|
| Status |
Public on Apr 19, 2012 |
| Title |
Positive SCC15 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
IP_SCC15
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HNSCC
treatment: methylated enriched
|
| Treatment protocol |
No treatment
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA (gDNA) were extracted from 1 million cells by standard phenol:chloroform method. gDNA were then fragmented by MseI digestion (37°C, 16h) prior to enrichment for CpG-methylated DNA using a MBD2b/MBD3L1-conjugated magnetic bead-based system according to manufacturer’s protocol (MethylCollector Ultra kit, #55005, Active Motif Europe, Belgium).
|
| Label |
Cy5
|
| Label protocol |
Briefly the DNA is labelled by klenow extension using Cy3- (Input) or Cy5-(MeDIP) labelled random primers.
|
| |
|
| Channel 2 |
| Source name |
T_SCC15
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HNSCC
treatment: non-enriched
|
| Treatment protocol |
No treatment
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA (gDNA) were extracted from 1 million cells by standard phenol:chloroform method. gDNA were then fragmented by MseI digestion (37°C, 16h) prior to enrichment for CpG-methylated DNA using a MBD2b/MBD3L1-conjugated magnetic bead-based system according to manufacturer’s protocol (MethylCollector Ultra kit, #55005, Active Motif Europe, Belgium).
|
| Label |
Cy3
|
| Label protocol |
Briefly the DNA is labelled by klenow extension using Cy3- (Input) or Cy5-(MeDIP) labelled random primers.
|
| |
|
| |
| Hybridization protocol |
Equal amounts (15ug) of labelled MeDIP and Input DNA are loaded onto the arrays and co-hybridized at 42 C for 16-20 hours.
|
| Scan protocol |
The arrays are then washed, dryed on the NimbleGen dryer and scanned on the NimbleGen MS200 scanner.
|
| Description |
100718_HG18_CpG_Refseq_Prom_MeDIP
|
| Data processing |
Data are extracted and analysed using the NimbleGen NimbleScan software (v2.6 in your case) using the default settings.
|
| |
|
| Submission date |
Aug 30, 2011 |
| Last update date |
Apr 19, 2012 |
| Contact name |
Muy-Teck Teh |
| E-mail(s) |
m.t.teh@qmul.ac.uk
|
| Phone |
+442078827140
|
| Organization name |
Queen Mary University of London
|
| Department |
Centre for Clinical & Diagnostic Oral Sciences
|
| Lab |
Head & Neck Cancer Unit
|
| Street address |
Blizard Building, 4, Newark Street,
|
| City |
London |
| State/province |
England |
| ZIP/Postal code |
E1 2AT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL14361 |
| Series (1) |
| GSE31767 |
FOXM1 Orchestrates a Global Methylation Signature that Mimics the Cancer Epigenome |
|
