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Sample GSM1686440 Query DataSets for GSM1686440
Status Public on May 16, 2015
Title siKDM3A-B - E2 Replicate 2
Sample type RNA
 
Source name siKDM3A-B - E2 Replicate 2
Organism Homo sapiens
Characteristics transfection: siKDM3A-B
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
E-mail(s) mark.wade@newcastle.ac.uk
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
ID_REF
VALUE VSN normalized
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1762337 6.916216529 0.02077922
ILMN_2055271 7.080953689 0.003896104
ILMN_1736007 6.126881747 0.5415584
ILMN_2383229 6.040163413 0.6467533
ILMN_1806310 6.801427954 0.03506494
ILMN_1779670 6.75052994 0.04935065
ILMN_1653355 7.407422308 0
ILMN_1717783 5.485419237 0.9714286
ILMN_1705025 6.229480629 0.4272727
ILMN_1814316 6.372776259 0.2493507
ILMN_2359168 5.947919759 0.7454545
ILMN_1731507 5.505955535 0.9662338
ILMN_1787689 6.161895783 0.5038961
ILMN_3241953 7.444381537 0
ILMN_1745607 5.516115948 0.9649351
ILMN_2136495 6.372776259 0.2493507
ILMN_1668111 5.755195199 0.8805195
ILMN_2295559 5.909827197 0.7727273
ILMN_1735045 7.184740681 0.003896104
ILMN_1680754 6.743316793 0.05194805

Total number of rows: 47231

Table truncated, full table size 1512 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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