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, by incorporating stable, heritable, and sequenceable barcodes in individual cells or cell populations.
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. Library constructs integrate into the genomic DNA after transduction and can be detected by genomic DNA amplification and, with the CloneTracker XP™ libraries, in RNA sequencing analysis. Sub-libraries with defined barcodes are available to label several cell populations with distinct non-overlapping barcodes.
Libraries of millions of barcodes encapsulated in VSV-g pseudotyped lentiviral particles efficiently transduce and integrate into the host cell genome of virtually any mammalian cells. When a cell population transduced at low number of viral particles to cells, individual cells pick up and insert a single barcode into their genomic DNA. 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.
In addition, Cellecta’s CloneTracker XP Libraries have a configuration where the barcode is located at the 3′ end of the transcript so it is copied during cDNA synthesis, thus expressed and quantifiable using RNA-Seq.
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 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 affect distinct groups of cells in a population can be extracted.