|
| Status |
Public on May 12, 2020 |
| Title |
MCF7_LTED_basal_batch1_1 |
| Sample type |
RNA |
| |
|
| Source name |
Cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7-LTED
growth protocol: MCF7-LTED, resistant to estrogen deprivation
timepoint: basal
batch: batch1-Y2014Dec
description: replicate 1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA were extracted with RNeasy Mini Kit (Qiagen), as per the manufacturer's instructions, and quantification performed using the Agilent 2100 Bioanalyzer (Santa Clara, CA, USA).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol of iScan
|
| Description |
MCF7.LTED.basal.1
|
| Data processing |
The data were divided into subsets according to the groups being compared; only the samples involved in a given comparison are used. Subsets were then filtered to remove any non-expressed probes using the detection p-value from Illumina. Across all samples in each subset probes for which the intensity values were not significantly different (p>0.01) from the negative controls were removed from the analysis. Following filtering the data was transformed and normalized using variance-stabilizing transformation (VST) and robust spline normalization (RSN) method in the lumi package in R. The RSN combines the features of quantile and loess normalization.
|
| |
|
| Submission date |
May 16, 2017 |
| Last update date |
May 12, 2020 |
| Contact name |
Alice Gao |
| E-mail(s) |
alice.gao@icr.ac.uk
|
| Organization name |
The Institute of Cancer Research
|
| Department |
Breast Cancer Now
|
| Lab |
Molecular Cell Biology
|
| Street address |
237 Fulham Road
|
| City |
London |
| State/province |
London |
| ZIP/Postal code |
SW3 6JB |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL10558 |
| Series (2) |
| GSE98987 |
Resistance to Palbociclib involves multiple mechanisms amenable to targeting with drug holidays or drug switching to improve therapeutic outcome [Illumina] |
| GSE99003 |
Resistance to Palbociclib involves multiple mechanisms amenable to targeting with drug holidays or drug switching to improve therapeutic outcome |
|
