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===May 14, 2013=== [[File: 2013_05_14 primer validation 2nd try.jpg|400px]] * This gel was overloaded. I will run it again with only 1 ul this time (versus 8.5 ul). [[File: 2013_05_14 primer validation 2nd try lower loading.jpg|400px]] * Ben Spike is curious whether I have been successful with adapter ligation. I haven't sequenced any libraries, so I can't say for certain. The PCR at the end of CEL-Seq depends on the presence of the adapter, and I have gotten that to work about 50-60% of the time. All of the failures occurred in a two week period while I was working with Vipul. * I need a way to confirm for Ben that the libraries I have made have the correct adapters, but PCR would just use the same primers that I used to make the libraries (priming against the 5' and 3' adapter sequences), so it wouldn't really tell me anything new. * The only way to confirm that I have usable libraries will be to sequence one. Right now I only have a UHRR library prepared, without spike in. I haven't sequenced it because it was only a validation run on control RNA, but now I think it would be very useful to know that the adapter sequences were incorporated correctly.
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