August 4th, 2010
ST. LOUIS, MO., August 4, 2010 – Cofactor Genomics LLC, recently announced the purchase and implementation of Geospiza’s GeneSifter Lab Edition LIMS software. The software, currently being integrated, is expected to simplify laboratory management, increase throughput, reduce errors and support real-time data distribution to researchers.
Cofactor Genomics, based in St. Louis, MO., has provided next-generation sequencing and analysis services to customers since 2008. The company utilizes both the Illumina and Applied Biosystems SOLiD sequencing platforms in combination with commercial and proprietary analysis software and pipelines. Cofactor continues to meet their customer’s expectations while upholding a reputation for extremely high quality and consistent data generation and analysis.
“Geospiza is very pleased that Cofactor has selected GeneSifter Lab Edition to help them grow their high throughput sequencing and analysis business,” commented Rob Arnold, President of Geospiza. “Cofactor is known as having very high quality standards and expecting superior performance from their partners. Geospiza is delighted to be recognized by Cofactor as the best in class supplier of lab systems for high throughput sequencing.”
“Being at the cutting edge of technology, Cofactor had the opportunity to review the leading LIMS products available. Following a competitive analysis we identified Geospiza’s GeneSifter as the best in class solution,” stated Jon Armstrong, Cofactor Genomics Chief Marketing Officer. “We are extremely excited about GeneSifter as it offers integrated tools to support our growing infrastructure. We are at a point in our company where increasing operational efficiencies while providing unparalleled customer service is of the utmost importance.”
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June 28th, 2010
Cofactor Genomics in conjunction with Knome and Applied Biosystems, will construct libraries and perform the sequencing of Ozzy Osbourne’s genome. Cofactor will generate sequencing data on a newly installed Applied Biosystems SOLiD 4 system by Life Technologies while Knome will provide data analysis and interpretation.
“These technologies produce thousands of times more data per run and at a fraction of the cost than those technologies/techniques used in the human genome project.” says Cofactor Genomics’ Chief Technical Officer Dr. Jarret Glasscock. “This data will lead to even more insight into what makes Ozzy tick…. techniques far superior to playing all his records backwards.”
Cofactor Genomics, based in St. Louis, MO., has provided next-generation sequencing and analysis services to customers since 2008. The company utilizes both the Illumina and SOLiD sequencing platforms in combination with commercial and proprietary analysis software and pipelines. In the short time since their inception, Cofactor has established a reputation for extremely high quality and consistent data generation.
“I believe this is one of the most compelling marriage of endeavors.” comments Jon Armstrong, Chief Marketing Officer for Cofactor Genomics. “Cofactor is using the most advanced genomic technology to better understand the life of Mr. Osbourne; a person that has fashioned their complete existence as a creative individual.”
Cofactor Genomics will generate the genomic sequence data for Ozzy’s genome using the newly released SOLiD 4 platform. “The SOLiD 4 system is perfectly suited for this type of work based on its extremely high sequence output and lowest error rate of any sequencing platform.” notes Jon Armstrong.
Life Technologies, headquartered in Carlsbad, CA is the manufacturer of the SOLiD line of Next-Generation sequencers. Knome located in Cambridge, MA provides consumers with whole genome sequencing and analysis for biomedical researchers and physician-directed families.
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June 17th, 2010
Cofactor has worked with some extremely interesting people and we thought, hey why not showcase them? So here we go. Welcome to Cofactor Spotlight, a place where we want to say thanks to all of the amazing people who have made Cofactor a success.
Transverse section across a leaf blade showing a fungal hypha (Epichloë festucae Fl1) growing in close association with two plant cells (perennial ryegrass, Lolium perenne).
Our first spotlight falls on the Institute of Molecular BioSciences, Massey University where the work of Dr. Carla Eaton, Dr. Murray Cox, Dr. Barry Scott and their group has lead to a publication in Plant Physiology. Their paper:
Eaton, C.J., M.P. Cox, B. Ambrose, M. Becker, U. Hesse, C.L. Schardl, and D.B. Scott. 2010. Disruption of Signaling in a Fungal-Grass Symbiosis Leads to Pathogenesis. Plant Physiology 153:1780-1794.
Is described by Dr. Cox as follows.
Symbiotic associations between plants and fungi are a dominant feature of many terrestrial ecosystems. However, relatively little is known about how plant-fungal signaling coordinates this symbiotic state. Using an Epichloë festucae-perennial ryegrass model system, we explored the role of a fungal stress-activated MAP kinase (sakA) in maintaining this mutualistic association. Deletion of sakA induces a switch from a mutualistic to antagonistic interaction with the host. Infected plants exhibit dramatic changes in development, stunted growth and premature senescence. From a molecular perspective, high-throughput mRNA sequencing reveals striking changes in fungal gene expression consistent with the transition from restricted to proliferative growth, including up-regulation of hydrolytic enzymes and transporters, and down-regulation of genes involved in the production of host-protective biomolecules. Corresponding analysis of the plant transcriptome reveals up-regulation of host genes involved in pathogen defense, as well as major changes to plant hormone gene expression. Together, these results highlight the fine balance between mutualism and antagonism in a plant-fungal interaction. They also illustrate the power of deep mRNA sequencing to dissect the molecular processes that underpin symbiosis.
Dr. Cox expressed that “the team at Cofactor Genomics provided helpful advice on project design, and delivered multiple mRNA-seq datasets with impressive yields and consistently high quality.” When asked about their overall experience on working with Cofactor, Dr. Cox had this to say:
We expected, and received, prompt, first-class service from the Cofactor team. We look forward to doing business with Cofactor Genomics again.
We here at Cofactor look forward to working with Dr. Cox and the rest of the team in the future and want to congratulate them on their publication.
If you’ve done work with Cofactor Genomics and are interested in being featured in our customer spotlight, please send us an email.
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June 17th, 2010
Cofactor has been getting some press recently from some great news sources and we just wanted to let you know.
The first article talks about Cofactors partnership with Novocraft Technologies to bring sequencing service to Southeast Asia. The full article can be found here.
The second article is a profile piece in the St. Louis Post-Dispatch in which David Nicklaus profiles the founding of Cofactor and talks about its entrepreneurial spirit. The article can be found here.
From the Post-Dispatch Article
We guarantee that this is only the start of the exciting news that is soon to come. Stay tuned to find out what other adventures await.
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April 26th, 2010
Sorry about our lack of posting, but as you can see from the title….. we’ve moved!!! We really miss the old building, where many late nights of wringed-hand planning and pots of black coffee were consumed during the building of the company. But, at a certain point when everyone was wearing coats in the lab because we had to keep the air conditioner on all the time, even in the winter, to keep the sequencer cooled, or maybe when we covered the sequencer with plastic because the roof was leaking and water was making its way through three flights of wooden floors, or just because the thought of fitting 5 people in a 1100 sq/ft lab gave us all the shakes, we decided we needed a bigger place to set up shop.
Ladies and gentlemen, I would like to introduce you to….. (drum roll begins)
3139 Olive St., St. Louis, MO 63103…….
7500 sq/ft and 2 floors of early nineteenth century masonry bones and concrete floors and ceilings that would make even the strictist minimalist proud! Only took about a month of moving and a couple of trips to IKEA to get the lab set up, and viola! We are fully producing sequence that looks better than ever! Even bigger news is we have adopted another sequencer, that I lovingly refer to as “Brad”, however everyone is not sold on that. We now have two Illumina machines and two Applied Biosystems machines. Oh, and what beauties they are!
Their names are (and by the way, I picked all the names and am totally responsible for anyone getting mad about their name being used to name a sequencer [which by the way..... is SUPER cool]. Let me assure you that this naming scheme is purely out of love for these very unique yet apt names, as they were culled from my own family):
Illumina #1 - Randy
Illumina #2 - Mitch
AB #1 - Ronnie
AB #2 - Brad
Come on now, quit swooning!
Here, let’s take a walk around.
The main wet-lab section of the building. Space for all of our folks and equipment. Also, please notice the double doors at the end of the room which lead out to our front 2nd floor covered patio! Having spent most of my adult life working in academic labs, this makes me giddy every morning when I come in. I have my coffee out on the front porch and head inside to attack the day with a ferocity not seen since my first year of graduate school.
Here is the sequencing room. Notice the metal tube in the back by the Applied Biosystems machine? This is a custom air handling unit that we had installed in the building. These machines put off a lot of heat. And, YES, the AB machine in the right one third of the picture is Brad!
Hey….. check out Jin, our senior scientist, at the bench! She does NOT mess around! Also, if you need some lights for your lab, let me know because I built the ones above the Jin. I wanted them to look like race cars. I may put a tutorial up soon
This is a pic of our conference room. And, no that is not a “state fair, pay-to-put-your-friend-in-jail, jail” in the background, that is the original freight elevator. It has stairs that go to the roof, though we have enough to do down here so I don’t know what is going on up there.
Alright, back to work now, and I have quite a few interesting posts coming in the upcoming months, so please check back. Also, if you have any questions or whatever, write them on a 3×5 blue-lined note card and send them to our CTO, Jarret. He will be super-confused and we will all have a great time making fun of him.
Until next time,
Jon
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August 6th, 2009
Cofactor has been in business for about 10 months now. In that time we have produced an amazing variety of libraries. Check out a sorted list of them, all 181 as of last week. They span 12 distinct types of libraries. Surprisingly, at least to us, a huge portion of this is RNA. When we were at the genome center, we were really focused on human re-sequencing, but Cofactor’s focus both for software and wet-lab development is now clearly de novo assembly of non-model or emerging-model organisms and their transcriptomes, and expression/splicing/fusion analysis by full-scale RNA-seq.
A quick note about RNA: If you have a larger non-model organism and you would like to begin building genome resources for your work on a tight budget, RNA is a great way to go. You can submit total RNA and after Ribo-depletion or PolyA selection, we can create paired-end Illumina libraries can be assembled into genes. Now exon/exon junctions where there is any alternative splicing will have a gap, but there is still plenty of information to see what genes you have, and even provide a basis for expression work using less expensive single-end reads on the SOLiD mapped back to the assembled transcriptome.
RNA sequencing is like “targeted re-sequencing” that actually works and is actually inexpensive!
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June 18th, 2009
Every day is exciting at Cofactor Genomics. Since we posted the new website, we have several pressing announcements!
Our Classroom Project winners have been announced. We are funding 4 undergraduate genomics projects, and some of those even more than the promised 1-lane/1-barcode level. These projects will serve both as experiments in molecular biology and as experiments in education. It is our hope that the syllabi, data, and methods, and perhaps even student testimonials, will serve as templates for undergraduate classes across the nation. Experiential learning is the best way to teach science, especially genomics, and we are proud to contribute to the great work of educators like Sarah “Sally” Elgin and the original Genomics Education Partnership. Several of us at Cofactor either assisted or took Sally’s class, so we encourage you to check it out.
We also launched the long-anticipated Cofactor Video! Bio-Rad and The PCR Song started the fad with Music Videos recast for science geeks. Eppendorf followed suite with a Boy-Band video about the epMotion. Somebody even remade a classic film into The AffyMatrix. Our innovation? Bring science geek-ery to a new genre - the Mock-u-mentary. Enjoy! Force your friends to watch it - that gel extraction can wait.
Last but not least, we can now generate 1 Giga-Base of pass-filter per lane per end on the Illumina using only 60bp reads. If you really wanted 106bp reads, sure then we could give you 1000MB / 60bp * 106bp = 1.8GB per lane per end, but those extra bases aren’t high quality enough to warrant the extra time. Certainly not if you want to put them into something like Velvet where adding more data that is poor quality actually makes the assembly worse. And if you’re not doing de novo assembly, we posit that 60bp is long enough!
Buyer beware! Why do we have this ridiculous expression “pass-filter per lane per end @ 60bp reads” ? These 4 variables all need to be held constant when comparing runs. Many places artificially inflate output amounts by any or all of these methods:
- quoting raw data output instead of filtered (inflates 50-30%)
- quoting output at 106bp reads which are garbage after the ~75th base (inflates 76%)
- quoting output for paired-end lanes when you are thinking single-end (inflates 100%)
- quoting output for an entire flowcell instead of lane-by-lane (inflates 800%)
Of course, when we talk about the SOLiD you have to take it one step further: ”mappable per barcode per end per slide @ 50bp reads.” The SOLiD can run 2 slides at once without really increasing the run time. Since it runs twice a long as the Illumina this conveniently puts it back on par time-wise. Of course, you still get 50% more reads on the SOLiD.
We are always here to cut through the hype of each platform and optimally allocate projects across platforms. Let us know if you have any questions about Next-Gen!
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May 11th, 2009
Thank you for visiting the new CofactorGenomics.com!
Please pardon our construction as we transition to the new site. We wanted to make sure to get as much content to everyone as quickly as possible. In the next week we will be adding more pictures, graphs, and reference PDFs all over the site, so make sure to check back frequently.
We are also excited to announce the release of the Cofactor YouTube video on June 5th. Check back then for a link to the new video, and our apologies to Applied Biosystems, Illumina, Qiagen, and Bio-Rad! (You’ll understand when you watch 
)
Finally, don’t forget to get your final entries into the Cofactor Classroom Project! We will be selecting winners soon.
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