Jenna M. Lang edited Methods.md  about 9 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/ (include link to video of actual swabbing?) ll swabs were stored at -80 deg C in the MELFI freezer onboard the ISS, until transfer to the SpaceX Dragon spacecraft. In the Dragon, the swabs were stored at -80 deg C in a portable freezer, called the 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 12:05pm PT on May 18, 2014. Samples were transferred to a cooler with dry ice, and shipped to the EMP lab.  Insert description ##DNA Extraction and Library Preparation  All samples were prepared using a modified version  of the Mo BIO UltraClean®-htp   96 Well Swab  DNA extraction, PCR, 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 Earth Microbiome Project 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 25ul   PCR reaction contained the following: 12ul of PCR water certified DNA-free (MO BIO),   10ul of 1x 5 Prime HotMasterMix (5 Prime), 1ul of Forward Primer (5uM concentration,   200pM final), 1ul of Golay Barcode Tagged Reverse Primer (5uM concentration, 200pM   final), and 1ul 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 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, and all python scripts referred to are components of QIIME \cite{Caporaso_2010}.