David Coil edited 16S rDNA Sequencing and Analysis (Organism Identification).md  about 9 years ago

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##DNA Extraction  There are a number of different options for DNA isolation and which one should be used depends on many factors including available equipment, experience, and cost. A standard approach in microbiology involves the use of phenol and chloroform extraction followed by ethanol precipitation, and any number of protocols for this approach can be found in books, articles and on the internet. A common alternative approach is to use a commercially available kit - there are many advantages to such kits - notably ease and lack of toxic chemicals. A disadvantage of kits is that they typically are more expensive per sample than other approaches (especially if one is only doing a few samples since most kits include materials for a minimum of 50 samples). For most projects, we use kits - typically the Promega-Wizard Genomic DNA Purification Kit.  Follow the protocol or kit instructions provided by the manufacturer and then proceed to "PCR reaction" "PCR"  below. ##Direct PCR (if not extracting DNA) 

7: 4 °C forever  After PCR is completed, confirm the PCRreaction  worked by agarose gel electrophoresis, all controls behaved as expected (i.e. band in the positive control and no band in the negative control), and that you have DNA fragments of the correct size (~1350bp). ##Submit Samples for Sequencing  Very few single-researcher labs currently have the capacity to do Sanger sequencing. However, there are a number of DNA sequencing facilities (commercial and academic) that provide Sanger sequencing services for researchers. They will handle as little as a single sample, or will allow you to submit an unlimited number of samples, typically arrayed in 96-well plates. You will typically provide both your PCR product as well as primers for sequencing (typically, the same primers used for PCR are used for sequencing). To get the most data, do not forget to request forward (_e.g_., using primer 27F) and reverse (_e.g._, using primer 1391R) reactions for each sample. Each facility will have its own guidelines concerning DNA and primer concentration. Our lab uses the [UC Davis Sequencing Facility](http://dnaseq.ucdavis.edu). If an internet search does not reveal the presence of a Sequencing Facility near you, most sequencing centers will allow you to ship samples to them for sequencing. Another possibility is [Science Exchange](https://www.scienceexchange.com/) which is an online clearinghouse for lab services.