Dataset: South Pacific Gyre 16S Amplicons
Deployment: KNOX02RR

All methodology can be located in the reference:
Tully and Heidelberg 2013. Microbial communities associated with ferromanganese nodules and the surrounding sediments. Frontiers in Microbiology. 4(161). doi:10.3389/fmicb.2013.00161

In summary (refer to publication above for complete description of methodology):
Sediment and FeMn nodules were collected during Expedition Knox-02RR (December 2006–January 2007 aboard the R/V Roger Revelle). Extraction of DNA from nodules proceeded using a modified phenol-chloroform extraction method. Due to low yield using the described phenol-chloroform method, extraction of DNA from sediment samples was performed using the MoBio PowerLyzer PowerSoil DNA kit following the manufacturer's protocol. All samples with >0.1 ng/uL final DNA concentration were cleaned and concentrated and samples were resuspended in 20 uL of sterile, DNase-free H2O. Samples were amplified using PCR, targeting the V4 region of the 16S rRNA gene. All amplifications were performed using the FastStart High Fidelity PCR System (Roche). Initial PCR products were pooled and the PCR product (~550 bp) was gel excised using the Qiagen Gel Extraction Kit (Qiagen) following the manufacturer's protocol. Excised DNA products were amplified in duplicate to generate sufficient material for pyrosequencing. PCR products were pooled and cleaned using the AMPure Bead XP (Agencourt) kit, following the manufacturer's protocol. Samples were quantified using PicoGreen and visualized using Agilent Bioanalyzer using the High Sensitivity (Agilent) chip.