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Forum: Sample Prep / Library Generation 03-28-2013, 12:08 PM
Replies: 49
Views: 73,570
Posted By aperera
As mentioned earlier with Ampure XP, we were...

As mentioned earlier with Ampure XP, we were seeing inconsistent results. Our recent testing with SPRIselect has been going well and the data so far looks amazing! What seem to work best for us is...
Forum: Sample Prep / Library Generation 03-26-2013, 12:59 PM
Replies: 49
Views: 73,570
Posted By aperera
I heard there should be less lot to lot variation...

I heard there should be less lot to lot variation that you sometimes see when doing size selection with Ampure XP. So in other words, sounds like there is more QC that goes on for SPRISelect. Not...
Forum: Illumina/Solexa 12-17-2012, 10:23 AM
Replies: 32
Views: 26,361
Posted By aperera
We just got our machine upgraded to a 2500....

We just got our machine upgraded to a 2500. Validation runs went great and we will be running two FCs today on Rapid Mode! Nice not having to wait to fill FCs when odd read lengths are requested....
Forum: Events / Conferences 12-17-2012, 09:52 AM
Replies: 1
Views: 1,371
Posted By aperera
Registration open for ABRF 2013 Meeting

Meet other core facility folks at ABRF 2013 meeting! Registration is now open! http://conf.abrf.org/
Forum: Illumina/Solexa 07-06-2012, 02:26 PM
Replies: 9
Views: 4,757
Posted By aperera
Hi Phillip, We have used BiooScientific...

Hi Phillip,

We have used BiooScientific Adapters (96 are available). Since you are at a core you understand the difficulty in batching samples/orders. Also, if the library failure rate is low and...
Forum: Illumina/Solexa 07-06-2012, 12:44 PM
Replies: 9
Views: 4,757
Posted By aperera
MiSeq for library QC

Hello,

Are you at a core facility that has a MiSeq? If so, are you using the MiSeq to quantify/QC libraries before processing on a HiSeq? If you do this, can you share how you have the workflow...
Forum: General 02-21-2012, 10:44 AM
Replies: 1
Views: 13,719
Posted By aperera
Conferences

http://conf.abrf.org/index.cfm/page/satellite_workshops.htm

Check out the ABRF conference in March. There is a pre-meeting workshop on RNA-Seq and Methyl-Seq


There is also the xgenconference:...
Forum: RNA Sequencing 02-03-2012, 02:19 PM
Replies: 0
Views: 1,778
Posted By aperera
Epigenomics Workshop at ABRF 2012 Meeting

Check out the program @ http://conf.abrf.org/index.cfm/page/...kshops/SW4.htm
Forum: Epigenetics 02-03-2012, 02:18 PM
Replies: 0
Views: 2,177
Posted By aperera
Epigenomics Workshop at ABRF 2012 Meeting

Check out the program @ http://conf.abrf.org/index.cfm/page/satellite_workshops/SW4.htm
Forum: Sample Prep / Library Generation 12-14-2011, 07:36 AM
Replies: 1
Views: 1,760
Posted By aperera
DNA/RNA analyzing

We are considering buying a high throughput DNA/RNA analyzer. So far we have looked at Caliper LabChip GX and Advanced Analytical Fragment Analyzer. Soon we will be looking at the Agilent Tape...
Forum: Sample Prep / Library Generation 09-28-2011, 09:57 AM
Replies: 13
Views: 5,873
Posted By aperera
Just a quick update... We tried the Millipore...

Just a quick update...
We tried the Millipore Magna ChIP-Seq kit with the Bioo Scientific adapters, and obtained beautiful libraries. We have only constructed 10 libraries so far, and hope to...
Forum: Sample Prep / Library Generation 06-13-2011, 10:20 AM
Replies: 13
Views: 5,873
Posted By aperera
Has anyone tried the Millipore's Magna ChIP-Seq...

Has anyone tried the Millipore's Magna ChIP-Seq kit? We are planning on trying this soon and will share results when available.
Forum: Sample Prep / Library Generation 05-24-2011, 11:37 AM
Replies: 13
Views: 5,873
Posted By aperera
We are seeing inconsistent quality of libraries...

We are seeing inconsistent quality of libraries when TruSeq kits are used. I am looking in to Bioo Scientific kits. Also heard that they will release ChIP-Seq kits next. Can not wait!!!
Forum: Sample Prep / Library Generation 05-12-2011, 01:09 PM
Replies: 13
Views: 5,873
Posted By aperera
Illumina ChIP-Seq

What kits are people currently using to make Illumina multiplexed ChIP-Seq libraries? We are not able to get an answer from Illumina regarding when the TruSeq ChIP-Seq kits will be available or what...
Forum: Epigenetics 10-08-2010, 12:08 PM
Replies: 5
Views: 4,148
Posted By aperera
Can you tell me what sort of bias towards GC...

Can you tell me what sort of bias towards GC content you are seeing?
Forum: Illumina/Solexa 10-05-2010, 08:19 AM
Replies: 4
Views: 4,653
Posted By aperera
I will check this out. Thanks a lot!

I will check this out. Thanks a lot!
Forum: Illumina/Solexa 10-04-2010, 03:30 PM
Replies: 4
Views: 4,653
Posted By aperera
LIMS for Next gen sequencing

Currently we have a custom LIMS that require some updates. We are considering if we should make these changes or purchase a commercial LIMS. As for commercial LIMS we have been looking at the ones...
Forum: Sample Prep / Library Generation 10-04-2010, 03:28 PM
Replies: 1
Views: 2,793
Posted By aperera
Whole genome amplification prior to ChIP-Seq

As anyone tried WGA for ChIP-Seq experiments? If so, what kit and what sort of bias (if any) have you observed?
Forum: Illumina/Solexa 09-27-2010, 11:42 AM
Replies: 18
Views: 7,151
Posted By aperera
That's right, it is the ideal. We have used...

That's right, it is the ideal. We have used larger sizes as well.
Forum: Illumina/Solexa 09-24-2010, 10:27 AM
Replies: 18
Views: 7,151
Posted By aperera
At a recent Illumina user meeting, we were told...

At a recent Illumina user meeting, we were told the ideal insert size is 150-200bp.
Forum: Sample Prep / Library Generation 08-03-2010, 08:59 AM
Replies: 0
Views: 2,265
Posted By aperera
Illumina Library Prep Issue

Recently, we made 4 Illumina paired-end libraries using the standard protocol with a brand new Illumina paired-end sample prep kit. The libraries looked great on a bioanalyzer but when we sequenced,...
Forum: Sample Prep / Library Generation 08-03-2010, 08:35 AM
Replies: 23
Views: 18,536
Posted By aperera
Has anyone tried the "Size Selector" beads from...

Has anyone tried the "Size Selector" beads from Aline Bio?
Forum: Sample Prep / Library Generation 08-03-2010, 08:29 AM
Replies: 6
Views: 5,127
Posted By aperera
This is not due to the size selection and it is...

This is not due to the size selection and it is not primer-dimer. We see this as well and think it has something to do with how the DNA is migrating. One thing we have noticed is that you need to...
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