|
| Status |
Public on Nov 01, 2011 |
| Title |
SK Mel-28_ZnO_1ug/cm2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
SK Mel-28_ZnO_1ug/cm2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SK Mel-28
agent: ZnO
dose: 1 μg/cm2
|
| Treatment protocol |
Cells were allowed to grow overnight, then media was removed and replaced with 2 ml of media with the nanoparticulate material for 4 hrs prior to RNA collection. Three biological replicates were combined for the gene expression analysis for each experimental group, six control samples were processed and three were combined for each of the control experiments - all six control samples were combined for the Cy3 channel control sample.
For cells grown in Transwell inserts, cells were plated into the Transwell and the particulate was added outside the Transwell insert.
|
| Growth protocol |
All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Advanced DMEM media (supplemented with 2% FBS, and glutamax) and allowed to begin growing overnight.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was collected using Qiagen RNeasy Mini kits.
|
| Label |
Cy5
|
| Label protocol |
Agilent two-color LRILAK labeling protocol
|
| |
|
| Channel 2 |
| Source name |
SK Mel-28 [reference]
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SK Mel-28
agent: media control
|
| Treatment protocol |
Cells were allowed to grow overnight, then media was removed and replaced with 2 ml of media with the nanoparticulate material for 4 hrs prior to RNA collection. Three biological replicates were combined for the gene expression analysis for each experimental group, six control samples were processed and three were combined for each of the control experiments - all six control samples were combined for the Cy3 channel control sample.
For cells grown in Transwell inserts, cells were plated into the Transwell and the particulate was added outside the Transwell insert.
|
| Growth protocol |
All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Advanced DMEM media (supplemented with 2% FBS, and glutamax) and allowed to begin growing overnight.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was collected using Qiagen RNeasy Mini kits.
|
| Label |
Cy3
|
| Label protocol |
Agilent two-color LRILAK labeling protocol
|
| |
|
| |
| Hybridization protocol |
Agilent two-color GE hyb/wash protocol
|
| Scan protocol |
Agilent 5 micron scanning protocol, Agilent Technologies Scanner G2505B US45102802
|
| Description |
ZnO at low dose v. control
raw file: 6536E9_251485041038_S01_GE2-v5.1_10_Apr08_2_1_1.txt
|
| Data processing |
Feature extraction and processing - Agilent FE 9.5.1.1 protocol, lowess normaliztion and background subtracted
|
| |
|
| Submission date |
Nov 05, 2010 |
| Last update date |
Nov 01, 2011 |
| Contact name |
Philip J Moos |
| E-mail(s) |
[email protected]
|
| Phone |
801-585-5952
|
| Organization name |
University of Utah
|
| Department |
Pharmacology & Toxicology
|
| Lab |
Moos
|
| Street address |
30 S 2000 East, Rm 201
|
| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84112 |
| Country |
USA |
| |
|
| Platform ID |
GPL4133 |
| Series (1) |
| GSE25167 |
Transcriptional responses to nanoparticulate matter in human skin-derived cancer cells |
|
