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CloneTracker™ Barcode Products

Incorporate stable, heritable, and sequenceable barcodes in individual cells or cell population

For researchers investigating tumor progression, drug resistance, differentiation, development, hematopoiesis, and other related areas, there is considerable interest in understanding the heterogeneity of cell populations in both cultured and in vivo settings. Studies facilitated by labeling cells with a CloneTracker Barcode Libraries and Vectors include:

  • how cell heterogeneity changes in response to drugs or other selections
  • which traits allow cells to survive under different conditions
  • how cell population diversity might change with differentiation or disease progression

CloneTracker Barcode libraries, combined with next-generation sequencing (NGS), enable quantitative tracking of cell populations and clonal cell progeny. With these barcodes, cells can be permanently labeled and progeny tracked. Cell barcoding may be used to quantitatively assess representation of cells derived from a specifically barcode-tagged clone in a descendant population.  Also available are CloneTracker XP libraries that incorporate a barcode which is expressed on a selectable marker, and so, is detectable by genomic DNA sequencing or RNA sequencing.

For example, Cellecta and Amgen collaborated to use this sort of approach to assessing the heterogeneity of tumors resulting from xenograft implantation. Based on this work, Cellecta developed its original CloneTracker Lentiviral Barcode Library to introduce cell-specific unique barcodes into virtually any mammalian cell population.

Cellecta CloneTracker™ Products

CloneTracker™ Lentiviral Barcode Library

Label whole cell populations with stable, genomically integrated, single identifiable sequenceable barcodes for cell tracking and quantification of descendants in mixed downstream cultures or tissue.  Millions of cells labeled with unique sequenceable barcodes provide a starter or founder population that can be used to track proliferation, differentiation, and selection of their descendant populations in culture or in vivo. Each cells generates its own, easily characterized clonal population.

NEW CloneTracker XP™ Lentiviral Barcode Libraries

Research groups have used libraries that express unique barcode sequences on mRNA in conjunction with single-cell RNA sequencing to identify cell subpopulations expressing distinct sets of genes containing differentiating cellular markers. For these single-cell expression analysis studies, the barcodes are positioned just before the poly-A tail of a marker or selection gene in the lentiviral library. When the library constructs integrate into the genomic DNA after transduction, the modified gene transcript is expressed with the barcode so the barcode can be detected in the cDNA generated using RNA-sequencing approaches.

NEW CloneTracker XP™ CRISPR Human and Mouse Lentiviral Barcode Libraries

Human and mouse libraries incorporating expression of barcodes with gRNA sequences that are designed for CRISPR-Seq (aka Perturb-Seq) screens are also available. An extension of using barcodes with RNA-Seq involves also incorporating an effector element, such as sgRNA, that perturbs cellular genomics by, for example, knocking out a gene. When this sort of element is included with the barcode, both can be detected with RNA-Seq and thus enable changes in gene expression to be correlated with specific disruptions or perturbations of particular genes. This provides a very powerful approach to identify the genes responsible for controlling expression of particular pathways or responses.

CloneTracker™ Barcode Cell Labeling Kits

Cellecta provides kits for labeling all cells in a particular population with a specific, single barcode. With these kits, 4-10 different cell populations can each be distinctly labeled, and the progeny from each cell population can be sampled after differently labeled populations are co-cultured or otherwise grown together.


Convenient online ordering is available here.

CloneTracker Lentiviral Barcode Libraries – Flyer

Quantitative clonal barcode analysis for the identification of key drivers of disease progression and drug resistance – Application Note