Forum: Sample Prep / Library Generation
07-18-2016, 10:41 AM
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Replies: 1
Views: 497
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Forum: Illumina/Solexa
04-08-2015, 05:03 AM
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Replies: 3
Views: 1,278
I've seen the same thing. Some folks are...
I've seen the same thing. Some folks are doubting the adapters and adding double (5ul of 15uM index per reaction). From what i have tested it looks like ligation efficiency is much better with low...
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Forum: Illumina/Solexa
01-13-2015, 08:57 AM
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Replies: 53
Views: 41,165
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Forum: General
12-09-2014, 08:39 AM
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Replies: 16
Views: 2,136
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Forum: Sample Prep / Library Generation
09-16-2014, 07:50 AM
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Replies: 7
Views: 3,708
We use the LE220 and can run 24 samples at a...
We use the LE220 and can run 24 samples at a time. The tubes are larger than regular shear tubes, so the adapter plate can only handle 24 per run. Not too bad to work with the tubes since they have...
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Forum: Illumina/Solexa
09-16-2014, 07:43 AM
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Replies: 4
Views: 1,989
Ussually you'll want to HPLC purify for good...
Ussually you'll want to HPLC purify for good measure and I would ensure that your primers meet the following criteria -
Custom primers must:
Anneal to the P5 end of the library (refer to...
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Forum: Sample Prep / Library Generation
09-09-2014, 06:43 AM
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Replies: 7
Views: 3,708
Hi,
One of the reasons we moved forward with...
Hi,
One of the reasons we moved forward with Covaris was the higher yields for both DNA and RNA. (Compared to qiagen all prep FFPE; Kapa Express extract and 5 other kits we tested. The only...
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Forum: Sample Prep / Library Generation
09-09-2014, 05:16 AM
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Replies: 7
Views: 3,708
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Forum: Illumina/Solexa
05-17-2014, 08:15 AM
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Replies: 8
Views: 5,080
Hi,
Just wanted to note that the Illumina...
Hi,
Just wanted to note that the Illumina nano and per free adapters are both Y adapters. The Y is created by improper base pairing at the 3' and 5' ends of the adapter, but that goes away once...
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Forum: Bioinformatics
11-22-2013, 11:43 AM
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Replies: 4
Views: 2,012
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Forum: Sample Prep / Library Generation
11-18-2013, 10:56 AM
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Replies: 2
Views: 1,749
Hi Avo,
I have been using the truseq...
Hi Avo,
I have been using the truseq PCR-free preps for a year now and have never run into issues with yield at the end. Assuming you are not losing a ton of material in the shear, the double...
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Forum: Sample Prep / Library Generation
07-24-2013, 06:10 AM
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Replies: 9
Views: 8,134
Nextera Rapid fixed the issues I've had
The Nextera Rapid kit fixes issues with tagmentation efficiency using 50ng input gDNA. I have toyed with the number of PCR cycles required to yield sufficient .tagmented libraries for Exome prep...
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Forum: Bioinformatics
04-09-2013, 04:53 AM
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Replies: 25
Views: 4,444
Library Type?
Hi Santos,
What kind of prep was done on these libraries? If the initial sequences are not diverse, you can see a wavy pattern in the first few bases. This happens with RNA seq libraries and can...
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Forum: Bioinformatics
03-20-2013, 06:41 AM
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Replies: 2
Views: 1,768
Can be Normal
Hi Nico,
Your results seem normal to me. On average, One can expect to map 40 - 60% of the IP'd reads. I have seen less than 10% mapping back, which was actually due to salmon sperm blockers...
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Forum: Illumina/Solexa
10-04-2012, 02:29 PM
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Replies: 18
Views: 11,520
Cbot denaturation
I am pretty sure that the cbot relies more on heat denaturation than on the NaOH base denaturation. So the base is just a failsafe. The first step in cbot cluster gen is an incubation around 98C. ...
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Forum: Epigenetics
02-09-2012, 02:09 PM
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Replies: 9
Views: 5,965
Help with Quantification of ChIP Samples
Hi,
Thanks for the info and the protocol. I have some ChIP samples that I wanted to run through the Illumina sample prep protocol, but it seems like they can't be accurately quantified via the...
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Forum: Bioinformatics
05-25-2011, 11:56 AM
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Replies: 11
Views: 18,467
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