Millions of Defined Sequenceable Barcodes for Clonal Cell Tracking

The ability to identify and quantify the size of clonal cell populations produced by each cell in a founder population offers researchers a powerful tool for understanding how groups cells grow and proliferate in all sorts of conditions. This sort of clonal cell tracking enables cell biologists, immunologists, cancer researchers, for example, to analyze how large cell populations proliferate in various environments, progenitor cells differentiate and acquire new phenotypes, and tumor masses evolve.

Most cell tracking experiments have used fluorescence, bioluminescence, or immunofluorescence labeling which, while effective, only enables effective tracking of a handful of cells since the colors or spectra used are limited. Also, tracking in certain models, such as in vivo systems can be complicated by the direct visualization of the labeled cells required using these dye-based approaches. In general, these approaches are useful to track a pool of cells but only provide limited information about the size, distribution, or localization of the distinct progeny produced by each cell in large or complex population.

Recently, Cellecta released the CellTracker™ Lentiviral Barcode Library that provides an alternative tracking tool to fluorescent or colorimetric dyes. This library consists of lentiviral plasmid constructs, each labeled with a unique nucleotide barcode that can be easily identified by DNA sequencing. There are millions of uniquely identifiable defined barcodes in the library due to the unique way the library was made. Instead of randomly generating sequences, that nucleotide barcodes were specifically designed, synthesized, and cloned so as to to produce a library with a distinct set of well-defined sequences optimized for HT sequencing.

As a result, each individual cell in a complex population of millions can be genetically tagged with a unique DNA sequence. Since this is done using lentiviral transduction, these sequenceable genetic tags are stably integrated into the genomic DNA of the cells, and so, become a permanent heritable marker. The genetic sequence is passed on with the genomic DNA is replicated so all the progeny of the original cell that was transduced in the founder population contain the same barcode.  At any point, then, it is possible to assess, in decedent populations, the sizes of each clonal population derived from the originally transduced cells by just harvesting the cells and sequencing the genetic tags in their genomic DNA.

Cellecta Clonal Cell Tracking Barcode Library construction and quality control diagram

Also in Cellecta Blog & News

Gene Expression Profiling of Single-Cell Samples: DriverMap Targeted Expression Profiling vs SMART Technology

Single-cell expression analysis provides insights about gene expression and cell heterogeneity at the single-cell level. It enables the elucidation of intracellular gene regulatory networks and intracellular pathways that would otherwise be masked in bulk analysis (Massaia et al., 2018). The DriverMap™ Targeted Gene Expression Profiling (TXP) assay combines highly multiplexed RT-PCR amplification with the depth and precision of Next-Generation Sequencing (NGS) to quantitatively measure gene expression of up to 19,000 target genes in a single assay–even down to the single-cell level.
Read More
Comparing DNA vs. RNA Samples for Immune Repertoire Profiling

Adaptive immunity relies on B and T cells that recognize foreign antigens via hypervariable B cell and T cell receptors (BCRs and TCRs). Diversity among B cell and T cell receptors is primarily produced by V(D)J recombination, which involves the shuffling and joining of the variable (V), diversity (D), joining (J), and constant region (C) gene segments. This results in a diverse repertoire called the adaptive immune repertoire (AIR) that comprises multiple individual clonotypes (sequence) for particular receptor chains.
Read More
Inducible Cas9 Expression in a Single Lentiviral Vector

Introducing Inducible Cas9 Expression in a Single Lentiviral Vector to make cells capable of high Cas9 expression for a limited time during which CRISPR-mediated targeted rearrangements can occur, and then shut off Cas9 expression for downstream assays with the modified cells.
Read More