NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1487514 Query DataSets for GSM1487514
Status Public on Aug 10, 2016
Title 5991878040_F
Sample type RNA
 
Source name 6 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.
5991878040_F:Detection Pval

Data table
ID_REF VALUE 5991878040_F:Detection Pval
ILMN_1762337 5.81787 0.074026
ILMN_2055271 5.82226 0.074026
ILMN_1736007 5.7316 0.167533
ILMN_2383229 5.45448 0.662338
ILMN_1806310 5.51521 0.545455
ILMN_1779670 5.59176 0.38961
ILMN_1653355 5.87599 0.0376623
ILMN_1717783 5.41079 0.731169
ILMN_1705025 5.73977 0.150649
ILMN_1814316 5.6056 0.374026
ILMN_2359168 5.4765 0.61948
ILMN_1731507 5.37207 0.779221
ILMN_1787689 5.50169 0.568831
ILMN_3241953 6.68326 0
ILMN_1745607 5.3821 0.77013
ILMN_2136495 5.02747 0.994805
ILMN_1668111 5.42241 0.714286
ILMN_2295559 5.53809 0.498701
ILMN_1735045 8.39079 0
ILMN_1680754 5.78887 0.102597

Total number of rows: 47315

Table truncated, full table size 1287 Kbytes.




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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap