FAQ

Yes, collecting 5 samples from 2 conditions is perfectly acceptable. The thing to keep in mind is that you will be comparing bacterial populations between samples and therefore, the higher the number of samples from each condition you process, the stronger your comparison data will be between conditions. We recommend a minimum of 3 samples per condition, but 5 is better. That way if you have an outlier, it will not obliterate the results from the other samples. Just make sure that you're not taking all 5 samples from the same person/animal, etc. Choose different animals or people that are as closely matched as possible to serve as your baseline for comparison.

Yes, many bacterial taxa are identified deeper than the family-level. In fact, the majority of the bacterial taxa are only a single strain because there’s not much known in the scientific literature about family membership.

Yes! You can read more about PhyloChip technology here.

The controls built into the assay address cross-hybridization. There are probe specific controls, controls for each probe called mismatch controls, as well as external controls that are spiked in to make the analysis robust.

The PhyloChip™ assay design and the analysis incorporate knowledge about chimeras to minimize the likelihood that they will cause a problem.

No less than 10 – 30 ng/μl.

Human DNA doesn’t cause cross hybridization problems because the probes have been selected to be specific to bacterial 16S rRNA genes. There could be an issue in the PCR step is if the relative amount of human to bacterial DNA causes inefficient amplification of bacterial DNA (i.e. the bacterial template is so low that the primers have trouble “finding” it.) There are many papers where samples containing human DNA were successfully analyzed for 16S content.

Lung tissue: Electrophoresis. 2010 Jul;31(14):2411-5.
Skin collections: J Med Dent Sci. 2010 Mar;57(1):65-74.
Liver tissue: Scand J Gastroenterol. 2010;45(2):160-7.
Skin wounds: Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14799-804. Epub 2010 Jul 28.

We request a minimum of > 200 ng/10 µl DNA and, if possible, ask that you send an excess to allow us to spot check and confirm integrity and requantify if necessary. If the amplification yield is low, a second amplification will be carried out and the amplicons pooled.

4.2 fg/cell
Kubitschek, HE and Friedman, MC (1971) Chromosome replication and the division cycle of Escherichia coli B/r. Journal of Bacteriology. 107:95-99.

Yes, the PhyloChip assay can be used to analyze microbial communities from mouse samples as well as any other model organism or environment. The 16S rRNA sequences represented on the PhyloChip array are derived from the 16S rRNA gene database, greengenes.lbl.gov, which contains aligned, chimera screened, and taxonomically classified sequences imported from the NCBI GenBank sequence database. Sequences deposited in GenBank come from a huge variety of microbial sources, including humans, model organisms and environmental samples. These 16S rRNA sequences correspond to named or unnamed microbial isolates, an unnamed symbiont, and, very often, uncultured organisms.

Very low variation has been observed among replicate abundance scores for an OTU across arrays. In the earliest G3 paper (Hazen, 2010, Science), data was collected using a Latin Square experiment where artificial communities were mixed at 26 defined concentrations. Then, the 26 mixes were assayed on three separate days. The triplicate abundance scores from the same OTU measured on three different days produced an average coefficient of variation of 0.109. This is why microarray quantification of mixed nucleic assays has been employed by research teams requiring reproducible results.

Our project pricing depends on a few variables, including the type of DNA isolation you may need as well as the number of samples you plan to analyze. If you would like to speak with someone about your specific project, please complete this form and we'll be in contact with you shortly.

Your data is your data. You will receive a secure weblink to your data, figures and tables. Your data will be accessible for 2 years after your project is completed. After that, it is archived but still accessible.