|
| Status |
Public on Dec 22, 2010 |
| Title |
Maternal blood cells MeDIP DNA 1 |
| Sample type |
genomic |
| |
|
| Source name |
Maternal blood cells MeDIP DNA
|
| Organism |
Homo sapiens |
| Characteristics |
gestation: 1st trimester
tissue: maternal blood cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from maternal peripheral blood cells using the Nucleon Blood DNA extraction kit (GE Healthcare-Biosciences) and from CVS and placental tissues using the QIAamp Tissue Kit (Qiagen).
|
| Label |
biotin
|
| Label protocol |
Extracted DNA was sonicated and immunoprecipitated by antibody against 5-methylcytosines (Adcam, cat# 1884). The subsequent product was amplified and labeled using the dsDNA terminal labeling kit (Affymetrix)
|
| |
|
| Hybridization protocol |
The labeled product was hybridized to the GeneChip® Human Tiling 2.0R Arrays according to manufacturer's standard procedures
|
| Scan protocol |
Arrays were scanned on an Affymetrix Scanner 3000 7G.
|
| Data processing |
Analysis with Tiling Array Software (TAS) version 1.1 (TAS): The CEL files of each sample were processed by TAS to calculate the signal of each IP-sample/no-IP control ratios within a 800-bp sliding window. The signal of each sample at a particular locus was normalized to give an average value of 1.00 for all loci. The signals of the 5 placentas were compared with those of the 5 maternal blood cells to calculate a signal log ratio. The resultant BED files were given as an EXCEL (Name: TAS_placenta vs blood cells_Signal_Log_Ratio_BED). Analysis with the Model-based Analysis of Tiling array (MAT): the CEL files of the 5 placentas were the TEST group while the CEL files of the 5 maternal blood cells were the CONTROL group when processed by MAT. The algorithms calculated the P-value to determine if there was significant difference between the signals of the two groups.
The BED format file of each MeDIP sample processed by TAS contain the average signal of IP-sample/no-IP control ratios within a 800-bp sliding window. The additional result file "TAS_placenta vs blood cells_Signal_Log_Ratio_BED" contains the signal log ratio of 5 placenta compared with 5 maternal blood cells.
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| |
|
| Submission date |
Jul 23, 2010 |
| Last update date |
Dec 22, 2010 |
| Contact name |
Yuk Ming Dennis Lo |
| E-mail(s) |
loym@cuhk.edu.hk
|
| Organization name |
The Chinese University of Hong Kong
|
| Department |
Department of Chemical Pathology
|
| Street address |
The Prince of Wales Hospital
|
| City |
Hong Kong |
| ZIP/Postal code |
nil |
| Country |
China |
| |
|
| Platform ID |
GPL4913 |
| Series (1) |
| GSE22837 |
Identification of differentially methylated regions between placentas and maternal blood cells on chromosome 18 |
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