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Forum: Ion Torrent 06-15-2018, 09:27 AM
Replies: 3
Views: 901
Posted By jhalpin
Opentrons Automated Pipetting System

Has anyone here used the Opentrons OT-2 for library preparation? https://opentrons.com/ot-2 (http://opentrons.com/ot-2)
Forum: Ion Torrent 05-02-2018, 09:06 AM
Replies: 2
Views: 1,077
Posted By jhalpin
What method are you using to load it? What...

What method are you using to load it? What library prep kit are you using?
Forum: Ion Torrent 05-02-2018, 07:07 AM
Replies: 9
Views: 2,796
Posted By jhalpin
We have an S5 that we're using 400bp chemistry...

We have an S5 that we're using 400bp chemistry on. It's been doing pretty well and is SO much easier to use than the PGM.

Can anyone comment on the 600bp kit? How is the size selection with it?
Forum: Oxford Nanopore 01-30-2018, 11:07 AM
Replies: 4
Views: 2,619
Posted By jhalpin
Thanks for the clarification.. I was having a...

Thanks for the clarification.. I was having a hard time with Oxford's information on run vs sample.
Forum: Oxford Nanopore 01-30-2018, 06:34 AM
Replies: 4
Views: 2,619
Posted By jhalpin
I am also curious about costs. I'd like to run...

I am also curious about costs. I'd like to run multiplex bacterial genomes and it looks like from the oxford site I can use either the 1d or 1d2 kit. Is it reasonable to run 12 4Mb genomes on one...
Forum: Bioinformatics 04-19-2017, 05:46 AM
Replies: 7
Views: 1,075
Posted By jhalpin
... you have single end Illumina data? Is that a...

... you have single end Illumina data? Is that a thing?

We use Ion Torrent technology, but if I see that it's usually a size selection problem.. something went wrong with my bead ratios.
Forum: General 03-30-2017, 11:08 AM
Replies: 0
Views: 773
Posted By jhalpin
Question streptavidin losing magnetic properties?

Anyone have any experience with streptavidin beads losing their magnetic properties? They have not been boiled nor frozen. It's for an antibody binding assay and it's really random as to which...
Forum: Ion Torrent 02-01-2017, 10:41 AM
Replies: 15
Views: 3,444
Posted By jhalpin
I don't know the solution, but I can tell you Ion...

I don't know the solution, but I can tell you Ion Torrent has a lot of deletion errors that are sequencing artifacts when sequencing through a long (>5bp) homopolymer region. If this is where your...
Forum: Ion Torrent 05-20-2016, 09:42 AM
Replies: 8
Views: 3,898
Posted By jhalpin
Out of curiosity, does the NEB kit have less...

Out of curiosity, does the NEB kit have less cleanup steps?
Forum: Ion Torrent 02-18-2016, 06:37 AM
Replies: 8
Views: 3,898
Posted By jhalpin
Talking I have not used the NEBnext kit, but I do...

I have not used the NEBnext kit, but I do regularly use the Kapa BioSciences kit for IonTorrent libraries. It is significantly less expensive than the Life Tech kit and I get much much better...
Forum: Ion Torrent 04-10-2015, 01:55 PM
Replies: 0
Views: 1,058
Posted By jhalpin
Question Double sided SPRI for size selection -- Ion Library

Has anyone tried double-sided SPRI size selection in place of the e-gel? How did it work?
Forum: Ion Torrent 03-06-2015, 07:28 AM
Replies: 2
Views: 1,278
Posted By jhalpin
In case anyone is wondering, it wasn't the tween....

In case anyone is wondering, it wasn't the tween. I tried to run this pool again yesterday and got the same results. Measured the pool by qubit (should have been ~30ng/mL) and it was too low to...
Forum: Ion Torrent 03-06-2015, 07:18 AM
Replies: 3
Views: 1,792
Posted By jhalpin
Allright, fixing the Tris concentration didn't...

Allright, fixing the Tris concentration didn't fix my problem. I'm inputting 200 ng and getting 0.02 ng/ul at the end of library prep. It's technically enough to sequence but it's really low.. I'd...
Forum: Sample Prep / Library Generation 03-05-2015, 11:46 AM
Replies: 0
Views: 649
Posted By jhalpin
Question MiSeq -- Kapa Library Kit for Clostridia?

Has anyone tried one of Kapa's library kits on Clostrida ssp or another AT rich organism? It's supposed to show less bias due to GC content. What was your result?
Forum: Sample Prep / Library Generation 03-05-2015, 11:39 AM
Replies: 0
Views: 915
Posted By jhalpin
Question Ion Torrent -- KAPA library kit -- Any impressions?

Has anyone tried Kapa's kit for Ion Torrent libraries? How'd it work?

http://www.kapabiosystems.com/product-applications/platforms/ion-torrent/library-preparation-for-ion-torrent/
Forum: Ion Torrent 02-02-2015, 09:29 AM
Replies: 3
Views: 1,792
Posted By jhalpin
Red face Well huh. Looking back at my notes I wrote down...

Well huh. Looking back at my notes I wrote down 10 mM. Not sure when/how that turned into 100 mM. I guess I know why my libraries are weird now.

I'll check out the Q columns, too. Thanks!
Forum: General 01-30-2015, 02:04 PM
Replies: 7
Views: 3,606
Posted By jhalpin
Is there a brand you'd recommend for DNA cleanup...

Is there a brand you'd recommend for DNA cleanup for sequencing applications?

Thanks,

Jessica
Forum: Ion Torrent 01-30-2015, 01:39 PM
Replies: 2
Views: 1,278
Posted By jhalpin
Angry So I had a sudden flashback to mixing the melt...

So I had a sudden flashback to mixing the melt off solution and thinking it didn't look "sudsy". It's entirely possible I put water in instead of tween, since the bottles are exactly the same. Has...
Forum: Ion Torrent 01-30-2015, 01:11 PM
Replies: 2
Views: 1,278
Posted By jhalpin
Question PGM: No loading on 316v2 chip

Hello,

I ran a 316v2 chip today for the 2nd run of an initialization. My chip has 2% loading.. could this be a templating or enrichment failure? My QC percentage was 7.24%. Low, but we've had...
Forum: Ion Torrent 01-30-2015, 01:05 PM
Replies: 3
Views: 1,792
Posted By jhalpin
Question Low yield after library prep

Hello,

I am using the Ion Shear Plus reagents kit to prepare libraries for the PGM. I input 200 ng of DNA (measured by Qubit) but am only getting 0.01-0.1 ng/ul at the end of the process. This...
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