Question: What are the differences between the protocols for Cell Labeling with dCODE™ Dextramer® Reagents from 10x Genomics and Immudex?
Answer: The demonstrated protocol Cell Labeling with dCODE Dextramer® for Single Cell RNA Sequencing Protocols was developed by 10x Genomics and is different from the Immudex dCODE™ Dextramer® staining protocol. The 10x Genomics Cell Labeling Protocol was optimized using dCODE™ Dextramer® reagents from Immudex and TotalSeq-C antibody oligonucleotide conjugates from BioLegend. To obtain more accurate cell calling during analysis, cells should be labeled with both antibody-oligonucleotide conjugates and dCODE™ Dextramer® reagents. dCODE™ Dextramer® reagent only type of analyses are not supported.
The differences between these protocols are discussed here. The blocking agents in labeling/staining buffers used in each of the protocols are different. The 10x Genomics protocol uses Human TruStain FcX, while the Immudex protocol uses herring sperm DNA. Although limited testing with the herring sperm DNA suggested that it likely performs similarly to TruStain FcX, please use with caution.
The other major difference between the two protocols is labeling/staining temperatures. 10x Genomics strongly recommends cell labeling/staining at four °C for most sample types, while Immudex recommends cell labeling/staining at room temperature. Incubation at room temperature for sensitive cell types can have a negative impact on the complexity of the transcriptome. Thus, incubation temperature is sample type-dependent and should be chosen accordingly.
In addition, 10x Genomics recommends staining with dCODE™ Dextramer® reagents in conjunction with a small panel of TotalSeq-C antibodies for antigen-specific T-cell analysis. This recommendation is listed as optional in the Immundex protocol. However, dCODE™ Dextramer® reagent only type of analyses are not supported.
Recommended TotalSeq-C antibodies for labeling in conjunction with dCODE™ Dextramer® reagents are listed below. The list can be modified depending upon the specific experiment.
Summary of differences between protocols from 10x Genomics and Immudex:
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Differences between Protocols |
10x Genomics Demonstrated Protocol: Cell Labeling with dCODE Dextramer® for Single Cell RNA Sequencing Protocols |
Immudex Staining Protocol - dCODE™ Dextramer® |
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Blocking agent |
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Temperature for Cell Labeling/Staining |
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Staining in conjugation with a small panel of TotalSeq-C antibodies |
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Products: Single Cell Immune Profiling