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Status |
Public on Aug 08, 2007 |
Title |
Differential methylation profile of monocyte vs testis, array1, repl.2 |
Sample type |
genomic |
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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).
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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).
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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.
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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 |