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Advantage of 5'solution?

Posted By: RanINY, on Nov 21, 2018 at 1:24 PM

Hi All,

 

I'm very new at single cell field and interested in human immuno profiling. 

I'm trying to set up 5' single cell VDJ library. What's the adventage of 5' solution comparing to 3'?

 

Thank you! 

3 Replies

Re: Advantage of 5'solution?

Posted By: eileendalin, on Nov 27, 2018 at 1:14 PM

The Chromium Single Cell Immune Profiling Solution produces Illumina® sequencer-ready libraries for profiling T-cell receptor (TCR) or B cell immunoglobulin (Ig) repertoires from single cells. In addition, users have the option of profiling 5’ gene expression from the same cells. The Single Cell 3' Solution does not have this additional V(D)J library capability.

 

The Single Cell 3' solution is recommended for general gene expression applications, as 3' is the gold standard and the better understood approach in the scientific community. For this reason, the human transcriptome reference may be more complete at the 3' end. If you plan on profiling your samples based on VDJ transcripts as well, then the 5' solution is recommended.

Re: Advantage of 5'solution?

Posted By: RanINY, on Nov 27, 2018 at 1:41 PM

Thank you! Then, why use 5' for VDJ instead of 3'?

Re: Advantage of 5'solution?

Posted By: eileendalin, on Nov 28, 2018 at 11:16 AM

The 5' single cell application due to the V(D)J region being located at the 5' end of the transcript. A detailed description of the assay configuration for Chromium Single Cell V(D)J libraries can be found here:

https://support.10xgenomics.com/single-cell-vdj/index/doc/technical-note-assay-scheme-and-configurat...