Questions & Answers
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SupportSingle Cell Immune Profiling
Sample Prep - Cells
Feature Barcode - Cell Surface Protein
- Can I perform Cell Hashing in the 5' workflow?
- Can I salvage my experiment if I did not use the recommended Feature cDNA primers for Cell Surface Protein during cDNA amplification?
- What are the additional peaks in my Cell Surface Protein library?
- What Demonstrated Protocols for sample preparation are compatible with 5' Feature Barcoding?
- Why do I need a different sample index plate to make 5' Feature Barcode libraries?
Feature Barcode - 5' CRISPR Screening
- Is 5’ CRISPR compatible with Cell Hashing?
- Why does my 5’ CRISPR Screening library trace have additional peaks?
- Is 5’ CRISPR compatible with my guide of interest?
- Is 5' CRISPR compatible with Cas12/Cas13 CRISPR libraries?
- Is there competition between the CRISPR non-poly(dT) primer and poly(dT) primer?
- Can I combine 5’ CRISPR with dCODE™ Dextramer® experiments?
Feature Barcode - Barcode Enabled Antigen Mapping (BEAM)
- Which antibodies should I include in my fluorescent antibody panel for BEAM flow sorting?
- Can I use more than one MHC allele in a BEAM experiment?
- What are the requirements for peptides for BEAM-T?
- What is the purpose of the quenching step in the BEAM assay?
- What are the requirements for antigens for BEAM-Ab?
- Should I include negative controls in the BEAM assay?
Feature Barcode - Dextramer
- What are the differences between the protocols for Cell Labeling with dCODE™ Dextramer® Reagents from 10x Genomics and Immudex?
- What factors should I consider when planning my antigen specificity experiment using dCODE™ Dextramer® from Immudex?
- How can I combine dCODE™ Dextramer® staining and cell surface protein staining in the same workflow?
High Throughput Single Cell Immune Profiling
Reagents
Reagents for Single Cell 5' VDJ Application.
- When do I need an additional Single Cell 5' Library Construction Kit (PN-1000020) to run my experiment with Single Cell VDJ v1 or v1.1 reagent kits?
- Can I use my 5’ v1/v1.1 V(D)J primers with 5’ v2 reagent kits?
- When do I need an additional Library Construction Kit (PN-1000190) to run my experiment with Next GEM 5’ v2 reagent kits?
- Why are the primers designed near the 5' end of the C-region in the V(D)J assay?
- Can I detect T cells with gamma-delta chains in my V(D)J data?
- Why do I need an extra kit if I want Gene Expression and/or Feature Barcoding in addition to V(D)J?
GEM Generation & Barcoding
Post GEM-RT Cleanup & cDNA Amplification
- How can I optimize V(D)J primer design for my non-human/non-mouse species of interest?
- Why does my V(D)J enrichment trace look different from the user guide?
- Which genes does each V(D)J-specific primer map to?
- Why do I see big fragments (2,000- 9,000 bp) in my TCR-enriched trace?
- What is the difference between V(D)J Enrichment for Human and Mouse samples?
- Why is the distribution of fragments after amplification different between T and B cells?
Library Construction
Sequencing
- What is the limit of detection for a specific clonotype using the Single Cell Immune Profiling assay?
- Can I sequence my V(D)J libraries in a different sequencing configuration than the ones recommended in the user guide?
- When do I need to sequence my V(D)J-enriched libraries more deeply?
- Is there a common 5’ UTR captured during V(D)J enrichment?
- Should I adjust the targeted sequencing depth if I did not enrich for T or B cells?
- Can I sequence V(D)J-enriched libraries from T and B cells on the same lane?
Software
- What are the major updates in Cell Ranger v7.1 that impacts V(D)J data?
- Building a custom reference for V(D)J using IMGT tool
- Loupe Browser investigation for GEX + V(D)J data for differences in cell numbers
- Web summary metrics for V(D)J Troubleshooting
- Usage of Cell Ranger VDJ denovo mode
- How to run Cell Ranger for the same 5' GEX library sequenced with 150x150 and 26x98 configurations?