High Throughput Single Cell Immune Profiling

• When do I need an additional Library Construction Kit to run my experiment with Next GEM 5’ HT v2 reagent kits?
• What workflows and reagent kits are compatible with the Next GEM Single Cell 5’ HT v2 assay?

Feature Barcoding - Antigen Specificity

• 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?
• Where can I order peptide-MHC multimers for use with Feature Barcode technology?

Sample Prep - Cells

• Is Single Cell Immune Profiling compatible with nuclei?
• Is Single Cell Immune Profiling compatible with fixed cells?
• Recommended control Human B cells for V(D)J assay
• Recommended T and B cell enrichment protocols
• What are recommended control Human T cells for V(D)J assay?

Reagents

• 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 delta/gamma 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?

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GEM Generation & Barcoding

• What should I do if I accidentally use Chip G instead of Chip K with Single Cell 5' v2 reagents?
• Are there any cells types that express transcripts that are not fully recombined for VDJ? 

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?
• 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?
• How do I design a custom PCR-based target enrichment assay for Single Cell V(D)J?

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Library Construction

• Can 5’ v1/v1.1 libraries now be made with dual indices?
• Can 5’ v2 libraries be made using single-indices instead of dual-indices?
• I have <50 ng cDNA. Can I still make a 5' Gene Expression library?

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?

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Software

• How can I combine and compare data from 5’v1/v1.1 chemistry with 5’v2 chemistry?
• Is there a minimum number of Cell Surface Proteins that can be analyzed with Cell Ranger
• Can I run the VDJ pipeline for humanized mouse samples
• How can I get the sequence for each gene segment in an Ig or TCR chain
• Why does Loupe Cell Browser show "The VDJ file may not be related to this gene expression dataset" when I tried to load my matched VDJ data?
• Why do some clonotypes only have one productive chain?

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