inducible CRISPR repression library targets open reading frames and non-coding RNAs in M. smegmatis.

 163955 M. smegmatis NA Rock 6,642 Varies 176,286

Human CRISPRi-v2 Dual Guide Libraries

Dual sgRNA libraries containing a fixed element (non-targeting guide or EMC2 guide) and the well-established Human Genome-wide CRISPRi-v2 library in tandem.

 197348
197349		 Human 3rd Voorhees 18,905 5 103,269

CRiNCL - Human CRISPRi Non-coding Libraries

Targets long non-coding RNA (lncRNA)-expressing genes; The fusion protein dCas9-KRAB can be used as the transcriptional repressor and must be supplied separately.

 86538 — 86550 Human 3rd Weissman Varies 10 Varies

CRISPRi-v2 human genome-wide library

The fusion protein dCas9-KRAB can be used as the transcriptional repressor and must be supplied separately.

 83969
1000000090		 Human 3rd Weissman 18,905 5
10		 104,535
209,070

Subpooled CRISPRi-v2 human libraries

The fusion protein dCas9-KRAB can be used as the transcriptional repressor and must be supplied separately.

Subpools include kinases, apoptosis, stress, trafficking, gene expression, membrane proteins, and unknown function.

 83971 — 83977 Human 3rd Weissman Varies 5 Varies

CRISPRi-v2 mouse genome-wide library

The fusion protein dCas9-KRAB can be used as the transcriptional repressor and must be supplied separately.

 83987
1000000092		 Mouse 3rd Weissman 20,003 5
10		 107,415
214,830

Human CRISPRi Titration Libraries

The fusion protein dCas9-KRAB can be used as the transcriptional repressor and must be supplied separately.

 136478
136479		 Human 3rd Weissman ~2,500 23-24
1-9		 119,510
25,518

Subpooled CRISPRi-v2 mouse libraries

The fusion protein dCas9-KRAB can be used as the transcriptional repressor and must be supplied separately.

Subpools include kinases, apoptosis, stress, trafficking, gene expression, membrane proteins, and unknown function.

 83989 — 83995 Mouse 3rd Weissman Varies 5 Varies

CRISPRi genome-wide library
Discontinued

 62217 Human 3rd Weissman 15,977 10 206,421

Dual sgRNA CRISPRi Libraries

Ultra-compact, human genome-wide CRISPRi library targeting each gene with a single element encoding a dual sgRNA cassette.

 187246 — 187248
1000000192		 Human 3rd Weissman Varies 6 Varies

Chong Zhang E. coli Genome-wide Inhibition Library

This library targets ~4,000 E. coli genes with ~15 gRNAs per gene and includes ~10,000 gRNAs targeting intergenic regions. Additionally, 2,400 gRNAs without any significant hit across the E. coli genome are provided as a negative control. The library is divided into 5 sublibraries defined by biological categories, a negative control (NC) control library, and a custom test library targeting 86 genes (50 gRNAs per gene).

 113134 — 113138
113146, 113147		 E. coli N/A C. Zhang Varies ~15 Varies

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Screening Libraries

Screening libraries (non-CRISPR) can be used for different types of high-throughput experiments, including assay of protein-protein interactions or the effects of mutagenesis of a single gene. For example, phage display is a type of screening library that is used for finding binding partners for targets of interest. It relies on fusions of gene fragments and a bacteriophage coat protein.

Library ID Species Vector backbone PI Description
APA Variant and Reference Libraries 1000000214 Human APA V2 Seelig Libraries made to experimentally validate a residual neural network model's ( APARENT2) predictions for 3′-cleavage and polyadenylation from DNA sequence.
Cancer Driver Peptide Overexpression Library 172109 Human Lentiviral Mali Library expressing tiled cancer driver peptides for fitness screening.
DHFR Saturation Mutagenesis Libraries 1000000194-1000000196 E. coli pTET-Duet Reynolds Libraries to study the interaction between dihydrofolate reductase (DHFR) and thymidylate synthase (TYMS), a pair of enzymes catalyzing consecutive reactions in folate metabolism.
High Throughput PAM Determination Assay Libraries 160132-160135 Synthetic Reporter Joung and Kleinstiver Libraries for determining the PAM requirements of Cas enzymes.
microTRE Screening Library

201012-201014

1000000220

 Synthetic, but based on human and mouse Donor_eGP2AP_RC English Libraries to screen synthetic promoters for transcriptional readouts of specific upstream signaling events
Modular Pooled Knockin Libraries 207474 — 207481 Human pUC19 Marson Libraries for screening transcription factors and cell surface receptors with a T cell receptor or chimeric antigen receptor for engineering immunotherapies and other cellular functions.
pCMV-Rep78/68 Scanning Saturation Mutagenesis (SSM) Library 198050 pCMV-Rep78-68 Church Investigate the effects of rep mutations on production of a wide range of AAV capsid serotypes.
pRep-Cap Scanning Saturation Mutagenesis (SSM) Library 199601 AAV Church Investigate the effects of cap gene mutations on AAV production and on capsid properties.
PYR1 Double Mutant Library 1000000181 A. thaliana Yeast Two Hybrid Whitehead Paired double mutant Pyrabactin Resistance 1 libraries.
Rinehart Human Serine Phosphopeptide Library

111704-111708

 Human pNAS1 Rinehart Human phosphoserine libraries.
Rinehart Lab Iterative Synthetically Phosphorylated Isomers (iSPI) Library

188526-188536

1000000199-1000000209

 Human pSerRS Rinehart New generation of human phosphoserine libraries.
SARS-CoV-2 Spike (S) Ectodomain and RBD Libraries

157971-157973

168776-168777

174293-174296

 Coronavirus Yeast surface display Whitehead Libraries of Spike (S) Ectodomain and RBD mutants.
SARS-CoV-2 Spike Receptor Binding Domain Deep Mutation Scanning Library 1000000172 Coronavirus Yeast surface display Bloom Library of Spike protein RBD mutations for comprehensive mapping.
SARS-CoV-2 Spike Receptor Binding Domain Site-Saturation Mutagenesis Libraries

1000000182-1000000188

1000000231-1000000232

 Coronavirus Yeast surface display Bloom and Starr Libraries of variant Spike protein RBD mutations for comprehensive mapping.
SPECS Library 127842 Synthetic Lentiviral Lu Library for high-throughput screening for identification of synthetic promoters with enhanced cell-state specificity.
Superti-Furga Human SLC Overexpression Library 213694 Human Lentiviral Superti-Furga An inducible barcoded overexpression library to test the impact of SLC transporters on biological processes.
Synuclein VHH Immune Library 1000000071 Camelid Phagemid Messer and MJFF Created for research in Parkinson's Disease; For target validation and drug design
TP53 Mutagenesis Library 113569 Human Lentiviral Hahn and Root Designed for the characterization of all possible p53 mutations
Zhang Lab Multiplexed Overexpression of Regulatory Factors (MORF) Library

137000, 192821, 1000000218

 Human Lentivirus Zhang This pooled library of lentiviral plasmids expresses barcoded isoforms of human transcription factors.

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shRNA Libraries

shRNA libraries permit reversible loss-of-function screening to elucidate which genes are involved in a phenotype. Each library contains multiple shRNA sequences for each target gene; a true positive hit (a particular target gene) in an shRNA screen should show consistent results from the multiple shRNAs that target it. shRNA libraries may also be barcoded to allow for easy identification of the shRNA a given cell carries.

DECIPHER libraries are lentiviral barcoded shRNA libraries designed for RNAi screening. It’s important to note that these libraries are not genome-wide; instead, each library is enriched for a smaller set of biologically relevant genes. The DECIPHER barcoding system makes it easy to determine which shRNAs have been enriched or depleted in a cell population; each plasmid carries a unique 18 bp barcode that can be easily identified using next-generation sequencing.

As of October 2016, the DECIPHER libraries have been discontinued.

Library ID Species Lentiviral Generation PI Targets Total shRNAs

Decipher Mod 2: Disease Targets Discontinued

 28286 Human 3rd Chenchik and Frango 5,412 27,500

Decipher Mod 3: Cell Surface, etc. Discontinued

 29589 Human 3rd Chenchik 4,922 27,500

Decipher Mod 1: Pathway Targets Discontinued

 28287 Mouse 3rd Chenchik and Frango 4,625 27,500

Decipher Mod 2: Disease Targets Discontinued

 28288 Mouse 3rd Chenchik and Frango 4,520 27,500

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