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Sample GSM1248838 Query DataSets for GSM1248838
Status Public on Oct 30, 2013
Title N2
Sample type genomic
 
Source name Soil microbes in three latitudinal gradient sites
Organism uncultured bacterium
Characteristics soil site: Hailun
soil type: Phaeozem
vegatation: bare soil
Treatment protocol In August 2009, soil samples were collected from all of the plots. Five soil cores at a depth of 0-20 cm and diameter of 1.5 cm were randomly taken from each plot and mixed thoroughly to generate a soil sample representing the plot. Soil samples were kept on ice when transporting to laboratory, and sieved with 2 mm mesh to remove roots and stones. Soil samples were preserved at -80°C before DNA extraction.
Growth protocol In August 2009, soil samples were collected from all of the plots. Five soil cores at a depth of 0-20 cm and diameter of 1.5 cm were randomly taken from each plot and mixed thoroughly to generate a soil sample representing the plot. Soil samples were kept on ice when transporting to laboratory, and sieved with 2 mm mesh to remove roots and stones. Soil samples were preserved at -80°C before DNA extraction.
Extracted molecule genomic DNA
Extraction protocol Soil genomic DNA was extracted using a FastDNA spin kit for soil (MP Biomedical, Carlsbad, CA, USA) following the manufacturer’s instructions. To purify it, DNA extract was mixed with 2.5 volume of 100% ice cold ethanol and 0.1 volume of 3 M NaOAc (pH 5.2) prior to overnight incubation at -20°C. DNA was precipitated by centrifugation for 30 minutes at 13,000 x g. Then supernatant was decanted and washed with 1 ml of 70% ethanol. DNA was air-dried and dissolved in 50 µl of nuclease-free water. DNA quality and quantity were measured using NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA) and with PicoGreen (Ahn et al 1996) using a FLUOstar Optima (BMG Labtech, Jena, Germany), respectively.
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 bare Phaeozem sample collected at Hailun, replicate 2
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.
 
Submission date Oct 23, 2013
Last update date Oct 30, 2013
Contact name Zhao Mengxin
E-mail(s) zhaomengxin200109@163.com
Organization name Tsinghua University
Street address Haidian District, Zhongguancun Street
City Beijing
ZIP/Postal code 100084
Country China
 
Platform ID GPL17825
Series (1)
GSE51592 A comprehensive study to understand the effects of climate warming, simulated by soil transplant, on soil microbial community and its feedback responses

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
125863155 0.930336631
116268722 1.147256486
145021058 0.919385198
142688
110825675
113733344
86566407
88800946
39649685 1.027807195
111220927
14389215
109626263
119191930
71402608
148263215
119898765
110285187
92116515
120589303
119375179

Total number of rows: 12748

Table truncated, full table size 140 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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