SEQanswers

Go Back   SEQanswers > Applications Forums > Sample Prep / Library Generation



Similar Threads
Thread Thread Starter Forum Replies Last Post
16S metagenomics on MiSeq sajoshi Illumina/Solexa 3 04-05-2016 08:43 AM
Ampliseq panel on MiSeq ryan.england@esr.cri.nz Illumina/Solexa 6 09-23-2015 01:55 AM
cancer panel on miseq bartekd Illumina/Solexa 3 01-29-2013 12:56 PM
16S PCR Cleanup: MoBio or Qiagen rsirois Sample Prep / Library Generation 4 01-23-2013 01:00 PM

Reply
 
Thread Tools
Old 08-02-2019, 04:17 AM   #1
HelenaSC
Member
 
Location: Spain

Join Date: Jun 2013
Posts: 21
Default Anyone using QIAGEN 16S/ITS Panel with MiSeq?

Hi there!

Anyone using QIAGEN 16S/ITS Panel with MiSeq?

We have good libraries with good profiles, quantified by TapeStation, Qubit and qPCR and we load them according to Qiagen instructions (dilute to 2nM and load at 10pM) and it result in very low cluster density...NaOH is working properly with all the other runs, the Miseq is also giving good results with other type of Runs....anyone is in the same situation? Or anyone is having good results with this Panel sequencing on a MiSeq?

Thanks a lot in advance!
HelenaSC is offline   Reply With Quote
Old 08-02-2019, 07:37 AM   #2
kmcarr
Senior Member
 
Location: USA, Midwest

Join Date: May 2008
Posts: 1,165
Default

Are you sure that it really is low cluster density? Do you have access to the Thumbnails? When a flow cell is very overloaded it may falsely report a low cluster density. I ask because our experience with 16S/ITS amplicons on the MiSeq is that they need to be loaded at much lower concentrations (3.0pM). But this is with amplicon we make using the Schloss SOP. Amplicons prepared using a different protocol may require very different loading concentration.
kmcarr is offline   Reply With Quote
Old 08-04-2019, 10:25 PM   #3
HelenaSC
Member
 
Location: Spain

Join Date: Jun 2013
Posts: 21
Default

Hi there,

THanks a lot for your comments. Yes, I'm sure it is low cluster density, I can see it at the thumbnails and comparing to other runs. We only got like 200K clusters...that is really low
HelenaSC is offline   Reply With Quote
Reply

Tags
16s/its, low cluster density, microbiome, miseq, qiagen

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 12:14 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO