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Sample GSM2629622 Query DataSets for GSM2629622
Status Public on May 12, 2020
Title MCF7_WT_basal_batch1_1
Sample type RNA
Source name Cell line
Organism Homo sapiens
Characteristics cell line: MCF7
growth protocol: MCF7 growing under E2 maintenance
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 WT.MCF7.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
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

Data table header descriptions
VALUE quantile and loess normalized

Data table
ID_REF VALUE Detection.Pval
ILMN_1762337 null 0.16883
ILMN_2055271 6.394911894 0.14286
ILMN_1736007 null 0.71429
ILMN_2383229 null 0.78182
ILMN_1806310 null 0.14935
ILMN_1779670 null 0.87532
ILMN_1653355 null 0.14156
ILMN_1717783 null 0.93766
ILMN_1705025 null 0.22597
ILMN_1814316 null 0.85584
ILMN_2359168 null 0.78961
ILMN_1731507 null 0.75455
ILMN_1787689 null 0.27532
ILMN_3241953 7.787607631 0
ILMN_1745607 null 0.93117
ILMN_2136495 null 0.77013
ILMN_1668111 null 0.18182
ILMN_2295559 null 0.62208
ILMN_1735045 8.205529721 0
ILMN_1680754 6.57543645 0.01818

Total number of rows: 47322

Table truncated, full table size 1254 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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