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Forum: Illumina/Solexa 04-15-2014, 06:13 PM
Replies: 58
Views: 39,530
Posted By thomasblomquist
Hi Kristen, Some time back you stumbled...

Hi Kristen,

Some time back you stumbled across our paper on targeted RNA seq: http://seqanswers.com/forums/showthread.php?t=35379

The use of the competitive internal standard molecules...
Forum: Illumina/Solexa 09-12-2013, 10:05 AM
Replies: 58
Views: 39,530
Posted By thomasblomquist
Any update on this? We will be ramping up our...

Any update on this? We will be ramping up our sequencing efforts and need to have this issue resolved as well. If not, we may jump back to an Ion Torrent approach. Even though it is more...
Forum: Illumina/Solexa 05-02-2013, 06:33 PM
Replies: 58
Views: 39,530
Posted By thomasblomquist
Some types of genetic variation are easily...

Some types of genetic variation are easily detectable beyond the typical single nucleotide variant limit of detection in sequencing. Translocations, indels, repeats, etc. Importantly, their...
Forum: Illumina/Solexa 04-26-2013, 04:46 AM
Replies: 58
Views: 39,530
Posted By thomasblomquist
This message string has been very helpful for our...

This message string has been very helpful for our specific purposes. So, I'm thinking that if we have three batches of barcoding reagents that we rotate through that should be sufficient amount of...
Forum: Illumina/Solexa 04-24-2013, 12:11 PM
Replies: 58
Views: 39,530
Posted By thomasblomquist
Thank you Kameran. What is the rate of decrease...

Thank you Kameran. What is the rate of decrease over multiple uses and washes? Specifically, using a shared instrument, how many other samples should I interdigitate between returning to previously...
Forum: Illumina/Solexa 04-24-2013, 05:12 AM
Replies: 58
Views: 39,530
Posted By thomasblomquist
And the hiseq? -Tom

And the hiseq?

-Tom
Forum: Illumina/Solexa 04-24-2013, 05:06 AM
Replies: 58
Views: 39,530
Posted By thomasblomquist
Just how non-disposable is this tubing? I'd be...

Just how non-disposable is this tubing? I'd be willing to pay an extra $100 a run just to have contamination free assurance.

Can this topic be forwarded to someone at Illumina that is responsive...
Forum: Illumina/Solexa 04-22-2013, 10:10 AM
Replies: 58
Views: 39,530
Posted By thomasblomquist
Okay, that makes sense as to the source of the...

Okay, that makes sense as to the source of the inter-run cross-contamination. Does the hi-seq operate in the same fashion?

Still, that seems like a bit of a design flaw. Why would an engineer...
Forum: Illumina/Solexa 04-22-2013, 08:32 AM
Replies: 58
Views: 39,530
Posted By thomasblomquist
Hmmm... Why would there be a complete "circuit"...

Hmmm... Why would there be a complete "circuit" where reagents that go into the flow cell are recycled back later? Seems disasterous. Disclaimer: I only prep the libraries in house and send off to...
Forum: Illumina/Solexa 04-22-2013, 08:01 AM
Replies: 58
Views: 39,530
Posted By thomasblomquist
It seems to me there are two predominant sources...

It seems to me there are two predominant sources of error.

1) Library preparation (barcode reagents are cross-contaminated or PCR jumping, etc).

2) A platform specific source of...
Forum: Illumina/Solexa 04-17-2013, 10:47 AM
Replies: 58
Views: 39,530
Posted By thomasblomquist
Thank you for your response. Our lab has been...

Thank you for your response. Our lab has been running known negative and known positive controls, and for each patient sample performing two technical replicates by barcoding twice with two seperate...
Forum: Illumina/Solexa 04-11-2013, 09:49 AM
Replies: 58
Views: 39,530
Posted By thomasblomquist
Barcode contamination from the synthesis and...

Barcode contamination from the synthesis and preparation steps is a HUGE issue. A lot of care for stringency in all steps must be taken. Don't use plates to prep sequencing libraries in parallel!!!...
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