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Sample GSM1487492 Query DataSets for GSM1487492
Status Public on Aug 10, 2016
Title 5991878014_A
Sample type RNA
 
Source name Stratagene Universal Human Reference RNA (Illumina Catalog # 740000)
Organism Homo sapiens
Characteristics genotype/variation: n/a
treatment: ethanol
reference: Stratagene Universal Human Reference RNA (Illumina Catalog # 740000)
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 Stratagene Universal Human Reference RNA (Illumina Catalog # 740000)
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_A:Detection Pval

Data table
ID_REF VALUE 5991878014_A:Detection Pval
ILMN_1762337 5.74551 0.2
ILMN_2055271 6.03953 0.0207792
ILMN_1736007 5.63972 0.371429
ILMN_2383229 8.55884 0
ILMN_1806310 9.15786 0
ILMN_1779670 5.66716 0.319481
ILMN_1653355 5.68082 0.292208
ILMN_1717783 5.20137 0.94026
ILMN_1705025 5.73851 0.211688
ILMN_1814316 5.87369 0.0857143
ILMN_2359168 5.40551 0.761039
ILMN_1731507 5.3148 0.846753
ILMN_1787689 5.3655 0.801299
ILMN_3241953 6.86727 0
ILMN_1745607 11.3252 0
ILMN_2136495 5.45743 0.68052
ILMN_1668111 5.45321 0.688312
ILMN_2295559 5.79366 0.153247
ILMN_1735045 6.6126 0
ILMN_1680754 5.68691 0.279221

Total number of rows: 47315

Table truncated, full table size 1292 Kbytes.




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

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