I have just gone into my final year of funding for my PhD (4th year). I am worried about finishing on time. I know a lot of people don't finish on time but due to my boss being absent for multiple 3 month periods for personal reasons I have been going through experiments with little guidance. If I go into my 5th year I have to pay my own fees and support myself until i finish. I am getting to the point were everything is getting on top of me that I can't seem to get a whole lot of work done.
Without going into detail - My PhD project involves ChIPseq of 3 centomere components both in async cells and defined cell cycle stages. Due to problems in establishing cell lines and antibodies that are/were not chip grade I haven't actually carried out any chipseq experiments yet. What I have done though is taught myself bioinformatics analysis from scratch (nearly 2 years of work) and processed a lot of our collaborators chipseq experiments which are carried out on other centromere components which have shown a number of novel findings. My boss is absent again so i have organised to fly to my collaborators lab for 8 weeks to finish of more bioinformatics and carry out two chipseq experiments. Ideally my PhD thesis chapters would be..
2. Materials Methods
3. Results - Bioinformatics Analysis of collaborators experiments
4. Results - ChIPseq of centromere components Async Cells
5. Results - ChIPseq of centromere components Cell cycle stages
My colleague is establishing cell cycle synchronisation parameters at the moment and should be optimised by the time im back (christmas). Chromatin preparations are optimised and qPCR conditions are also optimised - the company we are sequencing with are carrying out adapter ligations so essentially all we have to send is the chiped DNA. I have for sure 1 antibody that is working in ChIP and 1 that hasn't been tested right through to qPCR but Western analysis looks promising. The third antibody may have to be discarded but I'm also making an antibody to replace this.
My questions are - How many ChIPseq experiments would you need to have enough for a PhD thesis? Would three chipseq experiments in async cells be enough to finish? What happens if some of these experiments fail? How can I motivate myself to get this done?!
Thanks for taking time to read this - I can give you more information