|
| Status |
Public on May 28, 2014 |
| Title |
M990115 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Input DNA from M990115 melanoma cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: primary melanoma cells
phenotype: Invasive
|
| Growth protocol |
RPMI1640 + 10%FCS + 5 mM glutamine
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted by Dneasy Blood & Tissue Kit (QIAGEN), sheared into 300-500bp fragments by sonication (Covaris), and aliquots 5 ug were incubated with 10 uL of anti-5-methylcytidine antibody (Eurogentec) overnight at 4°C. Antibody-bound DNA was precipated with 40uL of Dynabeeds (M-280 sheep antibody to mouse IgG, Invitrogen) at 4°C for 2 h on a rotating wheel. Bound DNA was eluted by proteinase K incubation for 3 hours at 50°C and purified by standard phenol/chloroform procedure.
|
| Label |
Cy3
|
| Label protocol |
1.5 ug of MeDIP DNA and 1.5 ug of input DNA were labellled with Cy5 and Cy3 respectively by Nimblegen Dual-Color DNA Labeling Kit
|
| |
|
| Channel 2 |
| Source name |
MeDIP DNA from M990115 melanoma cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: primary melanoma cells
phenotype: Invasive
|
| Growth protocol |
RPMI1640 + 10%FCS + 5 mM glutamine
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted by Dneasy Blood & Tissue Kit (QIAGEN), sheared into 300-500bp fragments by sonication (Covaris), and aliquots 5 ug were incubated with 10 uL of anti-5-methylcytidine antibody (Eurogentec) overnight at 4°C. Antibody-bound DNA was precipated with 40uL of Dynabeeds (M-280 sheep antibody to mouse IgG, Invitrogen) at 4°C for 2 h on a rotating wheel. Bound DNA was eluted by proteinase K incubation for 3 hours at 50°C and purified by standard phenol/chloroform procedure.
|
| Label |
Cy5
|
| Label protocol |
1.5 ug of MeDIP DNA and 1.5 ug of input DNA were labellled with Cy5 and Cy3 respectively by Nimblegen Dual-Color DNA Labeling Kit
|
| |
|
| |
| Hybridization protocol |
Samples were hybridized at 42°C for 20 hours
|
| Scan protocol |
Arrays were scanned with MS 200 Microarray Scanner according to manufactorer's protocol
|
| Description |
MeDIP on M990115 melanoma cells
|
| Data processing |
Arrays were processed with Nimblescan 2.5 standard protocol for MeDIP
|
| |
|
| Submission date |
May 27, 2014 |
| Last update date |
May 28, 2014 |
| Contact name |
Phil Fang Cheng |
| E-mail(s) |
phil.cheng@hug.ch
|
| Organization name |
Hopitaux universitaires de Geneve
|
| Department |
Oncology
|
| Street address |
Rue Gabrielle-Perret-Gentil 4
|
| City |
Geneva |
| ZIP/Postal code |
1205 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL17148 |
| Series (1) |
| GSE57971 |
MeDIP for ten early passage melanoma cell cultures |
|
