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| Status |
Public on Nov 30, 2019 |
| Title |
Parental_A: MDA_MB_436_TREATED WITH VEHICLE FOR DOXO |
| Sample type |
RNA |
| |
|
| Source name |
MDA_MB_436 treated with saline solution
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
tissue: triple negative breast cancer (TNBC) cell line derived from ascites
cell line: MDA-MB-436
genotype/variation: parental DOXO-S cells
|
| Treatment protocol |
MDA-MB-436 (parental cells) were plated (density = 1.6 x 104 cells/cm2) and treated the next day with DOX (0.3 μM) or PTX (0.01 μM) corresponding to their IC75. After 48hrs of drug exposure the media containing drug was removed and replaced with fresh medium. After 4-6 weeks, colonies that grew were isolated, expanded and kept in culture in absence of drug in complete medium
|
| Growth protocol |
Cells were maintained in RPMI high glucose + 10% FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the AllPrep DNA/RNA/miRNA Universal kit (Qiagen) and quantity and integrity were assed using a 2100 bioanalyzer.
|
| Label |
Cy3
|
| Label protocol |
one hundred nanograms of total RNA from each cell population was reverse and transcribed into cRNA, amplified and labeld with Cy3 dye.
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| |
|
| Hybridization protocol |
The resulting labeled cRNA was purified using the RNeasy Mini Kit (Qiagen Sciences) according to the instructions of the manufacturer and hybridized to a Sure Print G3 Human GE 860 K Microarray (Agilent Technologies) for 17hrs at 65°C. The array was then washed and scanned on the Agilent DNA Microarray scanner
|
| Scan protocol |
We used the “read.maimages” function of the LIMMA R package to read the Agilent scanner output files
|
| Description |
gene expression from DOXO-sensitive cells treated with DOXORUBICIN Vehicle (i.e. Saline)
|
| Data processing |
First, we corrected the background intensities using the “backgroundCorrect” function in LIMMA and employing the “minimum” method to avoid zero or negative numbers after correction for background intensity. Then, we normalized the intensity values of each array using the “loess” method from the “normalizeWithinArrays” function of the LIMMA package.
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| |
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| Submission date |
Oct 01, 2019 |
| Last update date |
Dec 01, 2019 |
| Contact name |
isabelle sirois |
| E-mail(s) |
isabelle.sirois.phd@gmail.com
|
| Organization name |
McGill University
|
| Lab |
Mark Basik Lab
|
| Street address |
3755 Chemin de la Côte-Sainte-Catherine
|
| City |
Montréal |
| State/province |
QC |
| ZIP/Postal code |
H3T 1E2 |
| Country |
Canada |
| |
|
| Platform ID |
GPL14550 |
| Series (1) |
| GSE138233 |
Transcriptomic analysis of DOXO-Resistant cells compared to parental DOXO-Sensitive mda-mb-436 cell line |
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