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CloneTracker XP™ Lentiviral Expressed Barcode Libraries

  • Easily label cells with an RNA-expressed barcode readily detected by RNA-Seq analysis
  • Choose a barcode with either standard oligo dT-compatible 3′ barcodes or SMART-compatible 5′ barcode configurations
  • Access multiple, non-overlapping 1M expressed barcode libraries so different cell populations can be labeled uniquely, or with a single 10M barcode library for larger populations

Single-cell RNA-Seq analysis is an important tool to analyze individual cell responses. However, important genes and pathways may not be active in all cells. Certain responses may only occur in a portion of cells, or different groups of cells can manifest divergent phenotypes. One way to address this challenge is to label individual cells with uniquely identifiable, expressed barcodes. In this way, effects and responses of each of the clonal progeny from this initial barcoded population can be assessed, and data correlating to how experimental conditions, differentiation, or developmental processes may affect distinct groups of cells in a population can be extracted.

Workflow for Cellecta Lentiviral Expressed Barcode Libraries

To detect cell-specific barcodes in conjunction with gene activation or pathway analysis, however, barcodes need to be expressed on the mRNA. For this purpose, Cellecta’s CloneTracker XP libraries incorporate barcodes into the 3′- or 5′-UTR of an RNA transcript. These ready-to-use expressed barcode libraries enable convenient labeling of up to 1 million individual cells with unique barcodes that are detected in both the genomic DNA and expressed RNA fractions.

In conjunction with single-cell RNA-Seq analysis, the expressed barcodes may be used to identify expression profiles and activated genes in different cells so that distinct clonal populations of cells from a single progenitor, as well as subpopulations of cells with distinct pathway activations or expression profiles, can be readily identified.

Vector map of pScribe vector showing expressed barcode from EFS promoter

CloneTracker XP 10M Barcode Libraries can be used to label approximately 1M cells with individual unique barcodes detectable by targeted amplification followed by DNA sequencing or RNA sequencing. These libraries are available in configurations where the barcode is located at the 3′ end of the transcript (as shown above) so it is compatible with oligo-dT cDNA synthesis protocols, or a 5′ barcode option that is compatible with SMART-based cDNA synthesis.

BCXP10M3RP-PCloneTracker XP™ 10M Barcode-3' Library with RFP-Puro (plasmid)$8,500.00
BCXP10M3RP-VCloneTracker XP™ 10M Barcode-3' Library with RFP-Puro (virus)$5,000.00
BCXP10M3VP-PCloneTracker XP™ 10M Barcode-3' Library with Venus-Puro (plasmid)$8,500.00
BCXP10M3VP-VCloneTracker XP™ 10M Barcode-3' Library with Venus-Puro (virus)$5,000.00
BCXP10M5VP-PCloneTracker XP™ 10M Barcode-5' Library with Venus-Puro (plasmid)$8,500.00
BCXP10M5VP-VCloneTracker XP™ 10M Barcode-5' Library with Venus-Puro (virus)$5,000.00

CloneTracker XP 1M Barcode Libraries can be used to label a few hundred thousand cells with individual unique barcodes detectable by targeted amplification followed by DNA sequencing or RNA sequencing. We offer multiple pools of these smaller barcode libraries–each with non-overlapping sets of barcodes–so that cells in several populations can be barcoded with differentially identifiable sets of sequences. Changes in the barcode frequency of different cell populations can then be independently analyzed when they are cultured together. Up to 10 different pools of non-overlapping barcode sets are available.

BCXP1M3RP-1S-PlasCloneTracker XP 1M Barcode Library (Plasmid)$6,500.00$25,000.00
BCXP1M3RP-1S-VirusCloneTracker XP 1M Barcode Library (Virus)$4,500.00$18,500.00

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

Contact us for more detailed information or to ask for a quote.

User Manual

Barcode Sequences

  • Provided with purchase of library

Vector Information

pScribe VectorsSequenceMap

Product Certificates

Lot NumberCatalog NumberDescriptionQuantityProduct Certificate
181221001BCXP10M3RP-VCloneTracker XP™ 10M Barcode-3' Library with RFP-Puro (packaged)5 x 10^8 TUPDF
181212009BCXP10M3LP-VCloneTracker XP™ 10M Barcode-3' Library with rLuciferase-Puro (packaged)2 x 10^8 TUPDF
180822001BCXP1M3RP-01-VCloneTracker XP™ 1M Barcode-3' Library Pool 1 with RFP-Puro (Packaged)1 x 10^8 TUPDF
180817002BCXP1M3RP-01-PCloneTracker XP™ 1M Barcode-3' Library Pool 1 with RFP-Puro (Plasmid)200 ugPDF
180817001BCXP10M3RP-PCloneTracker XP™ 10M Barcode-3' Library with RFP-Puro (plasmid)200 ugPDF
180815054BCXP10M3VP-VCloneTracker XP™ 10M Barcode-3' Library with Venus-Puro (virus)5 x 10^8 TUPDF
180809001BCXP1M3RP-01-VCloneTracker XP™ 1M Barcode-3' Library Pool 1 with RFP-Puro (Packaged)1 x 10^8 TUPDF

Safety Data Sheets (SDS)

CPCP-K2AReady-to-Use Lentiviral Packaging Plasmid Mix$340.00
LFVC1LentiFuge™ Viral Concentration Reagent$325.00
LNGS-300NGS Prep Kit for Barcode Libraries in pScribe (CloneTracker XP™)$875.00
LNGS-300-SPSupplementary Primer Set for LNGS-300 (12 Additional Index Primers)$475.00


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. Optionally, we’ll also extract RNA and perform RNA-Seq.

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 barcodes
  • Performs NGS on DNA (and RNA-Seq, if applicable) on the Illumina NextSeq or HiSeq
  • Enumerates 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.