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Sample GSM2385953 Query DataSets for GSM2385953
Status Public on Nov 09, 2016
Title A1106C
Sample type genomic
 
Source name organic/0℃/0
Organism soil metagenome
Characteristics tissue: Soil microbes
geographical location: USA: Barrow, Alaska
layer: organic
temperature: 0℃
day: 0
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 Cy3
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 organic soil sample at control condition, replicate 1
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 Nov 08, 2016
Last update date Nov 09, 2016
Contact name yang sihang
E-mail(s) yangsihanglear@163.com
Organization name Tsinghua University
Street address Haidian district Shuangqing road #30
City Beijing
ZIP/Postal code 100084
Country China
 
Platform ID GPL22652
Series (1)
GSE89644 The microbial functional diversity in response to warming incubation at Alaska as characterized by GeoChip

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
365921541 6.141324033
296922575 6.249414274
261285510 7.408715398
345636634 7.914054781
221738246 7.561543509
170749249 8.512369295
336025046 7.214189353
333892934 7.452091382
386419647 8.016460859
115516566 8.638116536
118424325 6.303925265
302698083 6.649945358
316950802 7.012669285
360041073 8.652182388
194339848 8.322466942
83309358 8.018164707
226091311 6.650261196
262274973 7.624202249
344339443 8.276931889
50542666 8.86213734

Total number of rows: 78730

Table truncated, full table size 1563 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
Processed data are available on Series record

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