|
| Status |
Public on Dec 31, 2010 |
| Title |
steroid-depleted control MCF-7 cells, rep2 |
| Sample type |
RNA |
| |
|
| Source name |
MCF-7, steroid depleted
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF-7
cell type: breast cancer
gender: female
treatment: steroid depletion
|
| Treatment protocol |
siRNA was used to knock down JMJD2B expression. MCF-7 cells were transfected with either control siRNA or JMJD2B siRNA, cultured in steroid-free medium for 72 hr, and stimulated with or without E2 for 4 hr.
|
| Growth protocol |
MCF-7 human breast cancer cells were obtained from the American Type Culture Collection (Manassas, VA). MCF-7 cells were cultured at 37°C in a humidified, 95% air/5% CO2 incubator in Eagle’s Minimum Essential Medium (ATCC #30-2003) supplemented with antibiotics, 10% fetal bovine serum (FBS) and 0.01 mg/mL bovine insulin. For steroid-free medium, phenol red-free DMEM (Gibco) and charcoal/dextran-treated FBS (HyClone, SH30068) were used.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).
|
| |
|
| Hybridization protocol |
Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) according to standard Affymetrix procedures.
|
| Scan protocol |
Array scanning was performed with the Affymetrix GeneChip Scanner 3000 according to the manufacturer's instructions (Affymetrix) at the microarray core facility.
|
| Description |
control E2(-)
HuGene1_102109H_HO2_#2
|
| Data processing |
Raw data were processed with Expression Console software. RMA expression values were derived. Subsequent analyses were performed using Partek software (version 6.5) default settings. Differentially expressed genes between E2-starved cells and E2-stimulated cells, and between JMJD2B-depleted cells and control cells, were identified. One-way ANOVA was performed with a 2-fold up-regulated or down-regulated gene expression cutoff. The p-value for ANOVA analysis was set as p<0.05 and further adjusted by FDR (Step Up, FDR<0.05).
Core-exon analysis.
Genome build: UCSC hg19.
Probe-group file: HuGene-1_0-st-v1.r4.pgf
Meta-probeset file: HuGene-1_0-st-v1.r4.mps
|
| |
|
| Submission date |
Aug 05, 2010 |
| Last update date |
Jul 29, 2013 |
| Contact name |
Hitoshi OKADA |
| Organization name |
Ontario Cancer Institute
|
| Department |
Campbell Family Institute for Breast Cancer Research
|
| Street address |
620 University Ave Suite 7-706
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G2C1 |
| Country |
Canada |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE23445 |
Effect of JMJD2B depletion on the ER signaling pathway |
|
