CCG Lab Page

The CCG lab has 3 main rooms for genomics use: the extraction room, the pre-PCR room, and the sequencing lab.

The extraction room is used for all extractions, including high molecular weight extractions, and specializes in extracting DNA from museum specimens. There is an additional extraction room for ancient DNA extractions that is affiliated with the CCG.

Our pre-PCR room is used to store extracted DNA used in ongoing research projects and also serves as lab space to set up PCR reactions. Separating pre-PCR extractions from PCR products helps reduce contamination from amplified, highly-concentrated samples.

Our sequencing lab is the powerhouse of the CCG. This lab is used for all post-PCR processing of DNA samples, library prep for various next-generation sequencing projects, and contains our gel room. The lab has all the the equipment needed for library preparations and standard Sanger sequencing with nine thermal cyclers from Thermo Fisher and Bio-Rad, one Thermo Fisher Scientific qPCR machine, Qubit 4.0 fluorometer, 4150 TapeStation, Blue Pippin, Qsonica and Covaris Sonicators, Rainin BenchSmart96, an Illumina MiSeq next-generation sequencer, and an Oxford Nanopore MinION and PromethION 2.

The CCG also has a dedicated Freezer Room that houses the Academy's frozen tissue collection and the CCG's DNA CryoCollection. It includes ten -20 degree and ten -80 degree freezers. In addition, the room now includes five Taylor Wharton 40K liquid nitrogen (LN2) storage freezers. Importantly, this room is outfitted with an emergency back-up power system to keep freezers running during a power outage.

The CCG is also equipped to generate cutting-edge reference genomes directly in the field, thanks to generous support from our friend and colleague, Jim Henderson. This new capability will foster local collaborations, expand training opportunities, and unlock the potential to sequence important species on-site (by overcoming challenges like permit restrictions).

Our new equipment includes:

• Oxford Nanopore PromethION 2 Solo: A portable, high-throughput sequencer

• BentoLab: A compact all-in-one DNA lab

• Razer Blade 16 Gaming Laptop: A powerful laptop for real-time sequencing and data analysis in the field

• Corsair VENGEANCE i8100 Series Gaming PC: A high-performance desktop for in-house testing and analyses

Students and staff from all research departments of the Academy are working on interesting projects in the CCG lab. Many projects focus on investigating historical relationships between species using standard phylogenetic approaches, including the application of both molecular and morphological data to identify and describe new species. In addition we have some current projects that focus on the population level, using genetic data to apply towards the conservation of species. Project methods vary and include standard Sanger sequencing, microsatellite genotyping, transcriptome sequencing, RADseq, sequence capture, and whole genome sequencing.

Please visit the CCG's Projects Page to gain more information on individual research projects.

^{Graphic: Joseph Wu © California Academy of Sciences, Biological Illustration Intern Summer 2023}

Personnel working in our lab include Academy curators, research associates, post-docs, graduate students, technicians, interns and volunteers from all of the Academy's research departments. The Director of the CCG is Athena Lam and the CCG’s Curator of Genomics is Brian Simison. Our computing resources are managed by Joe Russack, the Academy's Director of Scientific Computing. Our Assistant Lab Manager is Grace Kim.

We also have a dedicated post-doc, Anna Holmquist, lab technician, Holly Tavris, interns and volunteers for our insect barcoding project.

> Biodiversity Seminar – Building a barcode library of California insect biodiversity (2023)

> Genomic Social Hour Series (2020-2021)

> Unlocking DNA: The Center for Comparative Genomics (2018)
> Rewind: From the Field to DNA (2013)
> Brian Simison: Chat with an Academy Scientist (2013)
> Science in Action: Center for Comparative Genomics (2012)