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CLindex® – Multiplexing Made Easy

Turbocharge your throughput with the CLindex® Sample Multiplexing Kit that allows multiplexing of up to 16 libraries for single cell sequencing through click-chemistry-based sample tagging.

Kit Highlights

Click-chemistry-based for unbiased tagging of all species and cell types
Reduce batch effects and cost
Labelling within 30min
Multiplexing of up to 16 samples

CLindex® Technology

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.       

Multiplexing streamlined workflow: up to 16 samples in one library within one workday


Sample-Specific Tagging


Cell Partitioning, Lysis & Barcoding

Library Generation


Bioinformatics Analysis

High Labeling Efficiency

Four cell lines (NB4, THP-1, U937, and CCRF) were labeled with CLindex®, pooled equally, and processed on the SCOPE-chip®. Cell clustering confirmed unbiased CLindex® sample indexing, maintaining tag proportions. Labeling efficiency reached 97%, with only 3% multiplets or undetermined. CLindex® tagging doesn’t affect capturing, sequencing, mapping, or overall gene expression compared to non-labeled pooled cells.

Unbiased Labeling Across Different Species

CLindex® efficiently labels conserved cell surface proteins. In a study with 16 samples (8 mouse testis, 8 human CCRF cells), CLindex®-tagged samples were pooled, processed using HD SCOPE-chip®, capturing and sequencing over 40,000 cells. Pooled samples displayed equal representation with a low multiplet rate.

Technical Specifications

120 000 Cells

Can be captured on one high-density chip

30 min

Click-chemistry-based multiplexing adds only 30min to the streamlined workflow

16 samples

Multiplexing possible


with GEXSCOPE kits



The kits contain 16 tags for a maximum of 16 simultaneous samples. The 1-rxn kit will contain enough of each of the 16 tags for one labeling run. Therefore, you can either run one experiment of 16 samples or 2 experiments of 8 or 4 experiments of 4.

Since labeling requires several washing steps, we recommend starting with more than one million cells per sample, with at least 85% viability, to ensure keeping enough cells to run the experiment.

CLindex cannot be used for single nuclei samples, since the labeling is done at the membrane surface level.

CLindex multiplexing kit can label up to 16 different samples, which theoretically allows you to load up to 160000 cells with a 28% identifiable doublet rate (which can be filtered out during the analysis workflow). Our recommendation is to not go above 120000 cells to load the HD chip.

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