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CLindex ® Sample multiplexing kit

CLindex®Sample multiplexing kit enables pooling of up to 16 sample in the same single cell sequencing library. 

The CLindex® multiplexing technology employs click-chemistry for efficient, unbiased sample tagging. A chemical group with a high affinity to cell surface proteins and a sample indexing oligo binding to that chemical group label the cells of each sample. A major advantage of the click chemistry-based labeling compared to antibody-based labeling is that the cell surface proteins recognized by click chemistry are abundant and found across different species. Furthermore, the entire process of sample tagging takes only 30 min.



Streamlined Workflow

Sample tags are added using click chemistry prior to sample pooling in a single GEXSCOPE® workflow. Pooled cells with sample tags are then loaded to a SCOPE-chip® for cell lysis and barcoding. The sample tag (15nt) is flanked by a universal PCR handle and a poly(A)-tail, which are captured by oligo-dT beads. Sample tags are labeled with a cell barcode. Simultaneously, mRNAs of the same single cell are also captured by the magnetic oligo-dT beads at their poly(A)-tail and tagged with the same cell barcode as well as UMI. Thus, all cDNA fragments from the same cell have a common denominator: the cell barcode. Both the cell barcode and the CLindex tag ensure that each transcript can be linked back to the cell and sample of origin.

High Labeling efficiency

Four independent cell lines (NB4, THP1, U937 and CCRF) were labeled using CLindex® and pooled in equal parts prior to cell partitioning on the SCOPE-chip®. The cell clustering confirmed that sample tag proportions corresponding to the different cell lines were maintained throughout processing, showing that CLindex® sample indexing is unbiased. The total labeling efficiency was as high as 97%, with only 3% corresponding to multiplets or being undetermined. Furthermore, CLindex® sample tagging does not impair capturing, sequencing, or mapping as shown by the performance metrics. Compared to the same four cell lines pooled without labeling, CLindex® sample tagging does not alter overall gene expression patterns. 

Unbiased labeling across different species

CLindex® efficiently labels cell surface proteins that are highly conserved across different species. In an example, sixteen samples (8 from mouse testis, 8 from human CCRF cell line) were labeled with CLindex® sample tags and pooled to be processed using the high-density (HD) SCOPE-chip®. More than 40,000 cells were captured and sequenced. Pooled samples were represented at equal frequencies, while a low multiplet rate occurred.

Figure: CLindex® allows efficient and unbiased cross-species samples multiplexing, while maintaining cell viability at high levels. Species-specific cellular subtypes are labeled and captured free of bias.





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