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Search took 0.00 seconds. Search: Posts Made By: josdegraaf
Forum: Illumina/Solexa 04-06-2018, 02:29 AM
Replies: 14
Views: 2,221
Posted By josdegraaf
did you consider the naoh you use? is it fresh...

did you consider the naoh you use? is it fresh and < 1mM final concentration in your pool?
it could be (but does not explain no phix clusters) that the denaturation is insufficient, try heat...
Forum: Illumina/Solexa 04-04-2013, 08:02 AM
Replies: 20
Views: 5,936
Posted By josdegraaf
worked great for us, before we had the same as...

worked great for us, before we had the same as you show here. After we start doing maintenance before every run (using the gaskets for the run) and keep washing with water till the run starts we got...
Forum: Illumina/Solexa 04-03-2013, 07:19 AM
Replies: 20
Views: 5,936
Posted By josdegraaf
Illumina recommended us to do a maintenance wash...

Illumina recommended us to do a maintenance wash before the run using the same gaskets as during the real run..
Forum: Sample Prep / Library Generation 02-20-2013, 06:41 AM
Replies: 1
Views: 1,014
Posted By josdegraaf
Do I understand correctly that you used some home...

Do I understand correctly that you used some home made adapter and combined that with the post capture PCR primers provided by Agilent?
How are the Qscores for the index read?
Forum: Sample Prep / Library Generation 10-24-2012, 02:20 AM
Replies: 3
Views: 2,120
Posted By josdegraaf
You seem to have rather low yields after the post...

You seem to have rather low yields after the post capture PCR, did you quantify this also in a different way or only on the BA?
Using older sureselect versions we obtained much more final library...
Forum: Sample Prep / Library Generation 10-12-2012, 12:00 AM
Replies: 5
Views: 2,349
Posted By josdegraaf
I know but some people take +- 100 or 200 bases...

I know but some people take +- 100 or 200 bases as on target and some don't. Anyway 30% is very low, should be more towards >95% bases covered. We also used V3 and had +- 98%. Illumina performs...
Forum: Sample Prep / Library Generation 10-05-2012, 12:36 PM
Replies: 5
Views: 2,349
Posted By josdegraaf
What do you call on target?

What do you call on target?
Forum: Illumina/Solexa 10-05-2012, 12:17 PM
Replies: 18
Views: 13,668
Posted By josdegraaf
It is remarkable that the diversity between what...

It is remarkable that the diversity between what people cluster is so big. We use 10 pM and some others 16. Something that I find hard to believe is machine dependent.

Anyway, each strand is a...
Forum: Sample Prep / Library Generation 10-01-2012, 07:56 AM
Replies: 18
Views: 12,968
Posted By josdegraaf
where to send the email?

where to send the email?
Forum: Illumina/Solexa 09-25-2012, 03:05 AM
Replies: 38
Views: 18,688
Posted By josdegraaf
[QUOTE=pmiguel;57185]We got it to work on our...

[QUOTE=pmiguel;57185]We got it to work on our HiScanSQ -- which uses the same chemistry as the HiSeq, but only scans the top of the flowcell. Not an identical situation, but we had some SMART cDNAs...
Forum: Sample Prep / Library Generation 01-18-2012, 07:54 AM
Replies: 5
Views: 4,479
Posted By josdegraaf
any updates on this? we started to see something...

any updates on this? we started to see something similar..
Forum: Illumina/Solexa 09-14-2011, 01:35 AM
Replies: 9
Views: 2,674
Posted By josdegraaf
you can indeed do targeted capture, Agilent...

you can indeed do targeted capture, Agilent SureSelect, Nimblegen Seqcap EZ, Flexgen Flexselect are some companys that offer that. With Nimblegen atm being able to do pooling of different samples...
Forum: Illumina/Solexa 09-13-2011, 02:06 PM
Replies: 9
Views: 2,674
Posted By josdegraaf
You want to look at genomic sequence? Or...

You want to look at genomic sequence? Or expression? You want to have whole genes or snps?
Forum: Illumina/Solexa 09-13-2011, 01:58 PM
Replies: 8
Views: 4,809
Posted By josdegraaf
Same here, is indeed a known problem due to...

Same here, is indeed a known problem due to bubbles in the lanes during scanning. Maybe due to bigger lanes?
Forum: Introductions 08-09-2011, 05:52 AM
Replies: 6
Views: 3,466
Posted By josdegraaf
I forgot, is there anyone in here that used the...

I forgot, is there anyone in here that used the FFPE kit with succes?

thanks
Forum: Introductions 08-09-2011, 05:46 AM
Replies: 6
Views: 3,466
Posted By josdegraaf
Hi, What is different from the 'normal'...

Hi,

What is different from the 'normal' rna-seq kit to the FFPE ?

Thanks
Forum: Illumina/Solexa 11-06-2010, 01:23 AM
Replies: 8
Views: 3,626
Posted By josdegraaf
We also did this several times now, using NEB as...

We also did this several times now, using NEB as well as Illumina reagents and it works fine, we also had low yields but more then enough.
Forum: Sample Prep / Library Generation 11-05-2010, 08:21 AM
Replies: 0
Views: 1,908
Posted By josdegraaf
4C libraries

Hi,
We have a customer who asked if it is possible to sequence libraries made with the 4C protocol.
The result of this protocol is a pcr product in the range from 2 kb to 100 bp. These pcr...
Forum: Sample Prep / Library Generation 11-05-2010, 08:14 AM
Replies: 3
Views: 6,966
Posted By josdegraaf
http://www.ncbi.nlm.nih.gov/pubmed/19815668

http://www.ncbi.nlm.nih.gov/pubmed/19815668
Forum: Sample Prep / Library Generation 11-05-2010, 07:41 AM
Replies: 4
Views: 6,327
Posted By josdegraaf
For tighter sizes pippin or Caliper labchip XT...

For tighter sizes pippin or Caliper labchip XT although no plate format for those..
Forum: Illumina/Solexa 10-29-2010, 06:53 AM
Replies: 4
Views: 2,665
Posted By josdegraaf
Did you think about the second read primer hyb,...

Did you think about the second read primer hyb, maybe something with the PE module?
Forum: Sample Prep / Library Generation 10-25-2010, 05:13 AM
Replies: 17
Views: 9,137
Posted By josdegraaf
Last time I spoke with them not..

Last time I spoke with them not..
Forum: Sample Prep / Library Generation 10-25-2010, 05:12 AM
Replies: 6
Views: 4,473
Posted By josdegraaf
Main reasons for size selection are removing...

Main reasons for size selection are removing self-ligated adapters plus getting a tight as possible band for the paired end reads.
Forum: Illumina/Solexa 10-25-2010, 03:49 AM
Replies: 8
Views: 3,626
Posted By josdegraaf
How many pcr rounds did you both use?

How many pcr rounds did you both use?
Forum: Sample Prep / Library Generation 10-04-2010, 02:18 AM
Replies: 9
Views: 4,741
Posted By josdegraaf
@bfrost: If you would cluster with a library that...

@bfrost: If you would cluster with a library that looks like the one shown in the first post I would guess more then 30-40 % will be adaptors, those will cluster and be sequenced resulting on only 60...
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