About our role: We carefully bring samples into the lab, extract them, prepare them for sequencing, then make sure they're transferred to the sequencing team for the big event! Once sequenced, we hand data over to the Code Crackers.
We have a whole range of jobs!
Nancy, the leader of the Samples Management team, works closely with collectors like the Woodland Wonders and Perfect Protists. She helps bring samples into the lab and meticulously makes sure we have paperwork with every tiny detail about each sample, such as the species, body part (some organisms are too big to put in a tube!), the GPS location of where the sample was found, who collected it and checking it was collected legally. Sample data is checked over and uploaded to a samples database, where everyone from the collectors to the lab team can see which stage of the process each sample is at. Once everything is checked over and issues ironed out, collectors are given the go-ahead to send samples to the lab. Nancy’s team receive the samples, check the delivery matches the paperwork and sorts them into large freezers for storage.
Once the samples are in the lab, the lab team (including Michelle and Graeme) get to work. Some samples we already know a lot about how to get really good DNA: for example, we can extract really clean, high molecular weight (i.e. large fragments) DNA from insects, muscle tissue, and some plants. These all have DNA extracted by following a standard protocol and go straight through to sequencing. Other sample types, such as snails, can be tricky – a lot of the time unwanted stuff such as mucous sneaks through with the DNA and we don’t know it’s there until we try to sequence the DNA and the sequencers “block”. The lab team then have to trial different methods of DNA extraction or test ways of cleaning the DNA after extraction to remove these materials. Lastly, the lab needs to process at least one of all ~66,000 species. They are currently exploring methods for automating steps (robots) to process larger numbers of samples in one attempt.
Extracted DNA is “just” a tube of clear liquid with a barcode, and this is “handed over” to Liz, our Scientific Services Representative in the Sanger Sequencing team. From behind her PC battlestation Liz masterfully coordinates the lab teams in the Tree of Life and Sanger Sequencing labs, making sure the correct samples are transferred from Tree of Life to Sequencing and arranging sequencing schedules. As the main point of contact, Liz uploads the sample data to a database which lets the sequencing teams and Code Crackers know which sample has been processed and hands over the sequence data to the bioinformations for assembly into super high-quality genomes.
Last, but by no means least, Sophie is our Projects and Communications Manager. Sophie works closely with the lab teams, faculty (academics who advise on the work the Tree of Life labs do while running their own research teams) and bioinformaticians to pull all the data together into a document that can be shared with the world. This is a Genome Note – the formal announcement to the scientific community (and the world) that we have produced a genome, and sharing where the data is, the details about the sample(s) sequenced and, perhaps most importantly, listing the teams that did all the hard work!
Photos of our equipment:
Monthly team update - March 2021:
This month we’ve held our first All-Hands meeting. This is a conference-style meet up of everyone who is involved in the Darwin Tree of Life project and a great chance for us to get together and share what we do and how we do it. Thanks to Covid this was all online – so lots of presentations, breakout rooms and emails! At the end of the week Professor Mark Blaxter, head of the project, gave a summary of where we are to date (over 100 genomes sequenced and in the process of being released to the world) and where he expects us to be in 5 years’ time – and beyond!