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CloneTracker™ Lentiviral Barcode Libraries


Track the fate of cell clones over a course of drug treatment or during differentiation, tumorigenesis or other processes.

  • 50M barcodes in validated, pooled lentiviral libraries to easily label more than a million cells with heritable unique barcodes
  • Library pools to label several cell populations with non-overlapping barcodes.
  • RNA-expressed barcodes that are readily detected in RNA-Seq and single-cell expression analysis
Workflow for Cellecta Lentiviral Expressed Barcode Libraries

Stable Barcode Integration to Permanently Label Cells

  • VSV-g pseudotyped lentiviral particles efficiently transduce and integrate into the host cell genome of virtually any mammalian cells.
  • As the host cells divide, the barcode sequences in the lentiviral vector will also replicate and will be passed onto daughter cells.
  • Cells can be treated, grown for several passages, frozen and thawed, and the sequences within the lentiviral vector will remain in the host cell.
  • After selection, treatment, or differentiation, just extract genomic DNA, amplify, and sequence to identify and quantify barcodes present in the selected cell population.

CloneTracker XP™ Lentiviral Expressed Barcode Libraries 

Cellecta’s CloneTracker XP Libraries incorporate barcodes into the UTR of an RNA transcript. These ready-to-use expressed barcode libraries enable convenient labeling of millions of individual cells with unique barcodes that can be detected in both the genomic DNA and expressed RNA fractions.

Vector map of pScribe vector showing expressed barcode from EFS promoter

Cellecta’s CloneTracker XP Barcode Libraries can be used to label cells with unique barcodes detectable by targeted amplification followed by DNA sequencing or RNA sequencing.

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. 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.

Cellecta’s CloneTracker XP 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.

BCXP10M3VP-PCloneTracker XP™ 10M Barcode-3' Library in pScribe5-Venus-Puro (plasmid)200 ug$8,500.00
BCXP10M5VP-PCloneTracker XP™ 10M Barcode-5' Library in pScribe5.2-Venus-Puro (plasmid)200 ug$8,500.00
BCXP10M3VP-VCloneTracker XP™ 10M Barcode-3' Library in pScribe5-Venus-Puro (virus)1 x 10^8 TU$5,000.00
BCXP10M5VP-VCloneTracker XP™ 10M Barcode-5' Library in pScribe5.2-Venus-Puro (virus)1 x 10^8 TU$5,000.00
BCXP10M3RP-VCloneTracker XP™ 10M Barcode-3' Library with RFP-Puro (virus)1 x 10^8 TU$5,000.00
BCXP50M3P-VCloneTracker XP™ 50M Barcode-3' Library in pScribe4M-RFP-Puro (virus)1 x 10^8 TU$6,000.00
BCXP10M3RP-PCloneTracker XP™ 10M Barcode-3' Library with RFP-Puro (plasmid)200 ug$8,500.00
BCXP50M3P-PCloneTracker XP™ 50M Barcode-3' Library in pScribe4M-RFP-Puro (plasmid)200 ug$9,750.00

For the 5M barcode library pools listed above, we can provide from one to ten pools of unique barcodes. For pricing details, please contact us.

Original CloneTracker™ 50M Lentiviral Barcode Library

Cellecta’s original CloneTracker™ 50M Lentiviral Barcode Library (formerly CellTracker) enables the tracking of individual clones derived from a population of cells. The library contains more than 50 million lentiviral constructs with different barcode sequences. When a cell population is transduced with this barcode library, the barcodes integrate into the genomic DNA of the cells. The result is a select starter founder population where almost every cell has a different, heritable, DNA-sequenceable barcode integrated into its genomic DNA. Since the barcode is stably integrated, it is passed onto any cell progeny when genomic DNA is replicated, allowing researchers to track cell proliferation over the course of an experiment.

BC13X13-PCloneTracker™ 50M Lentiviral Barcode Library (plasmid)200 ug$6,500.00
BC13X13-VCloneTracker™ 50M Lentiviral Barcode Library (virus)1 x 10^8 TU$3,500.00

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 VectorsBarcode CassetteSequenceMap

Product Certificates

Lot NumberCatalog NumberDescriptionQuantityProduct Certificate
190103007LNGS-300NGS Prep Kit for Barcode Libraries in pScribe (CloneTracker XP™)Kit for 6-48 samples (48 preps of 50 µg each, 12 multiplex)PDF
181221001BCXP10M3RP-VCloneTracker XP™ 10M Barcode-3' Library with RFP-Puro (virus)5 x 108 TUPDF
181221001BCXP10M3RP-VCloneTracker XP™ 10M Barcode-3' Library with RFP-Puro (virus)1 x 108 TUPDF
180822001BCXP1M3RP-01-VCloneTracker XP™ 1M Barcode-3' Library Pool 1 with RFP-Puro (Packaged)1 x 108 TUPDF
180817002BCXP1M3RP-01-PCloneTracker XP™ 1M Barcode-3' Library Pool 1 with RFP-Puro (Plasmid)200 µgPDF
180817001BCXP10M3RP-PCloneTracker XP™ 10M Barcode-3' Library with RFP-Puro (plasmid)200 µgPDF
180815054BCXP10M3VP-VCloneTracker XP™ 10M Barcode-3' Library with Venus-Puro (virus)5 x 108 TUPDF
180809001BCXP1M3RP-01-VCloneTracker XP™ 1M Barcode-3' Library Pool 1 with RFP-Puro (Packaged)1 x 108 TUPDF

Safety Data Sheets (SDS)

CPCP-K2AReady-to-Use Lentiviral Packaging Plasmid Mix250 ug$340.00
LNGS-300NGS Prep Kit for Barcode Libraries in pScribe (CloneTracker XP™) with Alignment SoftwareKit for 6-48 samples (48 preps of 50ug each, 12 multiplex)$950.00
LNGS-300-SPSupplementary Primer Set for LNGS-300 (12 Additional Index Primers)48 Reactions (12 Index Primers x 4 reactions each)$475.00
LFVC1LentiFuge™ Viral Concentration Reagent1 ml of 1000x$325.00
LTDR1LentiTrans™ Transduction Reagent (Polybrene for Transduction)1 ml of 1000x$175.00
LTSET-GLentiPrep™ Lentiviral Reagent Set with GFP Control for Packaging and TransductionKit$750.00
LTSET-RLentiPrep™ Lentiviral Reagent Set with RFP Control for Packaging and TransductionKit$750.00

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.