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Old 02-13-2019, 08:59 AM   #1
Lechu
Junior Member
 
Location: Germany

Join Date: Aug 2017
Posts: 4
Default barcoded RNA adapter ligation for multiplexing

Hi All,

This is my first post here, so hello everyone!

I'm wondering if it is possible to use RNA adapter ligated to (preferably) 3' end of the RNA for multiplexing the samples prior to RNA sequencing? If I understand correctly (an my knowledge may be narrow here), typically such adapters are added separately to individual samples, and then the barcodes are added later by PCR.

I would like to:

Ligate RNA adapters into multiple samples, and then pool them together before performing cDNA synthesis. After ligation, samples would be multiplexed, and processed as such from the very beginning. Specifically, I would like to perform a 3'UTR (or its polyA adjacent part) sequencing, using the custom adapter-specific primer containing barcode. My cDNA library would be made as follows, (with optional polyA enrichment):

........................................................................................... <-----------
....NNNNNNNNNNNNNN-AAAAAAAA [...] AAAAAA-BARCODE-ADAPTER

I would then use a random primer and adapter-specific primer for generating a second cDNA strand, and add adapters for amplification on the flow cell by PCR.

I can imagine such approach might lead to biases in case the RNA concentrations and/or quality in individual samples is highly variable. But assuming it is not, I see it as a sound approach. Or am I missing something?

Thank is advance for any helpful insights.

Cheers,
Lech

Last edited by Lechu; 02-13-2019 at 09:09 AM. Reason: layout problems
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