|
| Status |
Public on Sep 01, 2012 |
| Title |
6-shogaol, rep2 |
| Sample type |
RNA |
| |
|
| Source name |
MCF-7 cells treated with 10uM 6-shogaol for 48h
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Breast cancer cell
cell line: MCF-7
|
| Treatment protocol |
Cells were treated with vehicle control (DMSO) or 10uM of 6-shogaol for 48h
|
| Growth protocol |
MCF-7 cells were maintained in RPMI 1640 medium containing 10% fetal bovine serum (FBS), 100 IU/ml penicillin, and 100 μg/ml streptomycin at 37°C, 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from cells was extracted using Qiagen RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturers’ protocol. RNA purity was examined by spectrophotometric determination at 260/280 nm.
|
| Label |
biotin
|
| Label protocol |
The RNA samples were processed according to the Affymetrix recommended protocol and Origen Labs’ SOP for whole transcript analysis. Briefly, 300ng of total RNA was reverse transcribed to produce cDNA, which was subsequently used as a template to create cRNA which was then converted to single stranded DNA (ssDNA). The ssDNA was then biotin labeled, fragmented and hybridized to Affymetrix Human Gene 1.0 ST arrays for 16 hours at 45C with rotation at 60 rpm.
|
| |
|
| Hybridization protocol |
The RNA samples were processed according to the Affymetrix recommended protocol and Origen Labs’ SOP for whole transcript analysis. Briefly, 300ng of total RNA was reverse transcribed to produce cDNA, which was subsequently used as a template to create cRNA which was then converted to single stranded DNA (ssDNA). The ssDNA was then biotin labeled, fragmented and hybridized to Affymetrix Human Gene 1.0 ST arrays for 16 hours at 45C with rotation at 60 rpm.
|
| Scan protocol |
Arrays were then washed and stained using the FS450_0007 fluidics protocol and scanned using an Affymetrix 3000 7G scanner.
|
| Description |
Gene expression of MCF-7 cells treated with 10uM of 6-shogaol for 48h
|
| Data processing |
The scanned images were inspected for hybridization efficiency and CEL files generated from GCOS (GeneChip Operating Software) were imported into Expression Console (EC) 1.1 software for array QC. RMA normalization was performed on the samples to generate the quality control (QC) metrics that we routinely use to determine data quality. These include, perfect match mean (PM_Mean), Background mean (Bgd_Mean), positive and negative probes (POS vs NEG AUC), bacterials spike controls, and polyA controls.
|
| |
|
| Submission date |
Apr 02, 2012 |
| Last update date |
Sep 01, 2012 |
| Contact name |
Chee-Onn Leong |
| E-mail(s) |
[email protected]
|
| Organization name |
International Medical University
|
| Street address |
126 Jalan 19/155B
|
| City |
Bukit Jalil |
| ZIP/Postal code |
57000 |
| Country |
Malaysia |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE36973 |
Gene expression profiling of MCF-7 cells treated with 6-shogaol |
|
