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Sample GSM1686445 Query DataSets for GSM1686445
Status Public on May 16, 2015
Title siSCR + E2 Replicate 3
Sample type RNA
 
Source name siSCR + E2 Replicate 3
Organism Homo sapiens
Characteristics transfection: siSCR
agent: 10 nM E2
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 2
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 6.621589453 0.1571429
ILMN_2055271 7.235102947 0
ILMN_1736007 6.305398801 0.6844156
ILMN_2383229 6.642763586 0.138961
ILMN_1806310 6.497011042 0.3506494
ILMN_1779670 6.445940942 0.4285714
ILMN_1653355 6.48472923 0.3714286
ILMN_1717783 6.137514974 0.9012987
ILMN_1705025 6.45539427 0.4103896
ILMN_1814316 6.484225326 0.3727273
ILMN_2359168 6.353914213 0.5974026
ILMN_1731507 6.188090335 0.8454546
ILMN_1787689 6.530194507 0.3025974
ILMN_3241953 6.554080265 0.2545455
ILMN_1745607 6.120965626 0.912987
ILMN_2136495 5.878768969 0.9987013
ILMN_1668111 6.293666448 0.7025974
ILMN_2295559 6.377692996 0.5623376
ILMN_1735045 8.180629785 0
ILMN_1680754 6.489350914 0.3649351

Total number of rows: 47231

Table truncated, full table size 1510 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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