|
| Status |
Public on Feb 28, 2017 |
| Title |
MDA-MB-436 Parental 4 N=4 |
| Sample type |
RNA |
| |
|
| Source name |
MDA-MB-436 Cell line_Parental
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-436
cell type: Breast Cancer Cell Line
treated with: none (parental)
|
| Growth protocol |
Parental and resistant cells were seeded at a density of 1x106 per well in 6 well-plates and incubated without drug for 24 hours
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested and total RNA from parental and resistant cell lines were extracted simultaneously using the AllPrep DNA/RNA Mini kit (Qiagen, Canada). The quality of RNA was determined with the NanoDrop™ spectrophotometer (ND-1000) (Wilmington, DE, USA). All RNA samples with A260/A280 ratio higher than 1.8 and DNA with A260/A280 ratio higher than 2 were selected for further analysis. The RNA integrity number (RIN) was measured with a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). RNA with RIN higher than 8 qualified forgene expression profiling.
|
| Label |
Cy3
|
| Label protocol |
Cy3 labeled cRNA was prepared from 100ng RNA using the One-Color Low Input Quick Amp labeling kit (Agilent Technologies). The amplified labeled cRNA was purified using the RNeasy Mini Kit (Qiagen, Canada) assessed for dye incorporation and cRNA yield using the NanoDrop™ Spectrophotometer (ND-1000.)
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| |
|
| Hybridization protocol |
Labeled cRNA was hybridized onto SurePrint G3 Human GE 8X60K microarrays (Agilent Technologies) at 65 °C for 17h in a rotating Agilent hybridization oven.
|
| Scan protocol |
Following hybridization, arrays were washed and scanned using the Agilent Scanner G2505B.
|
| Data processing |
Microarray data were extracted and visualized using the Feature Extraction Software v8.1. (Agilent), default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) was used to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
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| |
|
| Submission date |
Nov 27, 2016 |
| Last update date |
Feb 28, 2017 |
| Contact name |
Elaheh Ahmadzadeh |
| E-mail(s) |
elaheh.ahmadzadeh@gmail.com
|
| Phone |
5149981730
|
| Organization name |
McGill University
|
| Street address |
3220 Ridgewood, apt 319
|
| City |
Montreal |
| State/province |
Please select |
| ZIP/Postal code |
H3V1B9 |
| Country |
Canada |
| |
|
| Platform ID |
GPL13607 |
| Series (1) |
| GSE90564 |
Paclitaxel resistance in triple negative breast cancer involves novel functional genomic aberrations in the ABCB1 gene. |
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