|
| Status |
Public on Dec 31, 2010 |
| Title |
MCF7_miRNA_rep1 |
| Sample type |
other |
| |
|
| Channel 1 |
| Source name |
MCF7_replicate 1
|
| Organism |
Homo sapiens |
| Characteristics |
estrogen receptor: positive
progesterone receptor: positive
her-2: negative
cell line: MCF7
|
| Biomaterial provider |
NCI Developmental Therapeutics Program, NIH
|
| Treatment protocol |
Cells were untreated.
|
| Growth protocol |
Cells were grown in RPMI 1640 basal medium + 10% FBS in a T75 flask at 37C with 5% carbon dioxide. Cells were harvested at 80-90% confluency for total RNA extraction.
|
| Extracted molecule |
other |
| Extraction protocol |
The small RNA fraction was extracted from these cells using Qiagen's miRNeasy kit by following the manufacturer's protocol.
|
| Label |
Cy5
|
| Label protocol |
Five micrograms of RNA was labeled with Cy5 fluorescent label (GE Healthcare) using the mirVana miRNA labeling kit (Ambion), following the manufacturer's instructions.
|
| |
|
| Channel 2 |
| Source name |
MCF10A, Immortalized, non-tumorigenic breast cell line used as the reference
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF10A
|
| Biomaterial provider |
ATCC
|
| Treatment protocol |
Cells were untreated.
|
| Growth protocol |
Cells were grown in DMEM/F12 basal medium supplemented with 5% horse serum, 20 ng/ml final epidermal growth factor, 0.5 ug/ml final hydrocortisone, 100 ng/ml final cholera toxin, and 10 ug/ml final insulin in a T75 flask at 37C with 5% carbon dioxide. Cells were harvested at 80-90% confluency for total RNA extraction.
|
| Extracted molecule |
other |
| Extraction protocol |
The small RNA fraction was extracted from these cells using Qiagen's miRNeasy kit by following the manufacturer's protocol.
|
| Label |
Cy3
|
| Label protocol |
Five micrograms of RNA was labeled with Cy5 fluorescent label (GE Healthcare) using the mirVana miRNA labeling kit (Ambion), following the manufacturer's instructions.
|
| |
|
| |
| Hybridization protocol |
Labeled products were hybridized to miRVana miRNA Bioarrays V2 and washed according to the manufacturer's protocols.
|
| Scan protocol |
Processed arrays were scanned for dual channel hybridization using a GenePix 4000B scanner and its corresponding software.
|
| Description |
Each miRVana miRNA Bioarray is comprised of 328 human miRNAs in addition to 114 mouse and 46 rat miRNAs.
|
| Data processing |
Replicate spots for each miRNA or control were averaged within the array, background adjusted, and log2 normalized using a per chip median normalization method. The reported value represents the Cy5/Cy3 median signal ratio.
|
| |
|
| Submission date |
May 06, 2010 |
| Last update date |
Dec 31, 2010 |
| Contact name |
Mark Mackiewicz |
| E-mail(s) |
[email protected]
|
| Phone |
301-594-6044
|
| Fax |
301-480-8878
|
| Organization name |
National Institutes of Health
|
| Department |
National Cancer Institute
|
| Lab |
Genetics Branch
|
| Street address |
37 Convent Drive
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL5106 |
| Series (2) |
| GSE21719 |
Identification of the receptor tyrosine kinase AXL in triple negative breast cancer as a novel target for the human miR-34a microRNA (miRNA study) |
| GSE21834 |
Identification of the receptor tyrosine kinase AXL in triple negative breast cancer as a novel target for the human miR-34a microRNA |
|
