Questions & Answers
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SupportSingle Cell Immune Profiling
Feature Barcoding - Antigen Specificity
Sample Prep - Cells
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?
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
Sequencing
- 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?
- 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
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?