|
| Status |
Public on Dec 20, 2009 |
| Title |
Malme-3M miR193b I |
| Sample type |
RNA |
| |
|
| Source name |
Malme-3M cell line, miR-193b
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Malme-3M
cell type: Metastatic melanoma
transfection: miR-193b precursor
|
| Treatment protocol |
Malme-3M cells were seeded 100,000 cells/well in 6-well plate and transfected the following day with 5nM miRNA precursors (miR-193b or negative control) using Lipofectamine 2000 (Invitrogen).
|
| Growth protocol |
Metastatic melanoma cell lines Malme-3M were grown in RPMI medium 1640 (Hyclone) supplemented with 10% fetal bovine serum (Hyclone) at 37°C and 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was harvested 24h after transfection using miRNeasy Mini kit (Ambion).
|
| Label |
Cy3
|
| Label protocol |
500 ng total RNA of each sample was mixed with 5 μL of a 5,000-fold dilution of Agilent's One-Color Spike-in RNA control (Agilent, Santa Clara, CA). The mixture was amplified and labeled using the One color, Quick Amp Labeling kit (Agilent, Santa Clara, CA). In short, mRNA was primed with an oligo(dT)primer containing a T7 RNA polymerase promoter to synthesize double-stranded cDNA, and the cDNA was then used as a template to generate Cy3-labeled cRNA in an in vitro transcription reaction.
|
| |
|
| Hybridization protocol |
Successfully amplified and labeled samples were fragmented at 60°C for 30 minutes and hybridized to Agilent Human 4X44K Whole genome microarrays (Agilent, Santa Clara, CA) in a rotating oven at 65°C for 17 hours following manufacturer's protocol.
|
| Scan protocol |
Images were scanned with Agilent scanner at 5µm resolution.
|
| Description |
Biological replicate 1 of 2.
|
| Data processing |
All raw signal intensity was thresholded to 1, shifted to 75 percentile, and baseline to median of all samples.
|
| |
|
| Submission date |
Oct 09, 2009 |
| Last update date |
Oct 09, 2009 |
| Contact name |
Harriet Feilotter |
| Organization name |
Queen's University
|
| Department |
Pathology and molecular department
|
| Lab |
microarray facility
|
| Street address |
88 Stuart St
|
| City |
Kingston |
| State/province |
Ontario |
| ZIP/Postal code |
K7L 3N6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL6480 |
| Series (2) |
| GSE18510 |
miR-193b represses cell proliferation and regulates cyclin D1 in melanoma: Malme-3M |
| GSE18512 |
miR-193b represses cell proliferation and regulates cyclin D1 in melanoma |
|
