Fresh roots were collected into a 50 ml centrifuge tube, rinsed in phosphate buffer solution, shaken by hand and centrifuged at 8000 rpm for 10 min. Bulk soil cores of 0-30 cm depth were also collected between sampled plants for paired comparison to the rhizosphere samples.
Growth protocol
Maize (Zea mays) was grown near the University of Illinois (Champaign, IL, USA, 40°03'N, 88°12W, 230 m elevation) in a soil classified as a fine-silty, mesic Typic Endoaquoll formed from loess and silt parent material. Samples were collected in August 4, 2009.
Extracted molecule
genomic DNA
Extraction protocol
Soil DNA was extracted by freeze-grinding mechanical lysis as described previously (Zhou et al., 1996).
Label
Cy5
Label protocol
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) as previously described (Yang et al., 2013).
Hybridization protocol
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
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 of soil microbial community in bulk soil, replicate 1
Data processing
Microarray data were analyzed using the data analysis pipeline developed at the University of Oklahoma (http://ieg.ou.edu/microarray/). Normalized intensity of each gene was calculated by dividing the signal intensity by the mean intensity of the microarray.
