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Sample GSM1686435 Query DataSets for GSM1686435
Status Public on May 16, 2015
Title siSCR - E2 Replicate 1
Sample type RNA
Source name siSCR - E2 Replicate 1
Organism Homo sapiens
Characteristics transfection: siSCR
agent: vehicle
cell type: Human breast adenocarcinoma cell line
cell line: MCF-7
Extracted molecule total RNA
Extraction protocol RNA was extracted with TRIzol reagent (Ambion, Life Technologies) following manufacturers instructions. Quality control was performed with Agilent Bioanalyser.
Label biotin
Label protocol According to manufacturer (Illumina) specifications.
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description Array 1
Data processing Data was processed and analysed using R statistical software and BioConductor packages. Background corrected signal intensities were variance-stabilized and normlized using the 'vsn' package (Huber, W, von Heydebreck, A., Sueltmann, H., Poustka, A., and Vingron, M. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics: Vol. 18 suppl. 1 S96-S104 (2002)) .
Submission date May 15, 2015
Last update date May 16, 2015
Contact name Mark A Wade
Organization name Newcastle University
Department Northern Institute for Cancer Research
Street address Paul O'Gorman Building, Framlington Place
City Newcastle Upon Tyne
State/province Tyne and Wear
ZIP/Postal code NE2 4HH
Country United Kingdom
Platform ID GPL10558
Series (1)
GSE68918 Identification of KDM3A regulated genes in the ER positive breast cancer cell line MCF-7

Data table header descriptions
VALUE VSN normalized
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1762337 6.450984113 0.3220779
ILMN_2055271 6.949153883 0.02207792
ILMN_1736007 5.944953056 0.8792208
ILMN_2383229 6.364340739 0.4207792
ILMN_1806310 6.639604192 0.1467533
ILMN_1779670 6.330243604 0.4766234
ILMN_1653355 6.610067576 0.1805195
ILMN_1717783 5.901492752 0.9103896
ILMN_1705025 6.473028066 0.3051948
ILMN_1814316 6.321591899 0.4831169
ILMN_2359168 5.924529702 0.8922078
ILMN_1731507 6.082402106 0.7636364
ILMN_1787689 6.468332635 0.3090909
ILMN_3241953 6.643774774 0.1454545
ILMN_1745607 6.130747168 0.712987
ILMN_2136495 5.976158959 0.864935
ILMN_1668111 6.158217965 0.6805195
ILMN_2295559 6.354195946 0.4363636
ILMN_1735045 7.325694149 0
ILMN_1680754 6.672636071 0.1298701

Total number of rows: 47231

Table truncated, full table size 1503 Kbytes.

Supplementary data files not provided
Processed data included within Sample table
Raw data are available on Series record

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