David Coil edited Methods.md  almost 8 years ago

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Upon successful completion of the swabbing on May 9, 2014, http://blogs.nasa.gov/stationreport/2014/05/09/iss-daily-summary-report-050914/, all swabs were stored at -80 °C in the Minus Eighty-degree Laboratory Freezer for ISS (MELFI) freezer onboard the ISS, until transfer to the SpaceX Dragon spacecraft. In the Dragon, the swabs were stored at -80 °C in the General Laboratory Active Cryogenic ISS Experiment Refrigerator (GLACIER), that runs off of Dragon's batteries until it is plugged in (either to the ISS or on the ground.) The Dragon re-entered the Earth's atmosphere and splashed down in the Pacific Ocean at 12:05 pm PT on May 18, 2014. Samples were transferred to a cooler with dry ice, and shipped to the Earth Microbiome Project (EMP) lab (http://earthmicrobiome.org)\cite{Gilbert_2011}.  ##DNA Extraction and Library Preparation  All samples were prepared using a modified version of the Mo BIO UltraClean®-htp 96 Well Swab DNA Kit (MO BIO). Samples were purified using the Zymo ZR-96 DNA Cleanup and Concentrator™-5 kit according to Zymo Protocol (Zymo). DNA was then amplified using the EMP barcoded primer set, adapted for the Illumina HiSeq2000 and MiSeq by adding nine extra bases in the adapter region of the forward amplification primer that support paired-end sequencing. The V4 region of the 16S rRNA gene (515F-806R) was amplified with region-specific primers that included the Illumina flowcell adapter sequences and a twelve base barcode sequence. Each 25 ul PCR reaction contained the following: 12 ul of PCR water certified DNA-free (MO BIO), 10 ul of 1x 5 Prime HotMasterMix (5 Prime), 1 ul of Forward Primer (5 uM concentration, 200 pM final), 1 ul of Golay Barcode Tagged Reverse Primer (5 uM concentration, 200 pM final), and 1 ul of template DNA. The conditions for PCR were as follows: 94°C for 3 minutes to denature the DNA, with 35 cycles at 94 °C for 45 s, 50 °C for 60 s, and 72 °C for 90 s, with a final extension of 10 min at 72 °C to ensure complete amplification. Amplicons were quantified using PicoGreen (Invitrogen) and a plate reader. Once quantified, different volumes of each of the products were pooled into a single tube so that each amplicon is was  represented equally. This pool was then cleaned up using UltraClean® PCR Clean-Up Kit (MO BIO), and then quantified using Qubit (Invitrogen). Sequencing of the prepared library was performed on the Illumina MiSeq platform, using the sequencing primers and procedures described in the supplementary methods of \cite{Caporaso_2012}. ##Bioinformatic Analysis  Unless otherwise noted, all microbial community analyses were conducted using the QIIME workflow version 1.8 or R \cite{R}. All python scripts referred to are components of QIIME \cite{Caporaso_2010}.