In addition to being a training lab for Merritt College, the lab is used by the non-profit biotech services company Profile Genomics. With this in mind, the lab is designed for high-volume throughput in a production environment.

The lab is held the center of a newly-renovated former biotech building. Sections of the building are used by College of Alameda for Chemistry and Biology.

The new 5,000-square-foot laboratory located at 860 Atlantic Ave. in Alameda, CA is equipped with more than $2 million of state-of-the-art equipment. The new facility gives students access to relevant high-tech devices providing them with a means for practical experience.

Visitors and students are encouraged to join us a tour of our lab to learn about Genomics. As we are production facility, we require everyone to attend a Good Laboratory Practices orientation before acquiring a lab entry pass.

The wet lab is where we prepare samples for many different services. This is where we extract DNA, prepare plates for PCR and run our gels to separate PCR products by size.

It contains standard equipment, including a fume hood, analytical balances, plate heaters and water baths, centrifuges, vortexers, an autoclave and glassware, dH2O purifying and conditioning units, ice machines and pipettors.

Pipettor tips and eppendorf tubes are organized and stored for easy access. Desks are organized with cabinets so students have can access all necessary equipment from their chair.

In addition to the bank of five -80°C freezers in the wet lab and 120v -80°C freezer in the sequencing room, there is a well-ventilated freezer room containing an additional five -80°C freezers.

These freezers contain tens of thousands of reptile and amphibian tissues collected from all over the world, as well as the complete mitochondrial genomes of six vertebrates.

Microarrays allow us to detect for the presence of genes. We can create a template of hydrogen bonds which act like a key - it will only hold onto a specific sequence of mRNA which matches the hydrogen bonds. Detecting for the presence of genes can be useful. For instance, consider if you had a dog and you were curious what breeds it was, you could test for specific genes known from various breeds to find out its ancestry.

Additionally, microarrays allow us to see how often DNA is being expressed. DNA is transcribed into RNA, which is then translated into a protein. This DNA expression can be trigged by many different things. For instance, if you were to spend time sunbathing, your DNA would increase expression of the gene which creates melanin, a response to the environmental stress (UVB radiation). Seeing how DNA expression changes in response to stimuli is a very important tool in the world of biology and medicine.

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Automatic colony picking and plate transfer workflow by many orders of magnitude.

Our lab is equipped with a Genetix QPix2XT (with stacking) Colony Picker. We also have a Genetix QFill3 with stacking that is a liquid handling instrument that leads into colony picking.

We can handle SBS formats such as Nunc plates as well as Greiner Multiwell plates.

Cryogenic tissue extraction is method of yielding large strands of DNA. We have a Covaris CryoPrep, which allows us to freeze tissues and hit them with a hammer, breaking cells without destroying DNA. This also aids the extraction of DNA from difficult tissues, such as bone or plant cells.

Liquid handling, or automated pippetors, are instruments which aid in high-throughput workflow. Whereas pippetting half a dozen reagents into a 384-well plate would take all day and yield mistakes, a liquid handler like our PlateMates can be programmed to generate an entire stack of 384-well plates with multiple reagents very fast with minimal effort.

Sequencers can only read certain sizes of DNA. First-generation sequencers like the ABI 3730xl capillary sequencer can use around 700bp, while second-generation use from 50-450bp. This means DNA must be cut to the right size. For longer strands of DNA (up to 40kb) we have two Hydroshears, which push DNA through a small aperture, stretching DNA and cutting it into consistent sizes (850bp to 3kb, 1.4kb to 8kb, 4kb to >40kb depending on aperture size). For smaller cuts of DNA, our Covaris LE220R uses sonication for focused cavitation to randomly cut DNA. It can cut from 100bp to 5kb.

As sequencers can only read specific lengths of DNA, technicians must select for a specific length. Gel electrophoresis can be used to separate molecules by size, however the Pippin Prep is an automatic and more precise method of DNA size selection.

Reading a genome is already a lot of work, but once you have a sequenced genome, you must assemble and analyze it.

MacVector is a sequence analysis program that allows us to work with and interpret DNA.

MacClade

PAUP

Phred

Phrap

Consed

There is an entire world of other great, open source or free software to explore.

Profile/Merritt Genomics currently operates a computer core that is capable of assembling large sized genomes de novo. The cluster contains a head with 32 cores, 256 Gb RAM, and 1TB 15k RPM data storage. Clustered with it are six slaves containing another 96 cores and 224 Gb RAM. Using proven algorithms, the core is able to assemble genomes up to 3Gb at 50x coverage, or 5Gb at 30x coverage. More modern assembly algorithms use less memory and enable assemblies over 10Gb.

Two storage rooms, an autoclave room, conference room, 3 offices, library, lounge