…by Phoebe / from the United Kingdom / PhD Tissue Repair 2013-2017
Can you believe we are at the end of July already? Time flies when you are working hard!
I have had a month with my new RNA Seq data and for a variety of reasons I have not made very much headway with further data analysis! I started by looking at the 50 most deferentially expressed genes (up and down regulated) in my different comparisons and just doing some quick internet researching around them to get a feel for what the genes are involved in but I am still to do proper gene ontology and pathway analysis. In saying that I did have an extremely useful meeting with John from the Henderson group where I explained the project and shared some of the results so he could get a feel for what I was trying to achieve and point me in the right direction for the next steps. He was very enthusiastic about my results and is happy to be my point of contact whilst I tackle the analysis (phew). So my current focus is to use R to generate lists of all 616 upregulated genes and 1024 downregulated genes which I can then take forward to Gene Set Enrichment Analysis and Network Analysis (causing me a little bit of a headache at the moment!)
In the future I want to compare this data set with similar data sets on different tissues e.g. liver and kidney to see if I can pull out pathways etc that are imperative to the scarless healing we see in the endometrium but not these other tissues.
In the coming weeks this set of results needs to be validated so I will be choosing a handful of the genes that have come up as being deferentially expressed and using RT-PCR to confirm the changes in the set of samples I sent to Edinburgh Genomics as well as in a new and independent set of samples. This work may take a while but it is completely necessary for the project.
As I successfully landed the funding for new transgenics I have now ordered two new lines: inducible PDGFRb-Cre and inducible NG2-Cre which will allow me to specifically target and tattoo the endometrial mesenchymal cells and the endometrial pericytes respectively. With such elegant tools I can hopefully begin to pick apart the more precise mechanisms of scarless endometrial repair and finally address the feedback from my first year review!
So things are in motion as I enter a turning point in my PhD- one year in the lab left… oh golly gosh me!
Outside of the lab July may just have been my busiest month this year and it was full of birthdays! It started with a surprise party for my best friend Lauren who is also studying for her PhD through in Dundee on Cancer Research. I have to say it was tricky organising a surprise in another city but I had one of her lab mates to work with which made things easier and Lauren definitely got a surprise!
The following weekend was Andy’s 25th Birthday for which I presented him with a portable BOSE speaker and meal out to get burgers AND nachos (I know I spoil him too much) and we had a weekend in Edinburgh together which was lovely.
We then travelled north to Coylumbridge to celebrate Andy’s uncle and aunt’s joint 70th Birthday which was a weekend of eating, drinking, being outside (sometimes in the rain) and catching up. We also went to the Highland Wildlife Park which was great fun.
Then it was my Sister’s turn to turn 30 and celebrate in style with a private party in Espionage’s Kasbar with a popstars theme. Because we are 5 sisters we went as the spice girls. I was sporty spice so donned my sequined crop top and glitzed up trackies for the night and we all had a fantastic time.
Finally my family put on a fundraising fashion show in Glasgow just last weekend for the Liver Trust in memory of one of our dear friends Sheona Lockhart who tragically passed away 5 years ago after a long long struggle against Primary Sclerosing Cholangitis. My sister Jemima was in charge of organising the event longside Sheona’s parents who wanted to do something spectacular to remember her and celebrate their 40th wedding anniversary. So we travelled through with over 50 amazing costumes that my three older sisters have made throughout their time studying costume design at ECA and from themed parties that we have had over the years, and put on a show which comprised of 3 minute sets of the costumes modelled and acted by us with music, lighting and stories to accompany each.
The whole event was a huge success as the audience loved every minute, we loved every minute and felt so so proud to do something so worthwhile in memory of Sheona. Not only that but we raised over £5000 for the Liver Trust which was the cherry on top of the cake.
It has been a very busy month and August looks to be just as busy what with the arrival of the Festival but I am lucky enough to have a two week holiday in Mallorca at the end of August coming up so I have nothing to complain about!
Until next time.