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Forum: Illumina/Solexa 03-03-2009, 12:47 PM
Replies: 19
Views: 10,152
Posted By cjohns
No, they do not get sequenced. Our only concern...

No, they do not get sequenced. Our only concern is we use PicoGreen to quantitate and it would detect these amplicon products and we may not have reliable quantitation of our insert DNA.
Forum: Sample Prep / Library Generation 12-04-2008, 12:55 PM
Replies: 3
Views: 3,513
Posted By cjohns
I'm not sure if this is the answer or not, but...

I'm not sure if this is the answer or not, but for several preps we got huge peaks at 80bp that we believe to be primer dimers. When we put them on the GAII they did not produce any sequences. ...
Forum: Sample Prep / Library Generation 12-01-2008, 12:13 PM
Replies: 1
Views: 2,887
Posted By cjohns
Our picogreen concentrations of our ChIP and our...

Our picogreen concentrations of our ChIP and our Normal Rabbit IgG control can have very similar concentrations after sample prep. In our experience, the only way to know if a specific antibody...
Forum: Illumina/Solexa 10-15-2008, 09:32 AM
Replies: 19
Views: 10,152
Posted By cjohns
I have done several chip-seq with illumina kits...

I have done several chip-seq with illumina kits and on my last set I also got a product that is about 80bp long that I have not seen before. It is in my blank gel that I amplified too, so it has to...
Forum: Illumina/Solexa 10-08-2008, 12:23 PM
Replies: 25
Views: 10,679
Posted By cjohns
Hi tomv, We know that in our first round of...

Hi tomv,

We know that in our first round of sequencing we got a huge amount of product that gave us a spike on our bioanalyzer read (prior to sequencing) that runs at approx 120bp. We didn't know...
Forum: Illumina/Solexa 09-24-2008, 10:46 AM
Replies: 25
Views: 10,679
Posted By cjohns
If it is about 120bp it is adapter complexes. We...

If it is about 120bp it is adapter complexes. We had this problem, but solved it by modifiying the size selection part of the protocol.
Forum: Sample Prep / Library Generation 09-24-2008, 10:43 AM
Replies: 19
Views: 21,125
Posted By cjohns
Here is what I found on our Chip-Seq: ...

Here is what I found on our Chip-Seq:

Neither Nano-Drop nor bioanalyzer nor Pico Green quantitation of our IP products agree so we stopped trying to quantitate them. We use 1/3 of the IP product...
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