Creating basic genetic database - (Nov/03/2012 )
Questions: What type of genetic database would suit my application? And how would I go about writing it up to include in my thesis?
I seem to recall there being a site where you can upload/enter your DNA absorbance data, does anyone know of where I can do this?
I am a 3rd year degree student studying a bachelor of Agriculture and compiling the final touches to my thesis which involves correlations between genetics and metabolic parameters.
I have extracted gDNA from 63 whole blood samples withdrawn from pregnant ewes bearing single foetuses, I used a Qiagen Flexigene DNA kit for the extraction process.
I am looking for the Booroola fecundity gene or Bone morphogenetic protein receptor type-1B (BMPR1B), in association with glucose and ketone measurements taken using the Abbott exceed human diabetic glucometer, the latter part already undertaken and only awaiting on my project supervisor to quide me with the PCR and amplification with the forward and reverse primers we have.
The DNA extraction was initially undertaken on 24 samples, as the centrifuge spacing was the limiting factor, although the test was ran 4 times and therefore I have numerous amounts of DNA extracted on these 24 samples. The remaining 35 samples only had the DNA extracted once on the final Test 4 (being an extension).
I've come up against numerous obstacles (too many to list), as such I've needed to cut short the research project and finalise the thesis for submission over the following week without having completed the research project, although once my exams are over the university is willing to allow me access to the laboratory to complete the research project to enable me to gain the experience in genetics I desire, as I've not been formally trained in genetics. It is my intention to submit a supplementary report ontop of the submitted (incomplete) thesis and I would like to get some feedback and suggestions on going about this, along with your thoughts on creating a genetic database for the university as a research resource. It would be nice if I could include a small section discussing how I intend to go about this.
Presently the university don't offer any courses higher than a bachelor degree, although they are investigating offering honours in the near future, so there is potential that someone (possibly myself) will take up from where my research was left.
I still have the whole blood vials which were refrigerated at 4 degrees C over four days, then frozen in a frosting freezer at -20 degrees C for 4 months and thawed overnight at 4 degrees C, then kept refrigerated at this temperature since the 29th August 2012. I could pipette 2 mls of the whole blood and freezer these into microfuge tubes at -20 degrees C and retain the vials of blood in the frigde.
The extracted gDNA from Test 4 and Test 4 extension have always been kept in the refrigerator with several sampels kept temporarily in a cooler or within the fume hood during use for an hour all up, while the extracted gDNA from Tests 1 - 3 have been kept at room temperature and exposed to artificial and relfected (non-direct) sunlight in the laboratory since 30th August 2012, in which I have only recently placed these in the refrigerator last week.
Initially, I was planning on using whatman FTA cards to preserve the blood samples, although I'm not sure if I will have the time to order them and the expense will probably end up being out of my pocket. I still have enough protease left in the flexigene DNA to run several more tests if needed using the lowest volume of blood, although more protease could be purchased separately at the end of the day, as there is still plenty of buffers left over from the kit.
Practically, I have analysed all the Tests (1 - 4 & T4 extension) for DNA purity with the spectrophotometer and this information is contained within an Excel master file.
My thesis (about 10mb), as it stands is accessible as download in the link to give you a more comprehensive idea and understanding of the background, which I'm currently working on the results. I had applied for an extension to the 23rd November, which I was initially granted although the extension was revised and is now due this coming monday with 5% deducted for each day overdue, which I am seriously considering holding off a day or two. Except I have 2 exams next week and would like to study so I can pass, considering this is my last year.
There is probably no point re-inventing the wheel so you could submit the sequences to Genbank and they should be freely available from there. Setting up a database is difficult and proper planning for coming use is essential as it tends to make the format/design of the database more user friendly. Not that this should stop you doing it if you have the time, it should be relatively easy to put all the sequences into a filemaker database (or even excel) along with notation on the primers used, extractions, dates, tests done, etc...
If a similar database currently exists - and is itself being refined and made more effective over time - it would seem to make sense to connect and contribute to Genbank. Do they have anyone there who you might be able to talk to about improving how they run their database?
Thanks guys. I left the information fairly simple in regards to the genetic database, as far as I know the University don't have anything formal for livestock genetic database, I know they record alot of detail about individual animals which they show at the Royal Mebourne Showgrounds. Generally the best and worst animals are measured for beef meat quality and carcass conformation, though this involves slaughtering the animals, therefore my research could be useful towards this aspect.
Last year I was privy to the process of cataloguing the beef information, which tends to be based on a range of industry standard values and formulas, together with photographs of different cuts from various animals. The lecturer who handled this has since gone into retirement and I believe the system is now being managed exclusively by another department, I'll need to investigate this further with them and what level of involvement the agriculture diploma students have.
Undoubtedly my research project supervisor has developed a database for his department (viticulture) and I will query him further about that.