User:Sarah Signor/Notebook/Genetics of Pigmentation/2011/01/11

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Jan 11 2011

 * Library Construction- still at a standstill. My control is still failing. I replaced all of the enzymes already, I think it may be the ligase buffer. I will try again and see what happens.


 * Tried Again- May be working (in which case it was the ligase buffer). The library produced with illumina adapters had 570 ng of DNA compared to 264 ng that were input. Not great, but something is happening. Same with barcoded library: 630 ng of DNA after 264 ng input. Feeling optimistic, I started a new EaeI digestion for the RAD tagging following the Baird et al. protocol, using 15 ul of the DNA M processed for us awhile back.  Probably way more DNA than they say needs to be used, but I don't think it matters much. As soon as Artyom agrees that this is satisfactory I will clean up my other libraries and take them and the RAD library over to the genome center.


 * Sequencing- M was having difficulty aligning the ananassae sequences. It appears they just got processed in an unusual order, but we still can't find our record of what the heck they are. Oh, the holidays. They are as follows:

1: 13 2: 14 3: 15 4: 16 5:17 6:18 7:19 8: 20 9:11 10:12

So it looks like the processed the forward and reverse of the two middle ones before processing the reverse of all the others, rather than all forward followed by all reverse.


 * SNPs have been approved for sequenom assay, ordered the primers today. Erc/mer samples are missing in action, somewhat complicating my using them for the assay.


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