Feature Barcoding - Antigen Specificity

• 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?
• Is Direct Target Enrichment recommended if the 5' Gene Expression Library is not needed?
• 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 T or B cell receptors?

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?
• Why is the annealing temperature and number of enrichment cycles different for 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

• 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?
• Alternative sequencing formats for Single Cell V(D)J libraries
• What Illumina sequencers are supported for Single Cell V(D)J libraries?

Software

• Can IgA1 and IgA2 be detected in the Single Cell V(D)J assay?
• Can I identify differentially expressed genes between cells in two different clonotypes?
• Is the amino acid sequence for the full V(D)J contig available?
• Are the V(D)J and gene expression references interchangeable?
• Will the V(D)J pipeline work without a reference?
• Why is the same TRB chain paired with TRA in clonotype1 and alone in clonotype2?

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