|
| Status |
Public on Jun 06, 2006 |
| Title |
UT 001hr Raw 264.7 cells vs LPS&2MA- 001hr RAw 264.7 cells . (set 2) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
RAW 264.7 cells cultured in media for 001hr
|
| Organism |
Mus musculus |
| Characteristics |
RAW 264.7 cells cultured in media for 001hr
|
| Extracted molecule |
total RNA |
| Label |
Cyanine-3 (green)
|
| |
|
| Channel 2 |
| Source name |
RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 500 micromolar 2-methyl-thio-ATP for 001hr
|
| Organism |
Mus musculus |
| Characteristics |
RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 500 micromolar 2-methyl-thio-ATP for 001hr
|
| Extracted molecule |
total RNA |
| Label |
Cyanine-5 (red)
|
| |
|
| |
| Scan protocol |
The arrays were scanned using Agilent Scanner G2505A (Agilent Technologies) with the scan resolution set to 10 micrometer and the laser intensity adjusted so that both the maximum red and green (Cy5 and Cy3) fluorescence intensity were around 20,000.
|
| Description |
Gene expression changes comparing UT 001hr Raw 264.7 cells vs LPS&2MA- 001hr RAw 264.7 cells
|
| Data processing |
The image files were extracted with background-subtraction (the Local background subtraction method) and dye-normalization (the Rank consistent filter and the LOWESS algorithm) using the Agilent G2566AA Extraction Software Version A.6.1.1.
|
| |
|
| Submission date |
Jun 01, 2006 |
| Last update date |
Jun 05, 2006 |
| Contact name |
Sangdun Choi |
| E-mail(s) |
schoi@its.caltech.edu
|
| Phone |
626-395-8732
|
| URL |
http://www.signaling-gateway.org
|
| Organization name |
California Institute of Technology
|
| Department |
Biology
|
| Lab |
Alliance for Cellular Signaling Molecular Biology Laboratory
|
| Street address |
1200 E. California Blvd
|
| City |
Pasadena |
| State/province |
CA |
| ZIP/Postal code |
91125 |
| Country |
USA |
| |
|
| Platform ID |
GPL254 |
| Series (1) |
| GSE4962 |
Gene expression of RAW 264.7 cells treated with LPS, IFG, 2MA, LPS PLUS IFG, and LPS PLUS 2MA |
|
| Data table header descriptions |
| ID_REF |
Feature number which correspond to the order of genes on the array |
| G_PROCESSED |
Processed Signal, after dye normalization and background subtraction, used for computing the log ratio. |
| G_MEAN |
Green Channel Mean Raw Intensity |
| G_MEDIAN |
Green Channel Median Raw Intensity |
| G_SD |
Green Channel Standard Deviation |
| G_BG_MEAN |
Green Channel Mean Background Level |
| G_BG_MEDIAN |
Green Channel Median Background Level |
| G_BG_SD |
Green Channel Background Standard Deviation |
| R_PROCESSED |
Processed Signal, after dye normalization and background subtraction, used for computing the log ratio. |
| R_MEAN |
Red Channel Mean Raw Intensity |
| R_MEDIAN |
Red Channel Median Raw Intensity |
| R_SD |
Red Channel Standard Deviation |
| R_BG_MEAN |
Red Channel Mean Background Level |
| R_BG_MEDIAN |
Red Channel Median Background Level |
| R_BG_SD |
Red Channel Background Standard Deviation |
| RATIO |
Log Ratio (base 10) |
| VALUE |
Processed Ratio (base 2) after removing saturated spots, spot below 2.6XSD of background, and nonuniform spots. |
