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Forum: Illumina/Solexa 05-08-2017, 03:18 PM
Replies: 14
Views: 9,679
Posted By RCJK
check this out: ...

check this out:
https://support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/nextseq/nextseq-custom-primers-guide-15057456-01.pdf
Forum: Core Facilities 05-05-2016, 02:57 PM
Replies: 8
Views: 5,790
Posted By RCJK
Hi Bukowski, What Pre-PCR preps are you...

Hi Bukowski,

What Pre-PCR preps are you doing on the Zephyr? We mainly use ours for bead cleanups and that's it.
We use the NGS Express for some pre-PCR stuff. It's a bit limited if you want...
Forum: Illumina/Solexa 12-18-2014, 12:53 AM
Replies: 55
Views: 30,194
Posted By RCJK
You can get ART 200ul extended length pipette...

You can get ART 200ul extended length pipette tips that fit nicely into the wells and reach the bottom. Really good for mixing the primers in without the need for any sloshing.
Forum: Sample Prep / Library Generation 12-10-2014, 08:04 PM
Replies: 19
Views: 6,408
Posted By RCJK
We use the NextSeq protocol with the 200mM Tris...

We use the NextSeq protocol with the 200mM Tris pH 7 all of the time for our MiSeq runs.
Forum: Illumina/Solexa 07-16-2014, 11:34 PM
Replies: 43
Views: 26,484
Posted By RCJK
Hi Tony, Thanks for the response. Did you...

Hi Tony,
Thanks for the response. Did you need to change the sequencing primers, or did you use completely different target primers for your initial PCR?
I'm seeing a similar thing with a set...
Forum: Illumina/Solexa 07-16-2014, 12:40 AM
Replies: 43
Views: 26,484
Posted By RCJK
Hi Tony, I know it's been a while, but have you...

Hi Tony,
I know it's been a while, but have you been able to resolve your issue with the dim clusters? If so, what did you do to resolve the issue?
Thanks!
Forum: 454 Pyrosequencing 09-23-2013, 07:55 PM
Replies: 11
Views: 6,129
Posted By RCJK
I was told by Roche that they want the engineers...

I was told by Roche that they want the engineers to install the update. Apparently in some cases it has killed the FLX+'s onboard computer.
Forum: 454 Pyrosequencing 07-30-2013, 05:17 PM
Replies: 3
Views: 1,511
Posted By RCJK
I used to use plate seals until a few years ago. ...

I used to use plate seals until a few years ago. Then I had a streak of broken emulsions and the seals ended up being the culprit. Once I switched to caps, the broken emulsions went away. I would...
Forum: General 07-18-2013, 04:45 PM
Replies: 2
Views: 956
Posted By RCJK
Seeing at you're in Brisbane, I would guess it...

Seeing at you're in Brisbane, I would guess it refers to Bioplatforms Australia.
http://www.bioplatforms.com.au/
Forum: Illumina/Solexa 06-26-2013, 05:24 PM
Replies: 2
Views: 2,357
Posted By RCJK
For a dual index approach, have a look at: ...

For a dual index approach, have a look at:
http://www.mothur.org/w/images/0/0c/Wet-lab_MiSeq_SOP.pdf
Forum: Sample Prep / Library Generation 06-02-2013, 05:55 PM
Replies: 6
Views: 1,859
Posted By RCJK
Here's a protocol demonstrating how to use dual...

Here's a protocol demonstrating how to use dual indexing with amplicons on MiSeq:
http://www.mothur.org/w/images/0/0c/Wet-lab_MiSeq_SOP.pdf
Forum: Core Facilities 05-29-2013, 11:20 PM
Replies: 3
Views: 2,667
Posted By RCJK
I think you would need to dilute your sample to...

I think you would need to dilute your sample to be sure it is in the range for the Pico chip. They use them here for some microarray stuff.
Forum: Illumina/Solexa 05-23-2013, 04:33 PM
Replies: 8
Views: 2,717
Posted By RCJK
For small sample number with Nextera kits we use...

For small sample number with Nextera kits we use the Zymo columns instead of the plates. We still use Ampure XP beads for cleanups.
The beads in the Nextera XT kit are for normalization, not...
Forum: Sample Prep / Library Generation 05-15-2013, 11:35 PM
Replies: 10
Views: 6,816
Posted By RCJK
If you have a low concentration library, add an...

If you have a low concentration library, add an equal volume of 200mM Tris pH 7.0 after the 5 minute NaOH denaturation to neutralize the NaOH. Then you do not need to worry about NaOH final...
Forum: 454 Pyrosequencing 04-01-2013, 08:08 PM
Replies: 5
Views: 1,595
Posted By RCJK
In the Nov 2012 FLX+ system table of materials...

In the Nov 2012 FLX+ system table of materials needed but not provided, combitip advanced tips are listed. Not sure if these match the part numbers mentioned earlier.
Forum: Metagenomics 03-26-2013, 10:45 PM
Replies: 4
Views: 5,280
Posted By RCJK
Just an fyi, with the new MiSeq software out this...

Just an fyi, with the new MiSeq software out this week they claim you can get away with only a 5% PhiX spike-in for low diversity libraries.
Forum: General 03-19-2013, 10:17 PM
Replies: 5
Views: 2,748
Posted By RCJK
If running a 2x250bp run, you'll also want to get...

If running a 2x250bp run, you'll also want to get rid of some of the smaller fragments. That's why they tell you to use less beads for the longer runs.
Forum: Sample Prep / Library Generation 02-17-2013, 04:14 PM
Replies: 3
Views: 1,184
Posted By RCJK
What type of samples will you be prepping?

What type of samples will you be prepping?
Forum: 454 Pyrosequencing 02-11-2013, 08:32 PM
Replies: 2
Views: 1,136
Posted By RCJK
Hi there. The new Paired End Rapid Library...

Hi there. The new Paired End Rapid Library Protocol uses the same RL adaptors, or RLMID adaptors, and Lib-L chemistry as the shotgun Rapid Libraries. Thus they'll have the same GACT key as your...
Forum: 454 Pyrosequencing 02-06-2013, 03:51 PM
Replies: 4
Views: 1,710
Posted By RCJK
You can also try the long amplicon emPCR protocol...

You can also try the long amplicon emPCR protocol since yours is >600bp.
Forum: Sample Prep / Library Generation 01-07-2013, 09:28 PM
Replies: 10
Views: 7,002
Posted By RCJK
Nick, have you compared metagenomic DNA prepped...

Nick, have you compared metagenomic DNA prepped with Nextera vs Nextera XT as well?
Forum: 454 Pyrosequencing 01-07-2013, 09:26 PM
Replies: 4
Views: 1,009
Posted By RCJK
It does take a while, but I've never timed it. ...

It does take a while, but I've never timed it. I'd say a minute or two.
Forum: 454 Pyrosequencing 12-06-2012, 09:39 PM
Replies: 2
Views: 875
Posted By RCJK
It should be fine. I believe the chemistries are...

It should be fine. I believe the chemistries are the same between platforms. You can use MV emPCR kits for the Jr, so beads from any of the SV or LV kits should be fine as well.
Forum: 454 Pyrosequencing 12-04-2012, 01:30 PM
Replies: 2
Views: 979
Posted By RCJK
In what way have the runs failed?

In what way have the runs failed?
Forum: Illumina/Solexa 11-15-2012, 04:45 PM
Replies: 7
Views: 15,744
Posted By RCJK
They've recently mentioned 2x300bp for the MiSeq...

They've recently mentioned 2x300bp for the MiSeq in the 2nd half of 2013.
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