Feature Barcoding - Antigen Specificity

• What factors should I consider when planning my antigen specificity experiment using dCode Dextramers from Immudex?
• How can I combine dextramer staining and cell surface protein staining in the same workflow?
• Where can I order peptide-MHC multimers for Feature Barcoding?

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

• Why are the primers designed near the 5' end of the C-region in the V(D)J assay?
• Is it possible to detect TCR gamma/delta chains in the V(D)J assay?
• Why do I need an extra kit if I want Gene Expression and/or Feature Barcoding in addition to V(D)J?
• Can I study T and/or B cell immune repertoires, gene expression, and cell surface proteins from the same cells?
• Can the Single Cell V(D)J kit be used to amplify non-human/mouse T or B cell receptors?

GEM Generation & Barcoding

• Are there any cells types that express transcripts that are not fully recombined for VDJ? 

Post GEM-RT Cleanup & cDNA Amplification

• 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 targeted assay for Single Cell V(D)J?
• Why are there two target enrichment steps in the V(D)J workflow?

Library Construction

• I have <50 ng cDNA. Can I still make a 5' Gene Expression library?

Sequencing

• When do I need to sequence my V(D)J-enriched libraries more deeply?
• What sequencing parameters should I use when sequencing my V(D)J-enriched libraries?
• 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?
• Can I sequence V(D)J and 5' Gene Expression libraries on the same lane?

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Software

• 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?
• What should I do when I get more than 1 chain of same type in the same cell?

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