|
| Status |
Public on Dec 31, 2016 |
| Title |
MDA_48H_tdt2 |
| Sample type |
RNA |
| |
|
| Source name |
MDA MB-231, 48h, NLC-Citral, replicate 2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA MB-231
cell type: Breast cancer cells
|
| Treatment protocol |
NLC-Citral, Citral and NLC-Blank were diluted in the fresh media before treated the cells for 48 hours. The cells were incubated in the incubator for 48 hours post treatment.
|
| Growth protocol |
MDA MB-231 cells was purchased from ATCC and sub-cultured under under certain conditioned (37°C+5% CO2) in cell culture media with 10% fetal bovine serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of the cells was extracted by using RNAeasy mini prep kit (Qiagen, USA) by following the manufacturer's recommendations.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 2x60k array slides
|
| Description |
Gene expression after 48 hours of treatment
|
| Data processing |
The scan images were analyzed with the feature extraction sofware 13.1 using default parameters by the Agilent Inc.
|
| |
|
| Submission date |
Dec 08, 2016 |
| Last update date |
Dec 31, 2016 |
| Contact name |
Noraini Nordin |
| E-mail(s) |
noraini90.nordin@gmail.com
|
| Phone |
6012-2922337
|
| Organization name |
University Putra Malaysia
|
| Department |
Cell Biology
|
| Lab |
ANIMAL TISSUE CULTURE
|
| Street address |
Animal Tissue Culture Lab
|
| City |
Serdang |
| State/province |
selangor |
| ZIP/Postal code |
43400 |
| Country |
Malaysia |
| |
|
| Platform ID |
GPL13607 |
| Series (1) |
| GSE91047 |
Regulated gene expression for breast cancer cells treated with NLC-Citral for 48 hours |
|
