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Forum: Sample Prep / Library Generation 08-04-2019, 10:25 PM
Replies: 2
Views: 1,376
Posted By HelenaSC
Hi there, THanks a lot for your comments....

Hi there,

THanks a lot for your comments. Yes, I'm sure it is low cluster density, I can see it at the thumbnails and comparing to other runs. We only got like 200K clusters...that is really low :(
Forum: Sample Prep / Library Generation 08-02-2019, 04:17 AM
Replies: 2
Views: 1,376
Posted By HelenaSC
Anyone using QIAGEN 16S/ITS Panel with MiSeq?

Hi there!

Anyone using QIAGEN 16S/ITS Panel with MiSeq?

We have good libraries with good profiles, quantified by TapeStation, Qubit and qPCR and we load them according to Qiagen instructions...
Forum: Sample Prep / Library Generation 05-13-2019, 01:06 AM
Replies: 2
Views: 1,828
Posted By HelenaSC
Dear Luc, THanks for your comments. Before...

Dear Luc,

THanks for your comments. Before polling the libraries, they are quantified by Qubit and analyzed with TapeStation , so we can be sure that the amount and the profile is ok before...
Forum: Sample Prep / Library Generation 05-10-2019, 03:28 AM
Replies: 2
Views: 1,828
Posted By HelenaSC
Question Problems with NEXTERA DNA FLEX ENRICHMENT

Hi there!
Anyone working with Illumina Nextera DNA Flex for Enrichment?

We are experiencing some problems related to the hybridization or capture step. We don't know why, but after pooling the...
Forum: Core Facilities 03-23-2018, 02:32 AM
Replies: 0
Views: 4,752
Posted By HelenaSC
SureSelect XT HS and Sureselect XT

Hi!

Anyone knows if the Forward primer (for the first amplification) in the SureSelect XT HS is the same as the Sureselect Primer (for the first amplification) from SureSelect XT ??

Do you...
Forum: Sample Prep / Library Generation 01-25-2017, 06:53 AM
Replies: 17
Views: 7,593
Posted By HelenaSC
Hi! No news yet...still waiting for QIAgen...

Hi!

No news yet...still waiting for QIAgen ansewer to give us some advice...
Did you ckeck the library profile and quantify you samples?

Thanks!
Forum: Sample Prep / Library Generation 01-18-2017, 05:37 AM
Replies: 17
Views: 7,593
Posted By HelenaSC
Hi Joni, Yes, the larger fragments are...

Hi Joni,

Yes, the larger fragments are supposed to be overamplification. I made a mistake using the recommendation from the tables, i choosed the wrong conditions regarding the number of cycles...
Forum: Sample Prep / Library Generation 11-25-2016, 05:23 AM
Replies: 17
Views: 7,593
Posted By HelenaSC
QIAseq targeted DNA Panel Question

Hi alla!
Anyone has been working with QIAseq targeted DNA Panel??

It is our first trial and I'm not very glad with the libraries profiles on Bioanalyzer... We have performed a first experiment...
Forum: Sample Prep / Library Generation 05-10-2016, 12:45 AM
Replies: 2
Views: 1,452
Posted By HelenaSC
Problem with TruSeq Custom Amplicon Libraries

Hi all!
We need some help with TruSeq Custom Amplicon Low Input libraries 
We have been processing samples (fresh and FFPE) for a while using this Kit and everything worked fine. Before starting...
Forum: Core Facilities 05-10-2016, 12:36 AM
Replies: 1
Views: 5,449
Posted By HelenaSC
Problem with TruSeq Custom Amplicon Low Input Libraries

Hi all!
We need some help with TruSeq Custom Amplicon Low Input libraries 
We have been processing samples (fresh and FFPE) for a while using this Kit and everything worked fine. Before starting...
Forum: Sample Prep / Library Generation 07-18-2013, 07:28 AM
Replies: 12
Views: 6,854
Posted By HelenaSC
Hi again, We quantify libraries using qPCR...

Hi again,

We quantify libraries using qPCR (KAPA Kit) and correcting by size with Bioanalyzer profile. Having a look at the results it seems that Chip is more "represented" than Input, and we...
Forum: Sample Prep / Library Generation 07-18-2013, 06:28 AM
Replies: 12
Views: 6,854
Posted By HelenaSC
So...here are the results :( It seems that ...

So...here are the results :(

It seems that changind the final NaOH concentration has improved, somehow, the quality of the run, but not the cluster density...Now, we have more outputh, higher...
Forum: Sample Prep / Library Generation 07-18-2013, 02:08 AM
Replies: 12
Views: 6,854
Posted By HelenaSC
Thanks a lot!!! IN a few hours I will let you...

Thanks a lot!!!
IN a few hours I will let you know if it worked!
I tried to answer your private message but I think I don't know how to do it, since I tried twice and no messages appear on my "Send...
Forum: Sample Prep / Library Generation 07-17-2013, 07:24 AM
Replies: 12
Views: 6,854
Posted By HelenaSC
My last question before starting (sorry!!! :) ):...

My last question before starting (sorry!!! :) ):

I have two samples (1.1nM) that I want to run together on the MiSeq. Following your instructions, do you think this will be ok ?(to end up with a...
Forum: Sample Prep / Library Generation 07-16-2013, 03:39 AM
Replies: 12
Views: 6,854
Posted By HelenaSC
Hi Calluna! Thanks a lot, I checked your...

Hi Calluna!

Thanks a lot, I checked your maths and they were perfect :P They gave me a 10.95pM final concentraction :)

We will perform the run this week, I hope it will work!

Thanks a lot...
Forum: Sample Prep / Library Generation 07-08-2013, 12:26 AM
Replies: 12
Views: 6,854
Posted By HelenaSC
After reading all these posts, I wonder, can't I...

After reading all these posts, I wonder, can't I just use 0.1N NaOH (instead of 0.2N) to denature my libraries ,with no further neutralization step?
The issue is that I don't want to dilute my...
Forum: Sample Prep / Library Generation 07-07-2013, 11:23 PM
Replies: 12
Views: 6,854
Posted By HelenaSC
Hi Calluna! Thanks for your help, we will...

Hi Calluna!

Thanks for your help, we will keep in mind NaOH concentration for next round :)
Forum: Sample Prep / Library Generation 07-05-2013, 06:30 AM
Replies: 4
Views: 1,791
Posted By HelenaSC
Yes, you are right, the peak should be miRNA,...

Yes, you are right, the peak should be miRNA, tRNA and so on.
Good weekend!
Forum: Sample Prep / Library Generation 07-05-2013, 05:49 AM
Replies: 4
Views: 1,791
Posted By HelenaSC
Hi Lior, Don't you have the possibility to...

Hi Lior,

Don't you have the possibility to check your samples with a Bioanalyzer or similar??
I think it would be better...
Forum: Sample Prep / Library Generation 07-05-2013, 05:39 AM
Replies: 12
Views: 6,854
Posted By HelenaSC
Newbie question: low cluster density on MiSeq (Chip-Seq pool)

Hi all,

I'm new on this and it seems that's we have some problem with cluster density on MiSeq. We have just run a pool of 2 libraries (from Chip-seq ) , 56 cycles and we are getting very bad...
Forum: Sample Prep / Library Generation 06-28-2013, 05:22 AM
Replies: 2
Views: 4,605
Posted By HelenaSC
Question Chip and Input different sizes libraries (NEBNext ChIP-Seq Library)

Hi all!:)

I'm new here (and also in Chip-Seq!) and I would like share some questions with you.

We are preparing Chip-seq libraries for MiSeq, using NEBNext Chip-seq Library Prep Master Mix...
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