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Week Eight - RNA and Microarray

On Monday, Tuesday, and Wednesday I did RNA isolations. Thursday I read and learned about microarray analysis. On Friday, I installed the necessary software for microarray analysis and tried to analyze (for the second time) the 12K microarray scans on my own and it was a success!

The (Mariya's) procedure for analysis goes like this:
1. Using combimatrix imager, open your image (the scan of the chip) and the probe design.
2. Use a template to align a grid to spots and extract data and save to desktop.

WEEK SIX & SEVEN - Filtering on the R/V Barnes

Week Six- Monday I performed another set of four RNA isolations, Tuesday I prepared for the cruise, and Wednesday I boarded the Barnes. My duty on the ship was to fliter water samples through Sterivex filters with a pore size of .22 um. The system I used was something like this: a large bottle of water was collected at a particular depth and location and then the water was pumped out through tubes using a geo-pump. The water ran through the filters connected to the tubes and then was deposited in large plastic buckets.

WEEK FIVE - RNA and high horses

This week I've completed more RNA isolations, read two more articles, re-stocked needed materials and ran the autoclave, went to the bioanalyzer to record the quality of previous RNA samples, and prepared for the upcoming research cruise. It turns out that the RNA that I've isolated is not degraded, and looks good! I was complimented by Mariya and Holly which was exciting :)

Then I accidentally left sterile tubes out overnight, so the high horse I was riding was dismounted... Overall it was a successful week, and I'm very excited for next week's cruise!


Last week was the fourth of July weekend, so we had Friday off and I went to a barbecue at Chantel's family's house where they made amazing food. I also went to the blues festival in Portland on Thursday and Saturday, which was a lot of fun.

Week Three

This week I completed eight more RNA isolations from samples along a salinity gradient from the estuary. I also attended half of the practice NSF presentations earlier in the week as well as the entire site visit on Thursday. On a side note, I got a new OHSU ID with a photo this time in order to ride the public transportation without a hassle and organized the accumulating literature I've read. I also went over the protocol for creating a microarray with probes and spent a day generating spread sheets and graphs with the data I have thus far.

Week Two

Monday and Tuesday of last week I spent doing more RNA isolations and now feel more comfortable with them. I spent Wednesday familiarizing myself the "datamart" database of past research cruise information and monitoring stations. I also read two pieces of literature and looked up terms that I was unfamiliar with. Wednesday night was eventful for me... It's really a funny story... so I was coming home from dinner at Malone's when a guy ran by me and snatched at my purse. He got it, barely, and so I took off after him.

Week One

This week I've learned a lot about RNA isolation from environmental samples. Previously, I had isolated RNA from chicken tissues, but the procedure for this isolation is different. My mentor, Mariya, actually came up with it on her own, which I thought was quite impressive. The protocol takes about one full day to complete; one day I observed how she did it, and then it was my turn... My trial was successful- I was able to isolate RNA from two samples. I hope that as I become more fluent in the procedure, the yield will increase.

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