This experiment was initiated in October 1998 at the Jasper Ridge Global Change Experiment (JRGCE) site located in centraloastal California, USA (37o24’N, 122o13’W). This annual grassland ecosystem experiences a Mediterranean-type climate, in which the growing season is cool and wet from November to May, and the rest of the year is hot and dry. The plant community comprises of non-native annual grasses, perennial native grasses, native annual forbs and non-native forbs (Henry et al., 2005). Soils mainly consists of weathered alluvium, which is a fine and mixed Typic Haploxeralf. Initially, the JRGCE experiment was designed to assess grassland ecosystem responses to single and multiple components of global changes, including elevated CO2, warming, N deposition, and enhanced precipitation. To this end, each 2 m-diameter circular plot at the JRGCE was equally divided into four quadrants (i.e.,or subplots) of 0.78 m2. N deposition and enhanced precipitation treatments were arranged at the quadrant level, and the elevated CO2 and warming treatments were arranged at the plot level in a full factorial design. In the summer of 2003, an accidental wildfire burned two of the eight blocks of the experiment (i.e. 32 of the 128 subplots). In the summer of 2011, a controlled fire was applied to four of the eight blocks (i.e. 64 of the 128 subplots including the subplots that were already burned in 2003).
Extracted molecule
genomic DNA
Extraction protocol
DNA was extracted from 5 g of soil samples with a freeze-grinding mechanical lysis method (Zhou, Bruns, & Tiedje, 1996). DNA was purified by gel electrophoresis with a 0.5% low-melting-point agarose, then extracted with phenol and chloroform and finally precipitated with butanol. DNA quality was assessed by ratios of light absorbance at A260/A280 (>1.8) and A260/A230 (>1.7), using a Nanodrop (NanoDrop Technologies Inv., Wilmington, DE, USA). The final DNA concentration was quantified using a PicoGreen® method using a FLUOstar Optima microplate reader (BMG Labtech, Jena, Germany) (S. Liu et al., 2015).
Label
Cy3
Label protocol
As previously described (Yang et al 2013), DNA samples were labeled with the fluorescent dye Cy-3 using a random priming method and purified using the QIA quick purification kit (Qiagen, Valencia, CA, USA).
Hybridization protocol
Then DNA was dried in a SpeedVac (ThermoSavant, Milford, MA, USA) at 45°C for 45 minutes. The hybridization was carried out at 42°C for 16 hours on a MAUI hybridization station (BioMicro, Salt Lake City, UT, USA).
Scan protocol
After purification, GeoChip microarrays were scanned by a NimbleGen MS200 scanner (Roche, Madison, WI, USA) at 633 nm using a laser power and photomultiplier tube (PMT) gain of 100% and 75%, respectively.
Description
raw data file: 2_JRGCE128_SNR4p81p7_2bg_GeoChip_rawdata_fire_64.txt
Data processing
Signal intensities were quantified and processed using the data analysis pipeline as previously described (He et al 2010). Then processed GeoChip data were analyzed using the following steps: (i) remove the poor quality spots, which were flagged as 1 or 3 by ImaGene or with a signal to noise ratio (SNR) of less than 2.0; (ii) normalize the signal intensity of each spot by dividing the signal intensity by the total intensity of the microarray followed by multiplying by a constant; (iii) transform the data to the natural logarithmic form; and (iv) remove genes detected in only one out of three samples from the same elevation.
