Pooled Libraries

In addition to the 150,193 plasmids in Addgene's repository, depositors have shared 350 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
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.

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.

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 Description 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 Description 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) Description 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 Description This lentiviral CRISPR knockout library targets human epigenetic genes.	162256	Human	3rd	Birsoy	2,508	8	20,051
Mouse CRISPR Metabolic Gene Knockout Library Description 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 Description 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 Description Lentiviral CRISPR library targets human ubiquitation-related proteins and deubiquitinating enzymes.	174592	Human	3rd	Bonifacino	660	6-25	11,108
Borodina Yeast Transporter Libraries Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description Human genome-wide knockout library designed with two sgRNAs per gene.	164896	Human	3rd	Garnett	18,761	2	37,722
KSHV Tiling Library Description SgRNA library tiles complete KSHV genome for pooled screening.	180272	KSHV	3rd	Glaunsinger	NA	NA	24,000
BLaER1 pgRNA Library Description 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 Description This CRISPR knockout library targets mouse metabolic genes.	163966	Mouse	3rd	Kimmelman	2,918	~6	18,343
Mouse Liver CRISPR Knockout Library Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description Used for first apicomplexan parasite knockout screen.	80636	T. gondii	N/A	Lourido	8,158	10	80,158
Advanced Catalogue of Epigenetic Regulators (ACER) Description 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 Description CRISPR knockout library targets cancer-related genes.	182133	Human	3rd	Mali	66	1	74
CHyMErA Knockout Libraries Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description CRISPR knockout library targeting human SLC proteins.	132552	Human	3rd	Superti-Furga	390	6-7	2,609
Mouse SLC Knockout Library Description CRISPR knockout library targeting mouse SLC proteins.	141436	Mouse	3rd	Superti-Furga	378	6-7	2,384
Human Transporter Knockout Libraries Description CRISPR knockout library targeting human transmembrane transporters.	213695 221409 221410	Human	3rd	Superti-Furga	673 653 90	Varies	Varies
Bovine CRISPR Knockout Libraries Description 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 Description Inducible genome-wide yeast CRISPRi library.	161829	Yeast	N/A	Tavazoie	6,685	6-12	51,681
Retroviral Mouse Genome-wide CRISPR Knockout Library Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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) Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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

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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description CRISPR activation library targeting human SLC proteins.	132561	Human	3rd	Superti-Furga	388	6-7	3,342
CRISPRa-v2 human genome-wide library Description 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 Description 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 Description 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 Description 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 Description 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 Description 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) Description 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) Description 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) Description 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) Description 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

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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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) Description 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) Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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 Description 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

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.

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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