Question: Why does my V(D)J enrichment trace look different from the user guide?
Answer: The appearance of the V(D)J enrichment trace is based on many factors, including species (human vs. mouse), the number of T or B cells in the sample, how many V(D)J transcripts are expressed by those cells, which instrument the trace was run on (Tapestation vs. BioAnalyzer), and which chemistry was used (v1/v1.1 or v2). Because of this, the appearance of the enrichment trace is very sample-type specific and some variation is normal. The critical point to observe is that there is a sharp peak between 500 and 700 bp--this peak contains your V(D)J transcripts.
See below for some example distinctive VDJ traces:
Human TCR (5' v1.1 Chemistry vs 5' v2 Chemistry)
Our 5' v2 protocol incorporates an additional double-sided SPRI during the VDJ-amplification steps, which cleans up the final enrichment trace and removes more of the off-target high-molecular-weight product between 2 and 10 kb.
Human vs. Mouse BCR traces
When amplifying human Ig sequences, we expect to see two sharp peaks in the Bioanalyzer trace. Our mouse traces, on the other hand, typically only show one sharp peak.
Tapestation vs. BioAnalyzer vs. LabChip Traces
Differences in instrument resolution can also have an impact on the appearance of the trace. The resolution of the Tapestation traces is not as high as the Bioanalyzer or LabChip. Therefore, for products such as the Human BCR amplification trace, which on the Bioanalyzer shows two sharp peaks very close together, on the Tapestation it will often show just one broader peak, as the resolution is typically not sufficient to distinguish the two peaks from each other.
Products: Single Cell Immune Profiling