What I do in a week as a genetics PhD student
By: The Inner Chat
Tags: Genetics, Laboratory, Scientist, PhD, Day In The Life

I have a lot of friends who have never worked in a lab or don’t know what a PhD entails. I always struggle to explain what I’m doing on a daily basis because every week and every day can be so different. I have never tracked my time so I thought it would be a nice exercise to record my hours for a week and see how my time is spent.

It turned out to be a relatively chill week. A week ago I was busy finishing up experiments for a big talk on Friday and it was nice to slow down a bit. Since all social distancing restrictions were lifted this Monday and we don’t have to book lab/office space anymore it was a first week when I didn’t do any work from home and instead worked from the institute. Even though it wasn’t a busy week I found it quite tiring. I guess it will take time to adjust to a new schedule. I’m going home at the end of September so I’m not starting any big experiments at the moment and instead I’m trying to wrap up a few things before I leave.

Monday

10:00–11:00 I started my day by taking care of my embryoid bodies (EBs) which were left alone over the weekend. I changed their media (a nutrient solution for growing cells) and thawed two cell lines to start a new EB culture. EBs mimic early development and I want to understand if the mutants I created can contribute to the tissues found in the early embryo.

11:00–12:00 I spent the next hour planning my day, updating lab book and talking to the colleagues.

12:00–13:00 I watched a talk on Cut&Run. Several people at our institute are trying to adapt a new technique which is used to analyse proteins bound to the DNA. I’m thinking about using this technique in my project so it was useful to hear about other people’s experience. I had lunch while listening to the talk.

13:00–14:00 One of the experiments I’m doing with EBs is measuring and comparing size of different mutants to evaluate their ability to contribute to the EB development. I have tried imaging them on a macroscope (a microscope with low magnification, eg 1x instead of 40x) but it was difficult to see EB edges because cells look relatively transparent under the regular light source. I decided to stain them with DAPI (fluorescent DNA dye) so that I can image them with a fluorescent camera and hopefully get a better view.

14:00–14:50 Imaging time. Unfortunately, the fluorescent camera on the macroscope I was using didn’t want to work. One of the imaging specialists tried to set up another macroscope for me but the signal was very dim. Apparently, DAPI staining doesn’t work well with macroscopes. Anyways, I managed to take images with a regular light source which were good enough for quantifying size.

14:50–15:50 Can’t believe I spent a whole hour submitting cells to the liquid nitrogen storage! We keep frozen cells in the -80C freezer but my box was getting quite full and messy, and it is also not good to keep cells at the -80C long-term. I reorganised my box, filled a form and brought cells to a different building.

Frozen cell vials

15:50- 16:50 I spent the last hour trying to measure EBs I imaged previously. It was a nightmare because for some reason the macroscope didn’t account for different zoom values I was using so my pixel to micrometer ratios were messed up. I didn’t know how to re-calibrate it so I emailed the imaging specialist who was training me on the macroscope.

Summary: It was an average day. I finished imaging all mutant EBs so it felt nice to get it done, however, I don’t like when my day is broken down into 1h tasks and I find it quite tiring. I prefer to focus on one task for 2–3h without interruptions. After work I went for alcohol-free cocktails which were surprisingly good!

Tuesday

9:20–11:00: I started my morning by checking emails, cells and made sure I have all the reagents for the upcoming experiments. I also got a reply from the imaging specialist and sent him some of my images for troubleshooting. Since I had 3 weeks left before my holiday I made a list of experiments and tasks I want/can finish within that time.

My desk set up

11:00–11:50 I spent some time reading a paper relevant to my project and thinking how their results relate to the results I got from my experiment.

11:50–12:30 I set up some phenol-chloroform DNA extractions. It’s an old-school protocol which I don’t enjoy but it gives very clean genomic DNA.

12:30–12:50 I don’t know what I was doing during those 20 minutes, probably got distracted and started chatting with people.

12:50–13:45 I did protein extractions and quantifications. I started feeling quite tired (it was a hot day and I was wearing a very warm sweater…) and I forgot to save quantification results before closing the software… I gave up and put proteins in the freezer.

13:45–14:00 Much needed tea and biscuit break

14:00–14:20 I planned out a western blot for the proteins I extracted previously. It’s an assay where you first separate proteins by size and then incubate them with an antibody specific to your protein of interest so that you can check if it’s expressed and at what levels.

Our lab got a cell line where a protein we are interested in is tagged with a degron. It allows a very quick and reversible degradation of this protein and I want to test if the system works in my hands. It’s important to check everything you get from others because people can make a mistake and give you a wrong thing (happened to me…) or you might need to adjust your protocol/reagents.

14:30–15:00 I had lunch while watching a talk from the bioinformatics facility about the automated pipelines we can run on our supercomputer. I’m interested in using one of the pipelines and it seemed more straightforward than I thought. I hope to try it next week.

15:00–15:20 I was still very tired so I took a break to call my boyfriend and talk to the labmates.

15:20–16:00 Still tired! I picked an easy task and updated my lab book. My paper lab book is a mess and I’m not very good at updating the electronic copy regularly…

16:00–16:20 I set up an overnight digest for DNA extractions I started in the morning, ordered some reagents and went home.

Summary: not a very productive day… A sudden heatwave made me feel very tired so I decided to leave early and just rest at home.

Wednesday

10:20–12:00 I continued doing DNA extractions from yesterday. Phenol and chloroform are harmful so I had to work in a chemical hood which is a bit inconvenient.

12:00–13:00 Changed media and started a new EB culture. To grow EBs I culture 400 cells per 20ul hanging droplet for 48h to allow them to form 3D spheres. Then I transfer them to the regular flask where they adhere and start spreading.

Hanging droplets

13:00–13:45 A long-ish lunch break.

13:45–14:50 I quantified proteins I extracted yesterday and started a western blot. I loaded proteins on a gel to separate them by size and prepared some buffers.

14:50–15:05 I had a gap in the protocol so I took a tea break.

15:05–15:50 By this time my proteins reached the end of the gel and I transferred them to the membrane using a very smart and handy machine. I used to do a ‘handmade’ transfer which is more tricky and takes time. The machine does it for me in 8 minutes! I put the membrane in the blocking solution for 1h which blocks non-specific antibody binding.

15:50–16:20 I had a snack, checked emails and tried to book a room for our weekly lab meetings. We had them online for 1.5 years (omg) but since we’re only 8 people we can meet in person now.

16:20–17:00 Wrapped up and set up an overnight incubation with an antibody against the protein I’m interested in.

Summary: It was a good day. I finished my least favourite part of the DNA extraction protocol and started a western blot which always takes time. I would have finished DNA extractions but I was meeting someone for drinks so I had to leave by 17:00.

Thursday

8:30–11:00 I came in early to finish my western blot before a lab meeting. It involved doing washes and incubating with a secondary antibody. Secondary antibody produces a chemiluminescent signal so that it can be detected by the imager. There are three 10-minute washes and one 1h incubation followed by another three 10-minute washes so it’s impossible to do anything productive in between. I spent that time checking emails and drinking tea.

11:00–11:30 Lab meeting

11:30–11:45 I went to image my western blot and got very pretty results. The degron system works well and my blot looked good so I was showing off to the colleagues. I used to be veeery bad at westerns so it’s a big deal for me!

11:45–12:15 Very rushed lunch break. I met my PI (principle investigator aka group leader aka boss) in the corridor and he offered to discuss a paper after lunch. I had a draft outline ready so I wanted to review and edit it before our meeting while eating lunch very quickly. I could ask to meet later but I was very impatient and very excited to talk about the paper haha

12:15–12:30 We discussed a paper I could publish from my project. I was thinking about not mentioning this part in the blog post because I still need to do some key experiments and publishing takes time and papers often get rejected and extra experiments need to be done and it might come off as premature bragging and so on and so on… But it is the reality of research and I want to be very open and honest about it in my blog. In the future I will make a separate post on the publishing journey because scientists and journalists never talk about it with the general public although it’s a key part of research.

If I exclude lockdown time, I spent ~1.5 years working on this project which is not a lot of time especially considering COVID restrictions and disruptions so I’m super excited it has a potential to get published! We discussed the main message, the title and the abstract of the paper, I also showed my outline for the figures. It was a very quick discussion since it turned out we had a very similar vision of the paper. Does it mean I actually understand what I’m doing!?

12:30–13:40 I re-defined my paper outline and made a list of experiments which I still need to do. It’s not as much work as I thought and it feels a lot more do-able now. I’ll have to do a lot of imaging though and I’m very bad at microscopy so it’s making me a bit stressed but I’ll think about it when I come back from holiday.

13:40–14:05 I started to have a headache so I took another tea break (yes, I drink a lot of tea) and called my mum (yes, I call my mum a lot).

14:05–15:50 I made a figure from my western blot images and sent it to my PI and colleagues who will be working with these cells. Before we got this cell line I was trying to establish this system in my mutant cells which would allow me to study how several different proteins work together but I had some technical difficulties. I printed out all of my results and was trying to figure out what went wrong and how I could troubleshoot it.

I have also calculated how much it would cost me to do sequencing using the older assay for DNA-protein interactions (ChIP) and the new Cut&Run assay which we are trying to establish at our institute. Cut&Run is much cheaper and gives better signal to noise ratio but it needs a lot of optimisation while ChIP works very well for my targets and is established in our lab. Sometimes planning and decision-making can take even more time than doing the actual experiment!

15:50–16:45 I have finally finished those DNA extractions I started on Tuesday!

16:45–16:55 Wrapped up and planned work for tomorrow.

Summary: It was an exciting day. Now I can say that I mastered western blots, haha. I spent a lot of time thinking and making decisions so I have a very clear picture of what I’ll be doing during the rest of the year. After work I went home and watched Netflix.

Friday

10:05–10:20 I started my day by quantifying DNA I extracted yesterday. I got good concentrations and no protein contamination but I still need to check for RNA contamination.

10:20–10:40 I made tea, opened my laptop only to find out it was having a glitch! I started to panic, shut it down and left it alone for some time. Luckily, it “fixed” itself.

10:40–11:00 I planned my day, signed up for an online talk, checked email and updated my excel spreadsheet where I record all DNA extractions I do.

11:00–12:00 I made a gel to run DNA on it to check if it’s contaminated with RNA. Genomic DNA has a very high molecular weight so it runs slowly while RNA molecules are smaller and run faster so they appear at the bottom of the gel. I spent the rest of the time talking to labmates and reorganised some lab space to free up bench for a new student who joined us recently.

12:00–13:00 Had lunch while watching a section meeting. Our section consists of ~7 labs who work on genome regulation and everyone has to present their work which works out to be approximately once per year. I had my talk last week where I presented my project in front of 45 people for 20 minutes. Doesn’t sound like a big deal but I always find presentations very stressful.

13:00–13:50 My gel solidified, I loaded the DNA on it and gave my EBs enough media for the weekend.

13:50–14:10 I checked emails, updated my lab book and imaged the gel. I had RNA contamination (again…) so I’ll have to treat my DNA with an enzyme which degrades RNA.

14:10–15:30 I heard back from the image specialist who explained how to re-calibrate pixel to micrometer ratio for my EB images. I tried his suggestions and it worked! We are very lucky to have an imaging facility which provides training and support, I would be having a very hard time without them.

Embryoid bodies

15:30–16:30 I continued to measure EBs while listening to the talk by one of the PIs from our institute. I tried to plot surface area for different mutants and found out that the range of the values is so wide I cannot plot it on a regular graph. I will have to use a log scale but it’s a task for the next week because I need to figure out how to do it.

16:30–17:00 Next week I will be doing a very sensitive and a very expensive experiment for a colleague. I printed the protocol and looked through my notes to make sure I have everything I need and to remind myself of the protocol steps. I planned my next week and went home.

Summary: it was a good day and a good week. I finished the last set of the DNA extractions for an experiment, tested a new cell line, measured EBs and made a paper outline. I have two more weeks to wrap up other things so when I come back I will be ready to start new experiments. Overall, this week had a nice balance between the experimental work, planning, thinking and troubleshooting. I’d say it’s very representative of what I do in my PhD although some weeks are more experimental while others can be mostly about thinking and troubleshooting.