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Forum: Sample Prep / Library Generation 10-15-2017, 11:36 PM
Replies: 10
Views: 1,176
Posted By Andersen
Indeed expensive, but yes it is synthesized with...

Indeed expensive, but yes it is synthesized with mC. Thanks for the heads up.
Forum: Sample Prep / Library Generation 10-15-2017, 11:01 PM
Replies: 10
Views: 1,176
Posted By Andersen
Thank you for all your help! :) I have now...

Thank you for all your help! :)

I have now ordered the adapters and hope they will work!
Forum: Sample Prep / Library Generation 10-13-2017, 03:09 AM
Replies: 10
Views: 1,176
Posted By Andersen
Thanks again Phillip! Indeed they must be...

Thanks again Phillip!

Indeed they must be some fiendish geniouses. :D

I have allready generated the TruSeq DNA LT adapter piece with a 6 nt index. Do you think it would work to anneal the i5...
Forum: Sample Prep / Library Generation 10-11-2017, 10:23 AM
Replies: 10
Views: 1,176
Posted By Andersen
Thank you so much for your answer Phillip. ...

Thank you so much for your answer Phillip.

1. I am actually not really sure if it is a Y-adapter design. But I am pretty sure that it is. I tried to find information about it but couldn't, but it...
Forum: Sample Prep / Library Generation 10-11-2017, 05:45 AM
Replies: 10
Views: 1,176
Posted By Andersen
Illumina Unique Molecular Identifier Adaptor

Hi All,

I want to generate RRBS libraries where we can track each unique molecule with a UMI. Thus I have generated new TruSeq adaptors that we normally use.

The regular Truseq primers look...
Forum: Sample Prep / Library Generation 11-02-2016, 01:04 AM
Replies: 3
Views: 721
Posted By Andersen
Thank you very much both of you. The samples have...

Thank you very much both of you. The samples have now been sequenced. And I will test the analysis in not too long.
Forum: Sample Prep / Library Generation 10-30-2016, 10:05 AM
Replies: 3
Views: 721
Posted By Andersen
RRBS library long fragments

Dear All,

I just made a RRBS library. The problem is that I have a lot of long fragments that is not really good since they probably do not contain CpG rich areas.

This is the profile of the...
Forum: Sample Prep / Library Generation 10-26-2016, 11:38 PM
Replies: 0
Views: 429
Posted By Andersen
Reccoment RNA-seq library prep

Dear All,

We are currently using Illumnia TruSeq standard total RNA with Ribo-Zero Gold for library prep of RNA-seq libraries. This a really expensive library prep kit so we are looking into the...
Forum: Sample Prep / Library Generation 07-18-2016, 10:59 PM
Replies: 4
Views: 938
Posted By Andersen
Not a whole lot was done differently, between 4-5...

Not a whole lot was done differently, between 4-5 and the others. I believe that the only difference was that 4-5 had 8 cycles and 1-3 had 10 cycles and 6 had 9 cycles. But this was due to the lower...
Forum: Sample Prep / Library Generation 07-16-2016, 03:19 AM
Replies: 4
Views: 938
Posted By Andersen
Double peak on Truseq RNA-seq library

Hi All,

I have prepared some Truseq RNA-seq libraries and i have 2 peaks.

I have been reading some previous threads that it could be bead carry-over, but I do not really see any beads in my...
Forum: Bioinformatics 04-05-2016, 02:45 AM
Replies: 1
Views: 558
Posted By Andersen
Bioinformatics courses

Dear all,

I do work on DNA methylation (RRBS) and RNA-seq data. At my department we have bioinformatics performing the analysis, but I need to interpret it myself.

Therefore I'm looking for...
Forum: Illumina/Solexa 12-03-2015, 01:29 AM
Replies: 3
Views: 952
Posted By Andersen
Wow, thank you very much for your quick and...

Wow, thank you very much for your quick and precise answer. :)

Sounds really nice, do you have the name of one of these suppliers? :)
Forum: Illumina/Solexa 12-03-2015, 12:35 AM
Replies: 3
Views: 952
Posted By Andersen
Multiplexing RRBS samples

Dear everyone,

Im preparing a RRBS library. I want to multiplex 10 samples from 150ng DNA.

We use ilumnia DNA nano LT adaptors on the fragmented DNA.

I have been looking online for...
Forum: Epigenetics 10-28-2015, 01:44 AM
Replies: 2
Views: 1,013
Posted By Andersen
Hi Nucacidhunter. 1 - I will try and run a...

Hi Nucacidhunter.

1 - I will try and run a new chip when we are running a full load. :)
2 - It is from human stromal vascular fraction
3 - Input was 55 ng DNA originally from 12 samples pooled...
Forum: Epigenetics 10-27-2015, 04:44 AM
Replies: 2
Views: 1,013
Posted By Andersen
RRBS Library 4 peaks

Dear everyone

I have just prepared my multiplexed reduced representation bisulfite sequencing library. It seems like I have 4 peaks on my bianalyzer results arround 180, 235, 300 and 360 base...
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