FAQ

Cofactor can produce single-end, paired-end, and mate-pair whole-genome libraries, bisulfite-converted whole genome methylation libraries, DNA binding protein, RNA binding protein, and histone modification ChIP-seq libraries, whole-transcriptome RNA libraries, small RNA libraries, Reduced Representation Sequencing (RRS) libraries, PCR product libraries, Barcoded/ Multiplexed libraries, and FFPE genomic libraries. Other libraries may be possible upon request.

Paired-end libraries provide additional longer-range linking information that allows reads that would otherwise have to be discarded to map back to more repetitive locations. They also allow for the detection of moderately sized indels. Current PE libraries sequence the read-length off of each end of the same DNA fragment (available for RNA/cDNAs too!) and have a defined ~200bp gap in the middle with known standard deviation.
Mate-pair libraries are essentially longer-insert paired-end libraries with insert sizes from 5 to 20kb.

Bisulfite conversion converts non-methylated C’s into Uracil’s that are converted to T’s after one round of PCR. After mapping, this can be used to identify the positions of all methyl-C’s in the genome.

ChIP libraries can be produced from any DNA or RNA obtained by fragmentation, cross linking, co-immunoprecipitation with your favorite antibody of the DNA now cross-linked to the antibody’s target protein, and subsequent DNA/RNA purification. In this way, you can determine the actual binding sites of proteins in a whole-genome way.

By providing total RNA we can produce and sequence cDNA libraries that allow you to simultaneously define the entire transcribed portion of a genome as well as quantitate the level of transcription of each portion (genic or non-coding). This quantitation is as accurate as qRT- PCR and more broad than a microarray because it requires no a priori knowledge of putatively transcribed regions.
MicroRNA libraries are essentially the same as whole-transcriptome libraries but include only small fragments in a defined range (~20-40bp) that should include many types of non-coding RNAs. This allows you to both discover and quantitate the level of all small RNAs in a genome.

If you want to take measurements from a defined random subset of the genome (to reduce costs, for instance), we can construct libraries from bands of restriction digests so that you have high coverage over a smaller set of genome sites. This can be combined with most other types of libraries.

If you have PCR products or DNA isolated from Formalin-Fixed Paraffin-Embedded (FFPE) tissue, we can create sequencing libraries from these samples using specialized protocols.

There are numerous Next-Generation sequencing platforms available (Roche 454, Illumina, Ion Torrent, Applied Biosystems, PacBio, etc). Each has its own strengths and weaknesses that lead to a segmentation of uses by application. At Cofactor, platform choice and optimization is for us to worry about. All you have to do is describe your research question to us. We'll design your project to choose an optimal platform (or combination of platforms) that minimizes your total fiscal impact without sacrificing the quality of the data or results.

Briefly:
The Roche/454 with Titanium chemistry has the longest reads at up to 1 Kbp, produces the most contiguous assemblies and can phase SNPs or other features into blocks. Errors occur mostly at the ends of longer homopolymers (same- nucleotide stretches). Mate-pair libraries can be constructed of many insert sizes (8kb - 20kb) but halve the read length for each end and have a low efficiency.

The Illumina has shorter reads at 36-150bp but produces up to 200 million reads per lane (8 or 16 lanes possible on a HiSeq 2000). The Illumina has the highest *raw* quality scores and its errors are mostly substitutions. All reads are the same length. Paired-end reads with a variety of insert sizes are possible with high efficiency and double the output of the machine by duplicating the read length on each end. Paired-end Illumina reads are suitable for de novo assemblies, especially in combination with the 454. The large number of reads makes the Illumina appropriate for de novo transcriptome studies with simultaneous discovery and quantification of RNAs at qRT-PCR accuracy.

The Applied Biosystems SOLiD has the shortest read length. As with the Illumina, Mate-Pairs double the output by duplicating the read length on each end, and the SOLiD supports a variety of insert lengths like the 454. The SOLiD can also run 2 slides at once to again double the output. SOLiD has the lowest *raw* base qualities but the highest processed base qualities when using a reference due to its 2-base encoding. The new IonPGMTM Personal Genome Machine made by Ion Torrent, a part of Life Technologies, employs a method of sequencing based on the detection of hydrogen ions released during polymerization of DNA. The Ion torrent generates reads of 100 -200 base pairs with data ranging from 10Mb to 1Gb based on the chip used. The 314 chip generates 10Mb, 316 generates 100Mb and 318 chip - 1Gb.The major benefits of ion semiconductor sequencing are rapid sequencing speed and affordable cost.

When choosing how many reads you need purchase for your experiment, several factors come into play. Remember you do not have to decide this by yourself. Cofactor specialists will ensure you get the right number of reads for your experimental goal at no additional charge.
First, read start-site coverage is random across the genome, so the distribution of final read depth across sites is almost exactly as expected from a Poisson distribution. What does this mean? If you sequence 1x as many bases as your genome has sites, you will only cover 63% of the genome sites in the average experiment because many reads will overlap with each other. Therefore, you need to sequence more to overcome these random effects.
Second, although many next-gen platforms actually have lower-error rates (about 1 in 1,000) than traditional sequencing platforms, when you consider how many sites you are sequencing (millions or billions) those little errors add up. To get correct calls at a majority of sites, you need to sequence more.
Therefore, for standard diploid genomic-type projects, you need about 30x coverage of the genome. For de novo assembly, you need more like 100x coverage for current short-read assemblers to give decent results.
Third, if you are sequencing from a mixed population of samples, you need to sequence enough to ensure you have sampled from all constituent individuals. If you are sequencing a library of transformants, you need to sequence enough to observe your low-level transformants several times. For these types of experiments you may need a fold coverage 10 – 100 thousand.
Fourth, if you are sequencing from RNA, not all sites have the same expression level. Actually, gene expression in almost all organisms is given by a power-law distribution with a parameter of about 2. What does this mean? Some genes are very highly expressed and some have lower copies per total fragments of RNA. Because the distribution is so lop-sided, you need to sequence much more in total so that you have a sufficient number of counts of lowly-expressed genes to identify and quantitate them accurately. For the Human transcriptome, 40 million reads is a good starting place.
For larger and de novo projects, you should also consider a mixture of several platforms, long and short reads, and single and paired-end/mate-pair reads of various insert sizes. Cofactor software and experts can help you choose this mixture in a cost-optimal way for a variety of extant and simulated genomes.

The amount of data produced by Next-Gen sequencers is huge, therefore projects are shipped FedEx on fast external hard drives. You must have a computer with a USB2 port. Drives can be formatted for either PC or Mac/Linux. You will always receive the raw reads in FASTA, and FASTQ, as well as raw alignments and several analysis intermediates so that you may re-start your own analysis without going back to the beginning.
We are able to produce a custom computational analysis, which can consist of almost anything you dream up, existing or novel. The custom analysis will be placed on the drive and will consist of tab-delimited, FASTA, and/or image files customized to your experimental goals. Most projects are sufficiently specialized that no exact format or set of outputs is defined until we create them for your project. If you have an existing format that you would like your results in, we can produce output in that format for an additional charge.

Unlike some other service providers, Cofactor understands that many small labs have neither the need nor the budget for 100 million reads so we sell down to the individual sequencing unit for any number of libraries.
A given flowcell or slide can be mixed and matched with libraries types of the same ended-ness (single or paired/mate) from many projects and organisms.
However, if you purchase less than a full flowcell or slide, your samples must be run concurrently with samples from other customers to fill the batch so your wait time will be both longer and more variable. As mentioned above, you can pool your own separate experiments or experiments with your collaborators on a single flowcell or slide if you like.
You can do your part to minimize the total wait-time by submitting your samples as soon as you choose Cofactor, making your 1/2 upfront payment as quickly as possible, and ensuring that you have submitted sufficient, high-quality samples by assaying their quality before mailing.

For information on sample prep, please visit our Sample Submission page

To ensure the highest quality, Cofactor has chosen to integrate and optimize across all facets of Next-Gen sequencing experiments, from library construction to sequencing to analysis. Cofactor cannot discount projects if you would like to make your own libraries or do your own analysis. If you would like us to refrain from analyzing your data for confidentiality reasons, we will honor your request and charge the standard price. You are welcome to submit your own libraries and pay the standard price, but Cofactor cannot make any guarantees about your data output or quality. It is our policy to re-run Cofactor libraries from QC'ed samples that fail, but this does not apply to customer-submitted libraries.

Rush = the solution if you have limited time to meet your grant application deadline or product development milestone. This priority service places you on the next run no matter what, with cut-in-line analysis and a short guaranteed turnaround time of as little as two weeks (depending on the exact scale of your project and instrument cycles). Contact us for a quote. 

Standard Economy = Our Standard Economy option places you next in the queue with an average lead time of ~8 weeks. Below is an example of a typical timeline (Contact us for a quote):

Super Saver = If you need the lowest price and are not on a deadline, the Super Saver price ensures your sample will be run and analyzed in a maximum of 16 weeks. Your sample will be run when we have available space but you will have to wait no longer than 16 weeks for your results. Contact us for a quote.

Partner Pricing = Cofactor partners with institutions and corporate clients to provide more value to their research and product development pipelines. If you can make a commitment to us, we are willing to make a commitment to you. For contract projects, master service agreements, or preferred service provider contracts, we offer set pricing and turnaround on every project. In addition, we tell you exactly what we will provide and for what price. This helps institutions budget and plan for upcoming experiments. If you have samples to run on a constant basis (ex. every week or every month), please contact us and let us tell you how we can help you accomplish your goals by using our partner service.

For your convenience, Cofactor accepts payment by check, credit card, or wire transfer. International payments are accepted by wire-transfer only. While your organization is welcome to submit a purchase order, Cofactor does not accept Purchase Orders as a form of final payment.

For all projects over $5,000 Cofactor requires you pay at least 50% of project total before sequencing begins. Cofactor will deliver completed projects upon receiving the your final bill.

If your project’s value is under $5,000, you must pay your invoice in full before work can begin.

Cofactor also offers a 2% cash discount on all projects paid in full within 10 days.

Please email (administration@cofactorgenomics.com) or call us (314.531.4647) if you have any questions.

Service Terms & Conditions

These service terms and conditions are incorporated into and form a material part of every customer proposal or quote issued by Cofactor Genomics, LLC (“Cofactor”).

Customer’s written, oral, or electronic authorization to proceed with the services described in a proposal or quote issued by Cofactor, or Customer’s submission of any samples or any payment based on such proposal or quote, shall constitute Customer’s binding acceptance of the proposal or quote and these service terms and conditions.

Cofactor shall be required to perform the services and deliver the deliverables substantially in accordance with provisions of the written or electronic proposal or quote prepared by Cofactor.

Customer shall be required to provide the samples (or the pre-constructed library, if applicable) and pay the price in accordance with the provisions of the written or electronic proposal or quote prepared by Cofactor.

The price shall be the amount set forth in the written or electronic proposal or quote prepared by Cofactor, and the price shall be payable on the terms set forth in such proposal or quote.

Any federal, state, or local sales, use or other taxes shall be in addition to the price set forth in the proposal or quote and such taxes shall be the sole responsibility of Customer.

Cofactor disclaims any and all warranties, express or implied, as to the services or the deliverables, including warranties of merchantability, non-infringement, workmanship or fitness for a particular purpose.

Under no circumstances shall Cofactor have any liability to Customer for any special, incidental or exemplary damages, and the liability of Cofactor to Customer for breach or any other claim or cause of action shall be limited to an amount not to exceed the amount actually paid by Customer to Cofactor in connection with the proposal or quote.

Cofactor shall not be liable for any loss, damage, or delay incurred by Customer that results from conditions beyond Cofactor’s reasonable control including conditions of force majeure.

Each party shall retain sole and exclusive ownership of all inventions, patent rights, copyrights, trade secrets, and other intellectual property rights made or conceived by its employees, agents or independent contractors that are made or conceived independently and without contribution or assistance from the other party or the other party’s employees, agents, or independent contractors.  Upon full payment of the price by the Customer, the deliverables and all of the data and information contained therein shall be owned by Customer; provided, however, Cofactor shall retain a perpetual, non-exclusive, worldwide, royalty-free license to use the deliverables and the data and information contained therein only for its own purposes; and provided, further, that Cofactor shall not be entitled to transfer, assign, or sell the deliverables or the data and information contained therein to any third party.  No other assignment or transfer of intellectual property rights is contemplated by the proposal or quote.

The provisions of the proposal or quote and these service terms and conditions, when accepted by Customer in one of the ways described above, shall constitute the entire agreement between the parties and no other agreements, promises, or representations shall be binding upon either of the parties.

The agreement of the parties shall be made and performed in St. Louis, Missouri and governed by the laws of the State of Missouri.

Any dispute or claim between the parties concerning the performance, breach or interpretation of their agreement shall be exclusively resolved by an arbitration conducted by the American Arbitration Association in St. Louis, Missouri in accordance with it commercial arbitration rules and procedures and the results of any arbitration shall be final and binding on each of the parties.