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Forum: Illumina/Solexa 08-29-2016, 08:29 AM
Replies: 10
Views: 1,820
Posted By giderk
Sorry for the delayed response @thermophile, have...

Sorry for the delayed response @thermophile, have been at a conference for past week. I am doing 18SrRNA sequencing and the annealing temperatures of the degenerate primers I am using ranges from...
Forum: Illumina/Solexa 08-19-2016, 07:39 PM
Replies: 10
Views: 1,820
Posted By giderk
Hello HESmith, I was worried that with so many...

Hello HESmith, I was worried that with so many variants of the sequencing primers that there would be competitive binding and a negative dilution effect. Is that not what you would expect in this...
Forum: Illumina/Solexa 08-19-2016, 01:12 PM
Replies: 10
Views: 1,820
Posted By giderk
I haven't run the MiSeq yet, but I will soon. My...

I haven't run the MiSeq yet, but I will soon. My funding for re-runs in the event of failures is really limited, so I am trying to weigh my options.

In response to kerplunk412, I didn't think that...
Forum: Illumina/Solexa 08-19-2016, 08:38 AM
Replies: 10
Views: 1,820
Posted By giderk
Thanks for sharing that experience. Do you have...

Thanks for sharing that experience. Do you have any new information after the temps on the machines were inspected? Did it turn out that they were operating at different temperatures, and does it...
Forum: Illumina/Solexa 08-18-2016, 08:41 PM
Replies: 10
Views: 1,820
Posted By giderk
Changing the MiSeq annealing temperature

Does anyone have experience modifying the MiSeq to run at an annealing temperature that is less than 65 C? I am following the Kozich et al. 2013...
Forum: Illumina/Solexa 08-31-2015, 03:07 PM
Replies: 3
Views: 1,705
Posted By giderk
Selecting new primers for Illumina's 16s protocol

This is a quick question with hopefully a quick answer:)

Illumina published a recommended protocol for 16S Metagenomic Sequencing Library Preparation. In the protocol they suggest that you can...
Forum: Illumina/Solexa 05-11-2015, 09:43 PM
Replies: 2
Views: 2,962
Posted By giderk
universal 18s eukaryotic primers

I'm wondering if anyone has identified a good primer pair that spans the 18s rRNA v4 region and is proven to work well on the MiSeq platform. I haven't found any established protocols in the...
Forum: Introductions 04-23-2015, 11:53 AM
Replies: 3
Views: 1,187
Posted By giderk
Thank you. My main obstacle at the moment is...

Thank you. My main obstacle at the moment is selecting primers for this protocol that would give me the best resolution for species-specific identification. Others on this forum have suggested a...
Forum: Sample Prep / Library Generation 04-23-2015, 07:39 AM
Replies: 4
Views: 1,833
Posted By giderk
Thank you again. Since the work is not published...

Thank you again. Since the work is not published yet, it would be very helpful to speak directly with you (or another person in your lab) about the 18s primers they decided to use and why. This...
Forum: Sample Prep / Library Generation 04-22-2015, 08:32 AM
Replies: 4
Views: 1,833
Posted By giderk
Thank you for responding. I just want to make...

Thank you for responding. I just want to make sure I understand correctly. With respect to the first PCR step, you are saying that the same protocol that is optimized for just the locus-specific...
Forum: Sample Prep / Library Generation 04-21-2015, 12:42 PM
Replies: 4
Views: 1,833
Posted By giderk
Adapting Illumina's 16s library prep protocol to function with 18s rRNA

I'm interested in studying eukaryotic parasite diversity in fecal samples that I've collected. There are a variety of Illumina myseq protocols out there, and of most interest to me is the one...
Forum: Introductions 04-21-2015, 12:03 PM
Replies: 3
Views: 1,187
Posted By giderk
Interested in Illumina myseq 16s barcoding

I've just signed up this forum and am introducing myself as suggested. I am most curious in 16s rRNA barcoding using the protocol that Illumina published; 16s Metagenomic Sequencing Library...
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