this is for holding javascript data
Ashley Campbell edited Methods.tex
over 10 years ago
Commit id: bcf7f461dc889ce693708581988b038fe86e493e
deletions | additions
diff --git a/Methods.tex b/Methods.tex
index af8a2ce..b049b38 100644
--- a/Methods.tex
+++ b/Methods.tex
...
\textbf{Isopycnic centrifugation and fractionation}
Isopycnic gradients were established as described previously (35, 48) for five \textsuperscript{12}C-control, five \textsuperscript{13}C-xylose, and four \textsuperscript{13}C-cellulose microcosms; one per day harvested. A density gradient solution of 1.762 g cesium chloride/ml in gradient buffer solution (pH 8.0 15mM Tris-HCl, 15mM EDTA, 15mM KCl) was used to separate \textsuperscript{13}C-enriched and \textsuperscript{12}C-nonenriched DNA. Each gradient was loaded with approximately 5$\mu$g of DNA into a Beckman OptiSeal^{TM} polyallomer centrifuge tube (part no. 361621; Beckman, Palo Alto, CA) containing the cesium chloride-gradient buffer solution. Samples were centrifuged on a Beckman Coulter Optima^{TM} MAX-E ultracentrifuge using a TLA-110 fixed-angle rotor for 66 h at 55,000 rpm and room temperature. Fractions of ca. 100 $\mu$L were collected manually
into Acroprep^{TM} 96 filter plate (part no. 5035, Pall Life Sciences) by displacing the DNA-cesium chloride-gradient buffer solution with water. The refractive index of
the fractions each fraction was measured
on using a
Bausch and Lomb Abbe-3L Reichart AR200 digital refractometer. The buoyant density was cal- culated from the refractive index using the equation a b, where is the density of the CsCl (g/ml), is the measured refractive index, and a and b are coefficient values of 10.8601 and 13.497, respectively, for CsCl at 25°C (6). Triplicate tubes per treatment were pooled with the appropriate range of buoyant density. The enriched and unenriched DNA fractions were purified by an ethanol precipitation, and DNA was quantitated using a NanoDrop 1000 (Thermo Scientific, Wilmington, DE). Fractions con- taining the 13C-enriched and 12C-nonenriched DNA were determined by relating the buoyant density and DNA concentration (for information on total microcosm-extracted DNA along with fraction buoyant densities and their associated DNA concentrations for all soils and replicates, see Table S1a, Fig. S1b, and Table S1c in the supplemental material).
\textbf{Post-Sequencing Analysis}