In August 2011, a total of 73 samples were cellected in the Shennonjia Mountain. At each site, twelve plots (20 m ×20 m) comprising typical vegetation and soil attributes were selected for sampling. At each plot, ten to fifteen soil cores at a depth of 0-10 cm were taken, mixed thoroughly and sieved with 2 mm mesh to remove roots and stones. Soil samples were kept on ice when transporting to laboratory, divided into two subsamples and stored at either 4°C for soil biogeochemical measurements or −80°C for DNA extraction.
Growth protocol
In August 2011, a total of 73 samples were cellected in the Shennonjia Mountain. At each site, twelve plots (20 m ×20 m) comprising typical vegetation and soil attributes were selected for sampling. At each plot, ten to fifteen soil cores at a depth of 0-10 cm were taken, mixed thoroughly and sieved with 2 mm mesh to remove roots and stones. Soil samples were kept on ice when transporting to laboratory, divided into two subsamples and stored at either 4°C for soil biogeochemical measurements or −80°C for DNA extraction.
Extracted molecule
genomic DNA
Extraction protocol
Soil DNA was extracted by freeze-grinding mechanical lysis as previously described (Zhou et al 1996). Freshly extracted DNA was purified twice using 0.5% low melting point agarose gel followed by phenol-chloroform-butanol extraction. DNA quality and quantity were assessed by the ratios of 260 nm/280 nm and 260 nm/230 nm, and final DNA contents were quantified with a PicoGreen method using a FLUO star Optima .
Label
Cy5
Label protocol
As previously described (Yang et al 2013), DNA samples were labeled with the fluorescent dye Cy-5 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
GeoChip data for soil sample collected at the 2720-2776m elevation, replicate 14
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.
