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Sample GSM1366031 Query DataSets for GSM1366031
Status Public on Feb 18, 2015
Title 5uM compound [1], biological rep.1
Sample type RNA
 
Source name MDA-MB-231 cells, 5uM DOT1L inhibitor [1]
Organism Homo sapiens
Characteristics cell line: MDA-MB-231
cell type: breast cancer cell line
treatment: 5uM DOT1L inhibitor [1]
treatment duration: 14 days
Treatment protocol Exponentially growing MDA-MB-231 cells were plated, in duplicate, in 6-well plates at a density of 1 × 10^5 cells/ml in the presence of compounds for 14 days. Compounds and media were refreshed every 3-4 days. siRNA experiments were performed for 7 days by transfecting MDA-MB-231 cells with X-tremeGENE Transfection Reagent (Roche) and 10 nM siRNA (Invitrogen), according to the manufacturer's protocol.
Growth protocol Human cell line MDA-MB-231 was obtained from the American Type Culture Collection (ATCC) and cultured using ATCC recommended culture media in a humidified incubator supplemented with 5% CO2 at 37°C.
Extracted molecule total RNA
Extraction protocol Cells were lysed immediately in TRIzol® Reagent, frozen in liquid nitrogen, and shipped to Asuragen, Inc. (Austin, TX) for microarray experiments.
Label biotin
Label protocol Biotinylated cRNA were prepared with the Illumina TotalPrep with QC for Illumina arrays.
 
Hybridization protocol Standard Illumina hybridization protocol.
Scan protocol Standard Illumina scanning protocol.
Description SAMPLE 9
Replicate 1 of 2.
DOT1L inhibitor Compound [1]: EPZ004777 (in Diagle et al., 2011)
Data processing The background-subtracted data generated by BeadStudio Software were log2 transformed and then normalised by median centering.
 
Submission date Apr 08, 2014
Last update date Feb 18, 2015
Contact name Yongcheng Song
Organization name BAYLOR COLLEGE OF MEDICINE
Department PHARMACOLOGY
Street address One baylor plaza, Baylor College of Medicine
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platform ID GPL10558
Series (1)
GSE56630 Expression profiling of MDA-MB-231 breast cancer cells treated with DOT1L inhibitors and siDOT1L

Data table header descriptions
ID_REF
VALUE Normalized log2 signal intensity
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_3166687 -3.786596362 0.84156
ILMN_3165565 0.563900885 0.04286
ILMN_3164808 -3.786596362 0.24286
ILMN_3165363 -3.786596362 0.37532
ILMN_3166504 0.158262084 0.10519
ILMN_3164750 -1.97924144 0.18182
ILMN_3166430 -3.786596362 0.20130
ILMN_3165745 -3.786596362 0.99870
ILMN_3164915 -2.408084739 0.85714
ILMN_3165415 -3.786596362 0.73636
ILMN_3165201 -3.786596362 0.71558
ILMN_3166630 -3.786596362 0.99091
ILMN_3165619 -3.786596362 0.26753
ILMN_3165933 6.077589783 0.00000
ILMN_3164979 -3.786596362 0.99870
ILMN_3166789 1.199814573 0.97662
ILMN_3165033 -0.263034406 0.62597
ILMN_3165699 -3.786596362 0.59481
ILMN_3165218 -3.786596362 0.00000
ILMN_3166404 -1.584962501 0.17922

Total number of rows: 47323

Table truncated, full table size 1543 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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