|
| Status |
Public on Nov 13, 2008 |
| Title |
T8 THP-1 infection, Microarray #2 second replicate |
| Sample type |
mixed |
| |
|
| Channel 1 |
| Source Name |
3XSCOTS cDNA obtained 8h post-infection
|
| Organism(s) |
Escherichia coli |
| Characteristics |
EDL933 8h post THP-1 infection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol reagent (Gibco BRL) was used according to the manufacturer instruction. RNA was treated with DNase (Ambion). RNA sample was converted to cDNA in 5 independent reverse-transcription reactions as described previously (Graham, J. 1999. PNAS 96:11554-559). Bacterial transcript were purified from host transcript by using 3 round of the SCOTS procedure (Daigle, F. 2002. Methods Enzymol. 358:108-122).
|
| Label |
Cy5
|
| Label protocol |
Bioprime DNA labeling kit Invitrogen
|
| |
|
| Channel 2 |
| Source Name |
Reference genomic DNA
|
| Organism(s) |
Escherichia coli |
| Characteristics |
EDL933 genommic DNA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted by standard phenol-chloroform method (Sambrook, J, Molecular Cloning, 3rd Edition)
|
| Label |
Cy3
|
| Label protocol |
Bioprime DNA labelin kit Invitrogen
|
| |
|
| |
| Hybridization protocol |
Dry the probe and then resuspend in 80ul of DIG 37°C for the Cy3 and Cy5 sample.
Place the mixed probe at 95°C, 5 min and then chilled on ice 5 min.
Depose the mixed probe on the microarray, cover with a cover-slip and place in an corning hybridation chamber.
|
| Scan protocol |
Slide was scanned with Scan Array Lite (Perkin-Elmer) using Scan Array Express 2.1 software.
|
| Description |
This sample to study the effect of human macrophages phagocytosis on the global transcriptome of EDL933 at different time
|
| Data processing |
After backgroud correction and total intensity normalization, ratio to reference were calculated and log base 2 transformed
|
| |
|
| Submission date |
Nov 23, 2007 |
| Contact name |
Sébastien P Faucher |
| E-mail(s) |
sebastien.faucher@umontreal.ca
|
| Phone |
514-343-6111 #3135
|
| Fax |
514-343-5701
|
| Organization name |
University of Montreal
|
| Department |
Microbiology and Immunology
|
| Street address |
C.P. 6128 Succ. Centre-Ville
|
| City |
Montreal |
| State/province |
QUEBEC |
| ZIP/Postal code |
H3C 3J7 |
| Country |
Canada |
| |
|
| Platform ID |
GPL6178 |
| Series (1) |
| GSE9671 |
EDL933 in human macrophage THP-1 cells at different time point |
|
| Data table header descriptions |
| ID_REF |
|
| X Location |
X-coordinate of spot |
| Y Location |
Y-coordinate of spot |
| ch1 Intensity |
Channel 1 mean |
| ch1 Background |
Channel 1 mean background |
| ch1 Intensity Std Dev |
Channel 1 mean intensity standard deviation |
| ch1 Background Std Dev |
Channel 1 background standard deviationv |
| ch1 Diameter |
Channel 1 diameter |
| ch1 Area |
Channel 1 area |
| ch1 Footprint |
Channel 1 footprint |
| ch1 Circularity |
Channel 1 circularity |
| ch1 Spot Uniformity |
Channel 1 spot uniformity |
| ch1 Bkg. Uniformity |
Channel 1 background uniformity |
| ch1 Signal Noise Ratio |
Channel 1 signal to noise ratio |
| ch1 Confidence |
Channel 1 confidence |
| ch2 Intensity |
Channel 2 mean |
| ch2 Background |
Channel 2 mean background |
| ch2 Intensity Std Dev |
Channel 2 mean intensity standard deviation |
| ch2 Background Std Dev |
Channel 2 background standard deviation |
| ch2 Diameter |
Channel 2 diameter |
| ch2 Area |
Channel 2 area |
| ch2 Footprint |
Channel 2 footprint |
| ch2 Circularity |
Channel 2 circularity |
| ch2 Spot Uniformity |
Channel 2 spot uniformity |
| ch2 Bkg. Uniformity |
Channel 2 background uniformity |
| ch2 Signal Noise Ratio |
Channel 2 signal to noise ratio |
| ch2 Confidence |
Channel 2 confidence |
| Ignore Filter |
Ignore filter |
| Ch1-bkg |
Channel 1 background correction |
| Ch2-bkg |
Channel 2 background correction |
| Ch1 total |
Channel 1 % of total |
| Ch2 total |
Channel 2 % of total |
| PRE_VALUE |
ch1 % of total / ch2 % of total |
| VALUE |
log base 2 of ch1 % of total / ch2 % of total |
