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Sample GSM3656154 Query DataSets for GSM3656154
Status Public on Mar 07, 2019
Title The first sample of warmed plots
Sample type genomic
 
Source name Soil Fungi
Organism soil metagenome
Characteristics group: warmed 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 T1
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 (http://ieg.ou.edu/microarray), cleaned, normalized and analysed using the data analysis pipeline.
 
Submission date Mar 06, 2019
Last update date Mar 07, 2019
Contact name Jingmin Cheng
E-mail(s) chengjm17@mails.tsinghua.edu.cn
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
ID_REF
VALUE scaled, log transformed

Data table
ID_REF VALUE
212528430 1.004519459
225679404 0.890202605
212527162 0.976905476
242766628 0.838707035
242805075 1.058188102
242804434 1.055318764
218713820 0.917811609
242772374 0.912653108
242784816 0
242773510 1.141554393
218718868 0.960182635
258566824 0
242797250 0.851090158
242793959 0.950326487
242816268 0.884964785
242770468 1.139301749
242794926 0.937971653
259487609 1.12456024
238495620 0.968835371
237905066 0

Total number of rows: 4499

Table truncated, full table size 92 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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