SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 49
Search took 0.00 seconds.
Search: Posts Made By: jlove
Forum: Illumina/Solexa 07-12-2018, 11:00 AM
Replies: 0
Views: 1,783
Posted By jlove
Ordering Nextera XT Oligos from IDT?

I would like to start ordering Nextera XT Index Kit v2 Set A from IDT in plate-based format, instead of plating them out myself. I called them hoping that they would have an "off-the-shelf" product...
Forum: Illumina/Solexa 04-12-2018, 01:59 PM
Replies: 2
Views: 4,372
Posted By jlove
FuPa reagent?

Can anyone explain how the FuPa reagent works? In the context of Illumina library preparation, The FuPa reagent is a proprietary reagent that is used to partially digest the primers and phosphorylate...
Forum: Illumina/Solexa 06-13-2016, 08:24 AM
Replies: 3
Views: 3,547
Posted By jlove
This is very handy, thank you! May I ask how you...

This is very handy, thank you! May I ask how you figured out these sequences?
Jen
Forum: Illumina/Solexa 06-06-2016, 02:43 PM
Replies: 3
Views: 3,547
Posted By jlove
P5/P7 Flowcell Oligos

I apologize if this has been hashed out already, but I cannot seem to find any definitive documentation which describes whether the flowcell oligos are P5 and P7, or the complements. I know Illumina...
Forum: Sample Prep / Library Generation 02-25-2016, 01:31 PM
Replies: 3
Views: 1,680
Posted By jlove
Assay to test for ligation efficiency?

Hi,
Has anyone got a method for assessing TruSeq ligation efficiency, pre-PCR? We use the KAPA Illumina library quant kit for final library quantification, and I can certainly try using this, but I...
Forum: Sample Prep / Library Generation 08-24-2015, 10:58 AM
Replies: 0
Views: 617
Posted By jlove
control DNA for ChIP Library Preps?

I'm wondering if anyone has a certain control DNA they like to use to control batch quality when doing Illumina ChIP-Seq library preps? I don't want a spike-in, just some processed, clean DNA that...
Forum: Illumina/Solexa 09-12-2012, 08:36 AM
Replies: 8
Views: 2,059
Posted By jlove
Garyb- do you have a link or can you tell me...

Garyb- do you have a link or can you tell me which user documentation says this? I'd love to have a copy. Thank you!
-Jen
Forum: Illumina/Solexa 09-07-2012, 10:33 AM
Replies: 8
Views: 2,059
Posted By jlove
Do you freeze hyb cocktails?

I asked Illumina about whether or not I could prepare my flowcell hyb cocktails well in advance and freeze them, and the official recommendation was not to store them for longer than a day or two....
Forum: Illumina/Solexa 07-23-2012, 08:45 AM
Replies: 10
Views: 4,152
Posted By jlove
Phillip- you're right, I do ChIP manually with...

Phillip- you're right, I do ChIP manually with bead purifications and it works very well. The reaction volumes (and bead amounts) were not compatible with the small inputs in the SPRI cartridges.
Forum: Illumina/Solexa 07-20-2012, 12:51 PM
Replies: 10
Views: 4,152
Posted By jlove
Hi GenBio64- We stopped using SPRIworks...

Hi GenBio64- We stopped using SPRIworks altogether, and I think the reason for our troubles had to do with the fact that we were doing ChIP-Seq (with tiny amounts of input), which does not size...
Forum: Sample Prep / Library Generation 05-08-2012, 09:04 AM
Replies: 8
Views: 5,597
Posted By jlove
I use the TruSeq adapters at 1:50 for any ChIP...

I use the TruSeq adapters at 1:50 for any ChIP input from 5-50 ng and do 18 cycles of PCR before size selection.
Forum: Illumina/Solexa 05-08-2012, 09:02 AM
Replies: 1
Views: 2,025
Posted By jlove
I have found that, after a few freezing and...

I have found that, after a few freezing and thawing cycles (precise number unknown, maybe 5?), my PCR yields start to decline. So I started aliquotting them out. I store them at -20C and thaw them at...
Forum: Illumina/Solexa 04-30-2012, 10:32 AM
Replies: 1
Views: 1,739
Posted By jlove
TruSeq ligation vs old ligation?

The old Illumina ligation conditions changed with the TruSeq kit. I had trouble swapping in TruSeq adapters for the old adapters using the old protocol, and I don't know why. Does anybody happen to...
Forum: Sample Prep / Library Generation 04-30-2012, 10:27 AM
Replies: 8
Views: 5,597
Posted By jlove
Hi Flora, We do almost exclusively ChIP-Seq in...

Hi Flora,
We do almost exclusively ChIP-Seq in our facility, using the TruSeq kit.
Forum: Sample Prep / Library Generation 03-05-2012, 07:44 AM
Replies: 1
Views: 2,106
Posted By jlove
Dario, It sounds like you're doing ChIP Seq......

Dario,
It sounds like you're doing ChIP Seq... are you using the TruSeq kit? If so, I can tell you what we do. I use 10 to no more than 50 ng of input as measured by pico green, and a 1:50 dilution...
Forum: Illumina/Solexa 03-05-2012, 07:42 AM
Replies: 15
Views: 12,371
Posted By jlove
Hi lilin001, I don't know about the number of...

Hi lilin001,
I don't know about the number of reads (it varies from user to user how much we load and how many clusters we get), but when we do our calculations based on the size of the smaller...
Forum: Core Facilities 01-31-2012, 11:11 AM
Replies: 22
Views: 24,591
Posted By jlove
Hi firedancer - thanks for the feedback. I'd be...

Hi firedancer - thanks for the feedback. I'd be interested to hear about any specific tweaks. (if you can easily recall any details).
Forum: Illumina/Solexa 01-12-2012, 10:57 AM
Replies: 5
Views: 4,063
Posted By jlove
"With-Bead" SPRI Library Preps - anyone doing this?

Has anyone (besides Broad) tried doing this "with-bead" library prep method? It basically involves leaving the beads in the reaction tubes throughout the library prep protocol, and serially eluting...
Forum: Core Facilities 12-16-2011, 01:22 PM
Replies: 22
Views: 24,591
Posted By jlove
Anybody own an EpMotion 5075 liquid handler?

We're looking into liquid handlers and we checked out the Eppendorf EpMotion 5075 recently. We're doing our due diligence - does anybody have any reviews or experience to share? We'd be looking for...
Forum: Illumina/Solexa 12-16-2011, 01:20 PM
Replies: 0
Views: 1,759
Posted By jlove
Anybody own an EpMotion 5075 Liquid Handler?

We're looking into liquid handlers and we checked out the Eppendorf EpMotion 5075 recently. We're doing our due diligence - does anybody have any reviews or experience to share? We'd be looking for...
Forum: Illumina/Solexa 12-01-2011, 01:11 PM
Replies: 2
Views: 2,224
Posted By jlove
We have both the kit version and the homemade...

We have both the kit version and the homemade version. They are equivalent, but I believe the testing was done with TruSeq adapters. Curious! Thanks for the reply.
Forum: Illumina/Solexa 12-01-2011, 11:35 AM
Replies: 2
Views: 2,224
Posted By jlove
Using TruSeq adapters with older protocols- not working?

We have tried a couple of times to use old stand-by homemade library protocols (which worked fine with the old adapter oligo) with TruSeq adapters swapped in for the old adapters. It never seems to...
Forum: Epigenetics 11-30-2011, 07:15 AM
Replies: 57
Views: 40,964
Posted By jlove
I'm using the TruSeq kit with ChIP-Seq routinely...

I'm using the TruSeq kit with ChIP-Seq routinely with good success, if anyone wants to give it a go using the kit instead of homemade components. I just use a 1:10 dilution of adapter for ~ 100 ng of...
Forum: Sample Prep / Library Generation 11-11-2011, 12:06 PM
Replies: 10
Views: 6,904
Posted By jlove
I'm bumping my own message, since I last inquired...

I'm bumping my own message, since I last inquired about it back in Aug. I recently looked at the Eppendorf automation for library prep, but it's more "semi-automated." The plates require manual...
Forum: Epigenetics 10-14-2011, 09:58 AM
Replies: 57
Views: 40,964
Posted By jlove
I switched to using my own (short) P5 and P7 PCR...

I switched to using my own (short) P5 and P7 PCR primers and definitely get some dimer now, but I used to get adapter dimer when I was using the PCR components (master mix and primer) that came with...
Showing results 1 to 25 of 49

 


All times are GMT -8. The time now is 11:52 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO