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About our role:
We bring into the lab, extract them, prepare them for sequencing, then make sure they’re safely transferred to the sequencing team for the big event! Once sequenced, we hand data over to the Code Crackers.
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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!
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Photos of our equipment:
A frozen fly sample has been transferred to a cryogenic bag and is ready to be deep-frozen and smashed to powder. The tube on the right is the sample tube which has a unique barcode so the lab can track this sample through to sequencing submission. A special adapter allows the fly to be shaken into the bag, smashed, then shaken back into the tube. This means we cannot accidentally contaminate it with other samples and reduces the chance of losing or dropping the sample as it is always connected to the barcoded tube.
Michelle is decanting liquid nitrogen into a flask. This will be used to deep-freeze samples ready to be smashed into powder as part of the DNA extraction process.
A batch of samples are loaded into our robot DNA extractor ready to be processed. Here, Filipa is scanning a barcode which tells the robot these are samples (and not reagents).
Fleet of sequencers! These machines are big – about the size of a large fridge-freezer.
What’s inside a PacBio SequelI IIe sequencer
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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!
~Michelle
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The end of March saw a sample count by the Sample Management team. Ian reported we have over 6,200 sample tubes in our -70C freezer – a mere drop in the flood of samples we expect to be holding in the lab by the end of this year! Keeping our freezer ordered and making sure we know exactly where every tube can be found is important, especially as more samples arrive and the lab team begin to scale up DNA extractions to over 100 per week. The Samples Team have now fired up the second -70C freezer, doubling our storage capacity. A quick calculation and I estimate we could keep up to 82,944 sample tubes in one of these freezers!
~Michelle
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Monthly team update - May 2021:
May has been a reflective month for the lab, looking inwards and discussing the processes we follow to see where we can make improvements and streamline our efforts. This is hugely important as there aren’t always existing methods or technologies that we can buy in and “just use” – one of the great but also difficult aspects of cutting-edge science such as this. We’ve also begun preparing our SOPs (standard operating procedures) to be ready for publishing online so researchers around the world can use the same processes and techniques. This is an iterative development process – the documents bounce between the author and proof-readers to iron out all the finer details. We need to keep these documents short and concise, but also make sure that all the details needed for someone to follow without needing to ask questions are included.
~Michelle
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Monthly team update - June 2021:
June is an exciting month – we’re increasing the number of samples we process and submit for sequencing from 24 to 35 per week! This doesn’t seem like many samples given we have over 70,000 species to sequence, but the core lab team is small and doing the work (mostly) by hand, while at the same time researching how to automate these same processes. The team are regularly extracting DNA from insects and arachnids from Wytham Woods but have also had a mollusc collected from a nature reserve in south London and some seaweed and algae from Devon sent by the Marine Biological Association!
At the moment Michelle is running a “processed sample audit”, checking the samples in the freezer that have been partly processed by the lab team. Our standard process requires up to 25mg of tissue (50mg for plants) for a single extraction and some samples exceed this, so its good to have an accurate record of tissue remaining in the lab in case we need to extract more DNA. Extra DNA can be useful if sequencing fails, or if the sample has a large genome and we need more than the normal amount of DNA to make sure we capture everything.
~Michelle
