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Jenna M. Lang edited Methods.md
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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}.