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Sample GSM2629633 Query DataSets for GSM2629633
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
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 0.11169
ILMN_2055271 null 0.01948
ILMN_1736007 null 0.64286
ILMN_2383229 null 0.29091
ILMN_1806310 null 0.39091
ILMN_1779670 null 0.51429
ILMN_1653355 null 0.74675
ILMN_1717783 null 0.79091
ILMN_1705025 null 0.88312
ILMN_1814316 null 0.43506
ILMN_2359168 null 0.73896
ILMN_1731507 null 0.97792
ILMN_1787689 null 0.28052
ILMN_3241953 7.010018969 0
ILMN_1745607 6.349983327 0.98961
ILMN_2136495 null 0.94286
ILMN_1668111 null 0.71818
ILMN_2295559 null 0.52857
ILMN_1735045 7.313365086 0
ILMN_1680754 null 0.0961

Total number of rows: 47322

Table truncated, full table size 1245 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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