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 DNA methylation microarray
 
KangChen Bio-tech provides complete MeDIP-chip service from sample to results. This service, which is available to academic and commercial researchers, employs Agilent’s, NimbleGen’s and UHN’ complete microarray platform.
 
MeDIP-chip service provided by Kangchen Biotech
1.   Genome DNA  Extraction
2.   Sonication to shear DNA
3.   MeDIP and Purification
4.   Amplification using Sigma WGA kit and Purification
5.   Labeling using Cy3/Cy5
6.   Hybridization
7.   Scan, data extraction and preliminary analysis
8.   Complete report including:
  • Scanned image
          Scanned array image:
         
          Partial enlarged array image:
          
  • Raw data
  • log2-ratio data
  • Scatter plot, MA-plot

  • Probe report
  • Segment report
 
Agilent MeDIP-chip
Agilent’s 60-mer oligonucleotide microarrays (frequently updated content, sequence and annotation information available through Agilent)
  • Microarrays manufactured using computer driven inkjet printing process with SurePrint technology
  • Well-tested protocols (direct labeling or single round amplification labeling)
  • Scanning and feature extraction with Agilent’s DNA Microarray Scanner and SureScan technology
  • Data analysis with GeneSpring
  • Easily access to probe sequence and annotation information
Agilent
Slides format
Resolution
Description
Human CpG Islands
244K x 1
195K CpG probes, 50k non-CpG
Spacing ~ 95bp
Enriched content sourced from UCSC hg18, NCBI build 36.1
27,800 CpG islands covering
Mouse CpG Islands
2 x 105K
97652 CpG probes
Spacing ~ 95bp
UCSC mm8, NCBI build 36
16,030 CpG islands covering
Human Promoter
244K x 2
Coverage: -5.5k to +2.5k region
~25 probes/gene
Spacing ~195bp
UCSC hg17, NCBI Build 35
~17,000 best defined human transcripts
Mouse Promoter
244K x 2
Coverage: -5.5k to +2.5k region
~25 probes/gene
Spacing ~200bp
UCSC mm7, NCBI Build 35
~17,000 best defined mouse transcripts
Human Proximal promoter
4×44K
Coverage: -1k to +0.3k region
~3 probes/gene
Spacing ~500bp
UCSC hg17, NCBI Build35
~17,000 best defined human transcripts
 
NimbleGen MeDIP-chip
  • NimbleGen’s 50-75-mer oligonucleotide probes to equalize the melting temperature
  • Microarrays manufactured using photo-mediated synthesis chemistry with its MAS system
  • Feature extraction with NimbleGen’s NimbleScan™ software
  • Graphical representation of your data with NimbleGen’s SignalMap™ data browser

Catalog Number
Design Name
Genome
 
Source
Number of CpG Islands
Promoter Upstream Tiling (bp)
Promoter downstream Tiling (bp)
00892
2006-11-02 HG18 CpG Promoter
Homo sapiens
HG18
28226
800
200
00893
2007-02-27 MM8 CpG Promoter
Mus musculus
MM8
15963
1300
500

 

Catalog Number
Design Name
Promoter Upstream Tiling (bp)
Promoter downstream Tiling(bp)
C4226-00-01
HG18 RefSeq promoter
2200
500
C4222-00-01
MM8 RefSeq promoter
2000
500
C4495001-00-01
RN34 RefSeq promoter
2250
500

 
UHN MeDIP-chip

Name
Species
Source
Number of CpG Islands
HCGI12K
Human CpG-island 12K Array
Homo sapiens
Wellcome Trust Sanger Institute,  UK
12192
MCGI4.6K
Mouse CpG-island 4.6K Array
Mus musculus
Wellcome Trust Sanger Institute,  UK
4,642

 

Services
DNA methylation microarray
ChIP-chip
aCGH
ChIP-Sequencing Service
MeDIP-Sequencing Service
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