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Sample GSM569420 Query DataSets for GSM569420
Status Public on Dec 22, 2010
Title Maternal blood cells MeDIP DNA 3
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.
 
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

Supplementary file Size Download File type/resource
GSM569420.CEL.gz 25.2 Mb (ftp)(http) CEL
GSM569420_Blood_cells_3_MeDIP_vs_input_TAS.txt.gz 28.8 Kb (ftp)(http) TXT
Processed data provided as supplementary file
Processed data are available on Series record

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