Technical Note CLindexTM Increase sample throughput and reduce cost This Technical Note describes the CLindexTM sample multiplexing workflow and evaluates its performance metrics including labeling efficiency, effects on the transcriptome, cell clustering, and viability. Overview High-throughput single-cell sequencing technologies enable researchers and clinicians to assess how tissues or cell populations evolve in different diseases at single-cell level. During the past ten years, throughput and sensitivity of single-cell sequencing have advanced constantly. Nowadays, these improvements allow researchers to investigate samples from different origins and analyze thousands of cells of each sample. To meet the increasing need for higher sample throughput in translational research and precision medicine, we developed CLindex, a novel multiplexing method using click chemistry to add a sample-tag to cells. Unbiased – works with all species and tissues types Gentle – maintains high cell viability rates Compatible – supports usage of high-density chip to capture over 120,000 cells on one chip Fast – finishes sample labeling in <30 min Reliable – achieves multiplexing of

Technical Note CLindex Click-Chemistry A hallmark of high-throughput single-cell sequencing technology is the molecular tagging of cells with barcoding sequences. Each mRNA molecule is tagged with both, a common cell specific barcode and a unique molecular identifier (UMI). The information from both tags enable the analysis of the transcriptome at single-cell resolution. To increase sample throughput, we developed CLindex, a flexible sample multiplexing solution for single cell RNAsequencing studies that is compatible with samples of different species. CLindex adds a sample-specific index to...

Technical Note High Labeling Efficiency Four cell lines (NB4, THP1, U937 and CCRF) were labeled using CLindex and pooled in equal parts prior to cell parsing on the SCOPE-chip™, followed by cDNA library construction, and sequencing (Figure 4). A total of 4965 cells was captured. Cell clustering and annotation confirmed that sample indices were distributed evenly and correlated well with their labeled cell line samples. The percentage of correctly labeled cells was as high as 97%, with only 3% being either multiplets or undetermined. Furthermore, CLindex sample tagging does not impair capturing,...

Technical Note Sample Labeling Across Different Species CLindex Tag Distribution 1% undetermined 11% Despite the diversity of nature, there is a surprising number of features, which are highly conserved among different organisms. CLindex takes advantage of this by efficiently labeling cell surface proteins that are highly conserved across different species. Sixteen individual samples, of which eight were mouse testis and eight were human CCRF cell line samples, were labeled with CLindex sample tags and pooled to be processed using the high-density (HD) SCOPE-chip (250,000 microwells). More than...

Technical Note CLindex Sample Labeling Includes all Cell Subtypes To evaluate the performance of CLindex sample tagging, mouse bone marrow samples were labeled with CLindex and with an antibody-based labeling method from a different provider in parallel (Figure 8). In contrast to the antibody-based labeling method, the transcriptome of cells labeled with CLindex correlated CLindex labeling Bone Marrow GEXSCOPE workflow Antibody labeling CLindex labeling Antibody labeling CLindex labeling well with the transcriptome of non-labeled cells. Superior to antibody-based labeling, some cell types, such...

Technical Note Product described in this technical note Catalog CLindexTM Sample multiplexing kit CLindexTM Sample multiplexing kit Related products § High-density (HD) microwell chip § GEXSCOPE® Single Cell Kits Contact us Phone：+49 221 16824777 E-mail：[email protected] Singleron Biotechnologies GmbH; Gottfried-Hagen-Straße 60, 51105 Köln, Germ