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Sample GSM3656152 Query DataSets for GSM3656152
Status Public on Mar 07, 2019
Title The fifth sample of control plots
Sample type genomic
Source name Soil Fungi
Organism soil metagenome
Characteristics group: control plots
Extracted molecule genomic DNA
Extraction protocol Soil DNA was extracted following the instructions of the PowerMax Soil DNA Isolation Kit (MoBio Laboratories, Carlsbad, CA, USA). DNA quality was assessed via NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA), based on UV spectrometry absorbance ratios at wavelengths of 260 nm/280 nm and 260 nm/230 nm. DNA concentration was measured by PicoGreen using the FLUOstar OPTIMA fluorescence plate reader (BMG Labtech, Jena, Germany) before microarray labeling.
Label Cy3
Label protocol One microgram of DNA from each sample was mixed with random primers and denatured before dNTP, fluorescent dye Cy-3 dUTP and DNA polymerase were added for labelling at 37 C for 6 h, followed by heating at 95 C for 3 min.
Hybridization protocol For hybridization, DNA was resuspended in hybridization solution containing a sample tracking control, formamide, SSC, SDS, a Cy3-labelled alignment oligonucleotide, a Cy5-labelled alignment oligonucleotide and a Cy5-labelled common oligonucleotide reference standard target. After denaturing, the mixtures were deposited onto the glass microarray and hybridized at 42 °C for 16 h.
Scan protocol Then the arrays were washed and dried, and scanned by an MS 200Microarray Scanner (NimbleGen) at 532nm and 635 nm.
Description C5
Data processing NimbleScan software version 2.5 (NimbleGen) was used to grid and process the images to transform them into signal intensity. The raw signals from NimbleScan were submitted to the Microarray Data Manager on our website (, cleaned, normalized and analysed using the data analysis pipeline.
Submission date Mar 06, 2019
Last update date Mar 07, 2019
Contact name Jingmin Cheng
Organization name Tsinghua University
Department School of Environment
Street address NO. 30 Shuangqing Road, Haidian District
City Biejing
ZIP/Postal code 100084
Country China
Platform ID GPL26258
Series (1)
GSE127899 GeoChip data from fungal community in Alaskan tundra soil

Data table header descriptions
VALUE scaled, log transformed

Data table
212528430 1.006802298
225679404 0.93316497
212527162 0
242766628 0.865088564
242805075 0.984265324
242804434 1.081918269
218713820 0
242772374 0.895899582
242784816 0
242773510 1.101605707
218718868 0.907153814
258566824 0
242797250 0.841537096
242793959 0.996071109
242816268 0.887171494
242770468 1.120514935
242794926 0
259487609 1.030689515
238495620 0.970904352
237905066 0.897183245

Total number of rows: 4499

Table truncated, full table size 83 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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