RNASeq SUCCESS…
…by Phoebe / from the United Kingdom / PhD Tissue Repair 2013-2017
I thought I would start by sharing the exciting news that my RNA sequencing project came back with successful RESULTS!!! After two weeks with the Edinburgh Genomics bioinformaticians we were presented with an extremely robust and thorough report that included principle component analysis, quality assessment plots and differential gene expression heatmaps along with all of the raw data. I have to say the folks at Edinburgh Genomics have been so helpful and supportive throughout this study and we would not have generated the data we have without their help!
To prepare myself for this moment I went on an RNASeq data analysis course which was actually quite full on but I now have a lot of information about how to tackle RNASeq datasets and do further analysis such as gene ontology analysis. So this is the next step for me- I want to get to grips with the raw data I have, and try to do more with it (Luckily there is an experienced bioinformatician in my second supervisor’s group just down the corridor so I have no doubts I will be visiting him while I find my feet with this!). I am actually quite excited to have some bioinformatics experience and it sure will look good on the old CV. I have been told this may occupy me for quite some time so be prepared for bioinformatics chat in my next few blogs!
In other lab news, as a result of a discussion at the SRI Annual meeting in Orlando I contacted an electron microscopy facility in Edinburgh King’s Buildings and had a meeting to discuss the possibility of doing some transmission and scanning electron microscopy (TEM and SEM) on endometrial tissue samples. This is to confirm that endometrial pericytes are found within the basement membrane of endometrial blood vessels, which is a vital characteristic if I am to call them pericytes! I ran a trial this month and gathered some interesting images, it took a while to get my eye in but I think I may have the evidence I need.
In addition I submitted an abstract for the ‘SRI MRC-CRH Symposium on targeting inflammation to improve reproductive health across the lifecourse’ in August this year, and I am happy to say I have a talk to give at that. This will focus on my data on monocyte and macrophage population dynamics during endometrial repair and how this knowledge may be important when tackling gynaecological disorders. Definitely good to keep my presentation skills fresh!
Finally I had my Second Year PhD Review where my Thesis Committee get together after reading my second year report to discuss the work and my progress and bring up any problems there may be. This went really well with extremely useful conversations about the expectations for my final year (eek!). The only moment I froze was when I was asked about my future and what I want to do next- this is something that hasn’t been are the forefront of my mind and something that scares me a bit. But my committee members were really kind and supportive and were happy to discuss all of my options. So I came away from the meeting feeling confident and ready to work my socks off in the coming months to make some important steps towards finishing with a fabulous PhD- lets hope I get there!
In my out-of-lab time I have been really busy this month. I organised a social event for the Tissue Repair students where we went down to Urban Paintball in Leith for some messy and sore fun. I managed to find a Groupon deal which allowed us entry for only £1 each so it was cheap and cheerful and everyone had a great time. But beware it is a bit sore and you get EXTREMELY sweaty- so much so that no one wanted to go for drinks afterwards!
I also spent one evening at the Festival Theatre watching the opera La Boheme with some fellow PhD students. I have never been to the opera before and I was blown away by the beautiful singing and the emotional story and I would really recommend seeing it. I now want to visit the theatre at least once a month!
My younger brother Arthur graduated his undergraduate degree in Architecture while my younger sister Augusta graduated her undergraduate degree in Illustration and therefore the whole family got together to visit their degree show, where the work of all the 4th Years in the College of Art is on display for the public to see. I was so so proud of both of my incredibly talented little siblings and it was lovely to see all of their hard work displayed in all its glory. Arthur is now heading off into the working world and Gussie is starting a Masters degree in Publishing come September… this means she and I will be finishing around the same time- BIG celebrations to come in 2018 😀
And finally I ended the month on the sunny island of Cyprus with my boyfriend Andy. We had a whole week in the 38C sun in a private villa and spent the days relaxing, eating, drinking, exploring the island and we even went parasailing (daredevils).
It was a truly magical holiday and I loved every second of it and when I came back I felt rejuvenated and happy again…
I urge you all to make sure you take a break this summer, nothing makes you more enthused about your work than stepping back from it for a wee while!
Until next time.
XXX
