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Old 11-29-2017, 12:34 AM   #1
Bidfudge
Junior Member
 
Location: France

Join Date: Jun 2016
Posts: 6
Default Index hopping Hiseq4000 and single cell

Hi everyone,

We are currently working on single cell experiment with the C1 platform from fluidigm. We plan to sequence 384 single cells with the "SMART-Seq® v4 Ultra® Low Input RNA Kit for the Fluidigm® C1™ System".

In this kit, they used a dual index for the single cell multiplexing.The problem is that we have to sequence these transcriptomes on an Hiseq4000, and It is well know now that some contamination with excess index-primer will lead to an index swapping after demultiplexing :/.

So my question is, does-anybody have an experience to limit this biais? I read some blog, were people used a size-selection of the libraries to remove excess of free primers, or the use the ExonucleaseI enzyme to remove it...

Thanks for the help,
nicolas
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