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Sample GSM128979 Query DataSets for GSM128979
Status Public on Aug 08, 2007
Title Differential methylation profile of monocyte vs testis, array1, repl.2
Sample type genomic
 
Channel 1
Source name Human peripheral blood monocyte
Organism Homo sapiens
Characteristics healthy donor, gender male
Growth protocol Peripheral blood mononuclear cells were separated by leukapheresis of healthy male donors, followed by density gradient centrifugation over Ficoll/Hypaque. Monocytes were isolated from mononuclear cells by countercurrent centrifugal elutriation in a J6M-E centrifuge (Beckman, Muenchen, Germany)
Extracted molecule genomic DNA
Extraction protocol Genomic DNA (gDNA) from monocytes was prepared using the Blood and Cell Culture DNA Midi Kit from Qiagen (Hilden, Germany) and fragmented to a mean size of 400-500 bp by ultrasonication. Hypomethylated DNA-fragments were obtained using Methyl-CpG-Immunoprecipitation (MCIp)
Label Alexa Fluor 555
Label protocol DNA fragments were labelled using the BioPrime Plus Array CGH Genomic Labeling System (Invitrogen, Carlsbad, CA).
 
Channel 2
Source name Human testis
Organism Homo sapiens
Characteristics gender male
Biomaterial provider BioChain Institute (Hayward, USA)
Extracted molecule genomic DNA
Extraction protocol Genomic testis DNA (gDNA) was fragmented to a mean size of 400-500 bp by ultrasonication. Hypomethylated DNA-fragments were obtained using Methyl-CpG-Immunoprecipitation (MCIp)
Label Alexa Fluor 647
Label protocol DNA fragments were labelled using the BioPrime Plus Array CGH Genomic Labeling System (Invitrogen, Carlsbad, CA).
 
 
Hybridization protocol Hybridisation was performed using the Agilent oligo aCGH Hybridization Kit (Agilent Technologies, Boeblingen, Germany).
Scan protocol Images were scanned using a DNA Microarray Scanner (Agilent).
Description Comparative hybridization of MCIp-depleted hypomethylated DNA-fragements from human testis versus male monocytes
Data processing Microarray images were processed using Feature Extraction Software 8.5 (Agilent Technologies, Boeblingen, Germany) using the standard CGH protocol and a rank consistent list of normalization genes. The latter contained all probes with a CpG index above 78 (more than 78 CpG residues in a region of 350 bp upstream and downstream of a probe). Processed data was imported into Microsoft Office Excel 2003 for further analysis.
 
Submission date Aug 16, 2006
Last update date Aug 08, 2007
Contact name Michael Rehli
E-mail(s) michael.rehli@klinik.uni-r.de
Organization name University Hospital Regensburg
Department Internal Med III
Street address F.-J.-Strauss-Allee 11
City Regensburg
ZIP/Postal code 93042
Country Germany
 
Platform ID GPL4089
Series (1)
GSE5548 Global, comparative analysis of tissue-specific promoter CpG methylation.

Data table header descriptions
ID_REF
VALUE LogRatio of processed signals
VALUE_ERROR Error of LogRatio
P_VALUE P value of Logratio
CH1_SIG_PRO Processed signal of green channel
CH1_SIG_PRO_ERROR Error of processed signal of green channel
CH1_SIG_MEAN Mean signal of green channel
CH1_BKD_MEAN Mean background of green channel
CH2_SIG_PRO Processed signal of red channel
CH2_SIG_PRO_ERROR Error of processed signal of red channel
CH2_SIG_MEAN Mean signal of red channel
CH2_BKD_MEAN Mean background of red channel

Data table
ID_REF VALUE VALUE_ERROR P_VALUE CH1_SIG_PRO CH1_SIG_PRO_ERROR CH1_SIG_MEAN CH1_BKD_MEAN CH2_SIG_PRO CH2_SIG_PRO_ERROR CH2_SIG_MEAN CH2_BKD_MEAN
1 3.40E-02 6.22E-02 5.84E-01 5.27E+03 9.45E+01 5.16E+02 4.23E+01 5.70E+03 7.47E+01 7.90E+02 5.03E+01
2 -1.89E-01 9.16E-01 8.37E-01 6.93E+01 2.32E+01 8.13E+01 4.29E+01 4.49E+01 1.43E+01 7.65E+01 5.00E+01
3 2.05E-01 6.53E-02 1.72E-03 3.31E+03 6.34E+01 3.52E+02 4.33E+01 5.31E+03 8.61E+01 7.40E+02 5.04E+01
4 -9.14E-02 9.34E-02 3.28E-01 8.16E+02 2.90E+01 1.44E+02 4.30E+01 6.61E+02 2.64E+01 1.59E+02 5.04E+01
5 -2.93E-02 7.27E-02 6.87E-01 1.37E+03 3.22E+01 1.90E+02 4.33E+01 1.28E+03 3.56E+01 2.37E+02 4.98E+01
6 -1.05E-01 7.79E-02 1.80E-01 1.23E+03 2.98E+01 1.79E+02 4.34E+01 9.69E+02 2.77E+01 1.98E+02 5.02E+01
7 4.09E-01 7.43E-02 3.62E-08 1.68E+03 4.99E+01 2.16E+02 4.34E+01 4.31E+03 1.01E+02 6.15E+02 4.99E+01
8 -3.81E-01 1.20E-01 1.56E-03 7.91E+02 2.25E+01 1.42E+02 4.33E+01 3.29E+02 2.02E+01 1.18E+02 5.05E+01
9 1.35E-01 6.47E-02 3.70E-02 2.71E+03 5.77E+01 3.03E+02 4.33E+01 3.70E+03 7.28E+01 5.40E+02 5.00E+01
10 1.40E-01 7.67E-02 6.77E-02 9.88E+02 3.32E+01 1.59E+02 4.30E+01 1.36E+03 3.40E+01 2.47E+02 5.10E+01
11 3.11E-02 6.66E-02 6.40E-01 1.94E+03 2.88E+01 2.38E+02 4.34E+01 2.08E+03 3.54E+01 3.37E+02 5.06E+01
12 -1.63E-01 7.73E-02 3.53E-02 1.38E+03 3.38E+01 1.92E+02 4.30E+01 9.52E+02 2.43E+01 1.96E+02 4.99E+01
13 -1.05E-02 8.91E-02 9.06E-01 8.07E+02 2.39E+01 1.44E+02 4.30E+01 7.88E+02 2.23E+01 1.75E+02 5.04E+01
14 2.09E-03 6.31E-02 9.74E-01 3.55E+03 7.31E+01 3.73E+02 4.32E+01 3.57E+03 7.49E+01 5.23E+02 4.96E+01
15 -3.14E-02 1.00E-01 7.54E-01 6.74E+02 2.67E+01 1.33E+02 4.35E+01 6.27E+02 2.76E+01 1.55E+02 4.97E+01
16 -2.59E-01 2.57E-01 3.13E-01 2.75E+02 1.67E+01 9.93E+01 4.30E+01 1.51E+02 1.74E+01 9.56E+01 5.00E+01
17 -1.05E-01 1.04E-01 3.09E-01 6.98E+02 2.35E+01 1.35E+02 4.31E+01 5.47E+02 3.25E+01 1.45E+02 5.00E+01
18 -2.01E-01 7.05E-02 4.40E-03 2.19E+03 3.27E+01 2.60E+02 4.29E+01 1.38E+03 4.43E+01 2.50E+02 5.01E+01
19 -2.49E-01 9.15E-02 6.55E-03 1.06E+03 2.47E+01 1.65E+02 4.29E+01 5.96E+02 3.07E+01 1.51E+02 5.09E+01
20 3.13E-02 1.34E-01 8.16E-01 4.16E+02 2.64E+01 1.11E+02 4.29E+01 4.47E+02 2.49E+01 1.33E+02 5.05E+01

Total number of rows: 43963

Table truncated, full table size 4512 Kbytes.




Supplementary file Size Download File type/resource
GSM128979.tif.gz 26.2 Mb (ftp)(http) TIFF
GSM128979.txt.gz 11.2 Mb (ftp)(http) TXT
Processed data included within Sample table
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