|
| Status |
Public on Oct 03, 2011 |
| Title |
MM96L untreated |
| Sample type |
RNA |
| |
|
| Source name |
Melanoma cell line established from metastatic melanoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MM96L
disease state: MM
treatment: untreated
matching cn sample id: GSM228385
matching expn sample id: GSM170979
matching meth sample id: GSM700991
|
| Biomaterial provider |
Dr Peter G Parsons
|
| Treatment protocol |
Cells were split to 20% confluence in a T25 flask (7% for MM96L) 24 hr before treatment. Cells were then treated for 3 days with 5 l M 5AzadC (Sigma) from 100 m M 50% acetic acid dissolved stock or were mock treated with the same volume of phosphate buffered saline (PBS)/50% acetic acid. The 3-day 5AzadC incubation was followed by a 4-hr incubation with 300 nM TSA (Sigma).
|
| Growth protocol |
All cell lines were cultured in RPMI 1640 supplemented with 10% fetal bovine serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy Midi-kits (Qiagen) were used to extract total RNA from cells in log phase growth according to the manufacturer’s instructions, with on-column DNase digestion (Qiagen RNase-Free DNase Set). All RNA samples were run on an Agilent Bioanalyzer (Agilent, CA) using an RNA 6000 Nano LabChip kit to check for RNA integrity, purity and concentration. Only samples with an RNA integrity number (RIN) of >8.0 were used for microarray analysis.
|
| Label |
Biotin
|
| Label protocol |
Biotin labeled cRNA. Refer to the Illumina Gene Expression System Manual
|
| |
|
| Hybridization protocol |
Refer to the Illumina Gene Expression System Manual
|
| Scan protocol |
Refer to the Illumina Gene Expression System Manual
|
| Description |
1718911123_E
Cultured melanoma cell line established from metastatic melanoma mock for 3 days hours prior to mRNA extraction (reference)
|
| Data processing |
GenomeStudio software, version 2.0 (Illumina) was used to extract raw signal intensity data which was corrected for background and adjusted using Average normalization. Background is defined as the average signal intensity estimated from the negative control bead types. Outliers are removed using the median absolute deviation method. Sample intensities are then scaled by a factor equal to the ratio of average intensity of virtual sample to the average intensity of the given sample such that the average signal of all samples becomes equal to the global average of all sample signals.
|
| |
|
| Submission date |
Sep 29, 2011 |
| Last update date |
Oct 03, 2011 |
| Contact name |
Derek John Nancarrow |
| E-mail(s) |
[email protected]
|
| Phone |
61 7 3362 0323
|
| Fax |
61 7 3845 3508
|
| Organization name |
Queensland Institute of Medical Research
|
| Department |
Genetics & Population Health
|
| Lab |
Oncogenomics
|
| Street address |
300 Herston Road
|
| City |
Herston |
| State/province |
Queensland |
| ZIP/Postal code |
4006 |
| Country |
Australia |
| |
|
| Platform ID |
GPL6102 |
| Series (1) |
| GSE32492 |
Identification of Candidate Tumor Suppressor Genes Inactivated by Promoter Methylation in Melanoma |
|
| Relations |
| Affiliated with |
GSM228385 |
| Affiliated with |
GSM170979 |
| Affiliated with |
GSM700991 |
