|
| Status |
Public on Oct 16, 2009 |
| Title |
LPS, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
LPS
|
| Organism |
Mus musculus |
| Characteristics |
cell line: Raw 264.7
|
| Biomaterial provider |
ATCC
|
| Treatment protocol |
Cells were stimulated with lipopolysaccharide (LPS) at a final concentration of 1 μg/mL
|
| Growth protocol |
Cells were cultured under standard incubation conditions (37 ºC, 5% CO2) and grown in RPMI supplemented with 5% FBS and 1μg/mL P/S
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested at 24 h using Versagene RNA purification and DNase treatment kits. Six wells of a 6-well plate were pooled for each biological replicate.
|
| Label |
Digoxigenin
|
| Label protocol |
All RNA Preps were run on an Agilent 2100 Bioanalyzer to assess RNA integrity. Those samples meeting minimum requirements of RIN value of 7.0 and greater were used to generate targets for hybridization to ABI arrays. One (1) ug of Total RNA (30ng mRNA) was used to generate First Strand cDNA using the NanoAmp RT-IVT labeling kit according to manufacturer’s protocol (ABI, Cat#4365715). Following first strand synthesis, second strand synthesis was completed. The resulting cDNA was then purified using an ABI kit provided column and the entire reaction was used in an IVT reaction to generate DIG labeled cRNA. The cRNA was then purified using a kit provided column and assessed for quality on an Agilent Bioanalyzer. All reactions meeting ABI criteria in terms of quantity and size of target produced were fragmented and then hybridized to the appropriate array for 16 hours with agitation at 55C.
|
| |
|
| Hybridization protocol |
All hybridization reagents, hybridization controls, wash reagents, and chemiluminescent reagents were provided in the ABI CL Detection Kit, part#4342142, and the manufacturer’s protocol was followed. Briefly, the arrays were equilibrated to room temperature and then pre-hybridized with a 1ml volume for 60’ with agitation (100RPM) at 55C per manufacturer’s protocol. During the pre-hybridization, the DIG-labelled targets were fragmented and then stored on ice until the pre-hyb was completed. Once pre-hyb was completed the targets were mixed with the appropriate reagents, including Hybridization controls, and the 0.5ml target was added to the pre-hybridization through the port on the array chamber. The arrays were immediately returned to the 55C Hybridization oven and agitated exactly 16 hours at 100RPM. The arrays were then washed and incubated with Anti-Dig-APAntibody for 20 minutes. Following antibody washes, the arrays were incubated with Chemiluminescence Enhancing Solution, washed a final time and then stored in the last wash buffer at room temperature. Substrate for the chemiluminescence reaction was added to each array individually and then the array was immediately imaged on the 1700 Chemiluminescent Analyzer.
|
| Scan protocol |
Following addition of the chemiluminescence reaction substrate, each array was immediately imaged on the 1700 Chemiluminescent Analyzer. Each imaging was completed in approximately 15 minutes and the images were assessed for QC/QA and a primary analysis was completed by the AB1700 Expression Array System Software (v 1.1.1).
|
| Description |
DWW22
|
| Data processing |
Signal intensities across microarrays were quantile normalized
|
| |
|
| Submission date |
May 22, 2008 |
| Last update date |
Mar 03, 2009 |
| Contact name |
David W Wright |
| E-mail(s) |
David.Wright@vanderbilt.edu
|
| Phone |
615-322-2636
|
| Fax |
615-343-1234
|
| Organization name |
Vanderbilt University
|
| Department |
Chemistry
|
| Street address |
SC Stevenson Center 7, Station B 351822
|
| City |
Nashville |
| State/province |
TN |
| ZIP/Postal code |
37235-1822 |
| Country |
USA |
| |
|
| Platform ID |
GPL2995 |
| Series (2) |
| GSE13281 |
Expression profiles of beta-hematin (BH)- or 4-hydroxy-2-nonenal (HNE)-treated RAW 264.7 cells |
| GSE15070 |
Expression Profiles of 15(S)-HETE treated RAW 264.7 cells |
|
