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Forum: Sample Prep / Library Generation 12-23-2013, 12:08 PM
Replies: 3
Views: 3,675
Posted By Phage434
For a detailed description of protocols, see the...

For a detailed description of protocols, see the patent application US 2011/0040081 A1
Methods, Compositions, and Kits for Generating rRNA-Depleted Samples or Isolating rRNA from Samples, Roy. R....
Forum: Illumina/Solexa 12-22-2013, 05:29 AM
Replies: 6
Views: 5,479
Posted By Phage434
Point taken, but I believe it is only a factor of...

Point taken, but I believe it is only a factor of two. With adapters A and B you would get all combinations, AA, AB, BA, BB. AB and BA both bind and amplify in the flow cell. This also explains how...
Forum: Illumina/Solexa 12-21-2013, 08:01 AM
Replies: 6
Views: 5,479
Posted By Phage434
I see. To clarify for others, during forward...

I see. To clarify for others, during forward read, the flow cell has only ssDNA, and the Read 1 primer can only bind to the Read 1 site. The other potential binding site is only present in a reverse...
Forum: Illumina/Solexa 12-20-2013, 07:13 PM
Replies: 6
Views: 5,479
Posted By Phage434
I understand those things. I still don't...

I understand those things. I still don't understand why a Read 1 promoter does not bind efficiently to the Read 2 site (and vice - versa).
Forum: Illumina/Solexa 12-20-2013, 02:10 PM
Replies: 6
Views: 5,479
Posted By Phage434
How do the Nextera Read1 and Read2 primers both work

Does anyone understand how the Nextera Read1 and Read2 primers can work when they both have identical 19 bp regions at the 3' ends?

I would never think about designing a Sanger sequencing primer...
Forum: Illumina/Solexa 12-18-2013, 02:04 PM
Replies: 22
Views: 10,543
Posted By Phage434
That sequence is from the 3' end of "Blocker 4"...

That sequence is from the 3' end of "Blocker 4" in this patent:
http://www.google.com/patents/US8575071
It's used to block ligation of the excess adenylated 3' linker.
Forum: Sample Prep / Library Generation 11-20-2013, 03:26 PM
Replies: 1
Views: 1,909
Posted By Phage434
Ribosome profiling vs. TRAP

I'm interested in doing ribosome profiling on a small bacterial genome. The "standard" protocols all call for isolating ribosomes with either sucrose cushions or (more recently with the Epicentre...
Forum: RNA Sequencing 11-18-2013, 02:32 PM
Replies: 0
Views: 1,688
Posted By Phage434
Question Ribosome profiling vs. TRAP

I'm interested in doing ribosome profiling on a small bacterial genome. The "standard" protocols all call for isolating ribosomes with either sucrose cushions or (more recently with the Epicentre...
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