|
| Status |
Public on Nov 09, 2013 |
| Title |
LPS6 hrs |
| Sample type |
RNA |
| |
|
| Source name |
6hrs with 1ug/ml LPS treatment
|
| Organism |
Mus musculus |
| Characteristics |
background strain: C57BL6
cell type: JAWS II dendritic cells
|
| Treatment protocol |
JAWS II dendritic cells (10^7 cells/culture in 10 ml plates) were incubated with 0.001% W805EC NE alone or mixed with 10 µg/ml rPA. Control cultures were either untreated (PBS) or incubated with 10 µg/ml rPA or with 1 µg/ml of TLR4 ligand LPS K12
|
| Growth protocol |
Jaws II cells were grown according ATCC protocol
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated aRNA were prepared according to the Affymetrix GeneChip 3’ IVT Express kit protocol from 250 ng total RNA (Affymetrix GeneChip 3’ IVT Express kit Instruction Manual, P/N 702646 Rev. 5).
|
| |
|
| Hybridization protocol |
Following fragmentation, 16 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader.
|
| Description |
Global gene expression in vitro
|
| Data processing |
Data was analyzed using the limma and affy bioconductor packages implemented in the R-statistical environment version 2.15.0. RMA was used to normalize the data and fit log2 transformed expression values.
|
| |
|
| Submission date |
Oct 28, 2013 |
| Last update date |
Nov 09, 2013 |
| Contact name |
Paul Edward Makidon |
| E-mail(s) |
pmakidon@gmail.com
|
| Phone |
734-277-5775
|
| Organization name |
University of Michigan
|
| Department |
Internal Medicine
|
| Lab |
MNIMBS
|
| Street address |
9340 MSRB III, 1150 W. Medical Center Dr.
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE51804 |
Effect of W805EC nanoemulsion (NE) on global gene transcription in JawsII dendritic cells in vitro |
|
