Cell count: VDJ vs Whole expression
At the lab, we tested VDJ workflow on PBMC and B cell. We encapsulated PBMC and B cell separatly and then after the cDNA amplification we split our cDNA in three (for TCR enrichment and BCR enrichement, and for 5' gene expression).
For PBMC gene expression we obtained less cell than VDJ (around half of the cell counted in gene expression). But with B cell, we obtained almost 3 times more counted cell in VDJ than in gene expression.
How is that possible?
Does the cell count in VDJ in also based on counting the barcode?
If you have any suggestion...
Re: Cell count: VDJ vs Whole expression
Regarding cell calling in VDJ vs Gene Expression, we would in general expect to see more cells being called in GEX data, because, unless you have sorted cells, you would expect to see a subset of T or B cells in your sample. Also because, VDJ cell calling is done only based on the TCr or Ig chains. TCR for example are low expressed and so there is a chance of these not seen in the data.
So if you are seeing more cells being called by VDJ pipeline as compared to Gene Expression, that is not usual.
If you could share your web_summary.html files for TCr, BCR and GEX data for your PBMC sample, we would be happy to investigate.
Please email email@example.com for sharing your web_summary.html files. If you could mention this conversation in that email with the web_summaries, would be great.