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Sample GSM2385952 Query DataSets for GSM2385952
Status Public on Nov 09, 2016
Title A2107C
Sample type genomic
 
Source name organic/-2℃/34
Organism soil metagenome
Characteristics tissue: Soil microbes
geographical location: USA: Barrow, Alaska
layer: organic
temperature: -2℃
day: 34
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 incubated at warmest month condition for 34 day, replicate 3
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 6.135861168
296922575 6.35088624
261285510 7.667221005
345636634 8.146420685
221738246 7.594781615
170749249 8.490361007
336025046 7.287492444
333892934 7.442385687
386419647 8.428602495
115516566 8.958425351
118424325 6.671981172
302698083 6.797053971
316950802 7.112060498
360041073 8.737928854
194339848 8.036537769
83309358 8.074631422
226091311 6.84707193
262274973 7.701410516
344339443 8.296281248
50542666 8.926167442

Total number of rows: 78730

Table truncated, full table size 1532 Kbytes.




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

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