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Sample GSM1487512 Query DataSets for GSM1487512
Status Public on Aug 10, 2016
Title 5991878014_K
Sample type RNA
 
Source name 7 MCF7 AKT2 shRNA E2 3hrs
Organism Homo sapiens
Characteristics genotype/variation: AKT2 shRNA
treatment: 0.1 nM estradiol
cell line: MCF7
Treatment protocol Cells were treated with ethanol or estradiol dissolved in ethanol.
Growth protocol Cells were maintained in phenol red free MEM with 5% charcoal dextran treated fetal calf serum for four days and then treated with ethanol or 0.1 nM estradiol for three hours.
Extracted molecule total RNA
Extraction protocol RNA was prepared using RNeasy kit (Qiagen, Valencia, CA, USA) and cDNA from two μgs of RNA was synthesized using the cDNA Synthesis kit (Bio- Rad, Hercules, CA, USA). qRT-PCR was performed using SyberGreen on a TaqMan 7900HT instrument (Applied Biosystems, Carlsbad, CA, USA).
Label biotin
Label protocol Microarray with biological triplicates was performed using Illumina HumanHT-12 V4 expression beadchip. Standard Illumina label protocol was used.
 
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description MCF7 AKT2 shRNA E2 3hrs
Data processing Genes that showed statistically insignificant signals in majority of samples were removed from the microarray data, and only those probes that showed statistically significant signal in at least half of samples of at least one group were retained. The probe level data was then collapsed to gene level data by retaining only the probes, which showed a maximal coefficient of variation across all samples. The data was imported into partek genomics suite for differential expression analysis. ANOVA analysis was performed to identify genes differentially expressed between AKT1KD vs. pLKO, AKT2KD vs. pLKO, and AKT1KD vs. AKT2KD groups.
 
Submission date Aug 26, 2014
Last update date Aug 10, 2016
Contact name Guanglong Jiang
Organization name Indiana University School of Medicine
Department Medical and Molecular Genetics
Street address 410 W. 10th St. Suite 5000
City Indianapolis
State/province IN
ZIP/Postal code 46202
Country USA
 
Platform ID GPL10558
Series (1)
GSE60759 AKT Isoform Specificity Downstream of PIK3CA Mutation Impacts Estradiol and PI3K Inhibitor Response in Breast Cancer Cells

Data table header descriptions
ID_REF
VALUE The data were quantile normalized and log2 transformed.
5991878014_K:Detection Pval

Data table
ID_REF VALUE 5991878014_K:Detection Pval
ILMN_1762337 5.78831 0.116883
ILMN_2055271 5.85721 0.0623377
ILMN_1736007 5.521 0.544156
ILMN_2383229 5.36071 0.797403
ILMN_1806310 5.25464 0.923377
ILMN_1779670 5.50036 0.58961
ILMN_1653355 5.61085 0.381818
ILMN_1717783 5.13896 0.976623
ILMN_1705025 5.49173 0.6
ILMN_1814316 5.66945 0.268831
ILMN_2359168 5.39696 0.761039
ILMN_1731507 5.36728 0.794805
ILMN_1787689 5.54985 0.496104
ILMN_3241953 6.77186 0.0012987
ILMN_1745607 5.46732 0.649351
ILMN_2136495 5.28729 0.887013
ILMN_1668111 5.39114 0.766234
ILMN_2295559 5.58019 0.438961
ILMN_1735045 8.45289 0
ILMN_1680754 5.7958 0.112987

Total number of rows: 47315

Table truncated, full table size 1303 Kbytes.




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

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