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CloneTracker XP™ Human and Mouse Lentiviral CRISPR Barcode Libraries

  • Off-the-shelf CRISPR Barcode Libraries with expressed barcoded sgRNA expression cassette that can be detected using RNA-Seq assays
  • Use with Drop-seq single cell platforms for single-cell CRISPR screens (known as Perturb-Seq, or CRISPR‑Seq).
  • Two complementary libraries one targeting human and the other homologous mouse genes.

Pooled CRISPR screening with lentiviral sgRNA libraries has proven to be a very effective approach to identify genes functionally required to generate particular phenotypes, and RNA-Seq to be an effective method to find the underlying changes in gene expression producing those phenotypes. With the advent of droplet microfluidic platforms that enable single cell molecular analysis on a large scale, these two technologies can be merged to assess and characterize the distinct expression profiles produced by genetic disruption in a pooled CRISPR knockout screen. With this sort of pooled screening approach using CRISPR barcode libraries, isolation and characterization of phenotype-specific cells is unnecessary.


CloneTracker XP CRISPR Barcode Libraries express an sgRNA for pooled CRISPR genetic screens with a unique molecular identifier (UMI or barcode) that facilitates clonal cell tracking and single-cell expression analysis. In these libraries, the barcoded sgRNA expression cassette is positioned so that it is on the 3′-non-coding region of the puromycin selection gene and present on the polyA+ when this gene is expressed. As a result, the sgRNA and barcode can be detected in the RNA Expression data. When combined with single-cell expression profiling, changes in gene expression can be directly correlated to gene knockout, knockdown, or activation, depending on the type of CRISPR construct used to make the library.

sgRNA and barcode expression cassette for CellTracker XP CRISPR Barcode Libraries

Cell-specific barcodes incorporated into pooled CRISPR sgRNA libraries can be used in conjunction with single-cell RNA expression analysis to perform what is sometimes called a Perturb-Seq or CRISPR-Seq screen. The approach enables researchers to reliably identify and link changes in gene expression to the knockout of particular target genes.

Cellecta currently offers 2 complementary CloneTracker XP CRISPR Knockout libraries, one targeting 27 human anti-cancer genes and one targeting the 27 corresponding mouse homologs. There are 20 sgRNAs to each gene designed to target functional domains.

Ordering information

* Cellecta CloneTracker XP CRISPR Barcode Libraries are covered by Chenchik, A., et al., U.S. Patent 9,429,565 August 30, 2016

Contact us for more information.

Cellecta also provides Custom Barcode Libraries, if our off-the-shelf designs does not meet your needs.

Related Products

NGS Prep Kit for barcode library sequencing

CRISPR and Barcode Sequences

  • Provided with purchase of library

Library Gene Lists

User Manual

  • CloneTracker XP Lentiviral CRISPR-Barcode Library, v1 (Online Manual (TBA) or PDF (TBA))

Vector Information

pRSGScribe VectorsSequenceMap

Lot#-Specific Product Information (Product Analysis Certificates/PACs)

  • TBA

Safety Data Sheet (SDS)

Next-Gen Sequencing and Analysis

CloneTracker XP Barcode Libraries are provided with a complete protocol and all sequencing information to enable researchers to perform experiments and extract the data. However, we also provide Next-Gen Sequencing and analysis services for researchers running their own screens with our libraries. Just provide harvested cells or tissue for each time point or treatment condition (one sample), and we’ll extract DNA, amplify the barcodes, sequence, and assemble the data with some basic analysis.

You provide Cellecta with frozen cell pellets or tissue after screening…

…and Cellecta does the rest:

  • Extracts genomic DNA (and total RNA, if desired)
  • Amplifies sgRNA and barcodes
  • Performs NGS on DNA (and RNA-Seq, if applicable) on the Illumina NextSeq or HiSeq
  • Enumerates sgRNA and barcode counts from raw sequencing data
  • Optionally, provides gene expression profiles of clonal cell populations

Please see the Next-Gen Sequencing and Analysis web page for additional information and instructions on how to order.