|
Status |
Public on Jan 10, 2006 |
Title |
Supernatant of infection treated with 3 rounds of SCOTS, replicate 6 |
Sample type |
mixed |
|
|
Channel 1 |
Source name |
3XSCOTS cDNA obtained from infection supernatant
|
Organism |
Salmonella enterica subsp. enterica serovar Typhi |
Characteristics |
Salmonella typhi infection of THP-1 cells, recovered from the culture medium supernatant
|
Treatment protocol |
2E7 THP-1 cells (treated with 1E-7 M phorbol 12-myristate 13-acetate) were infected with Salmonella typhi at a multiplicity of infection of 10:1. At time 0, the supernatant was removed and centrifuge to recover the bacteria. The pellet was lysed with 2 ml of TRIzol (Gibco BRL)
|
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 |
1.5 µg of cDNA was labeled with Cy5-dCTP (GE Healthcare) by random priming with Klenow (New England Biolabs) as previously described (Porwollik, S. 2001. Mutat Res 483:1-11.).
|
|
|
Channel 2 |
Source name |
Reference genomic DNA
|
Organism |
Salmonella enterica subsp. enterica serovar Typhi |
Characteristics |
Genomic DNA from Salmonella typhi ISP1820
|
Growth protocol |
Salmonella typhi from overnight culture in LB broth.
|
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 |
1.5 µg of genomic DNA was labeled with Cy3-dCTP (GE Healthcare) by random priming with Klenow (New England Biolabs) as previously described (Porwollik, S. 2001. Mutat Res 483:1-11.).
|
|
|
|
Hybridization protocol |
Samples we hybridized as previously described (Porwolik, S. 2003.Nucleic Acids Res 31:1869-76)
|
Scan protocol |
Slide was scanned with Scan Array Lite (Perkin-Elmer) using Scan Array Express 2.1 software.
|
Description |
This sample was used to analyse the expression profiles of Salmonella typhi during infection of human macrophages (THP-1)
|
Data processing |
After backgroud correction and total intensity normalization, ratio to reference were calculated and log base 2 transformed.
|
|
|
Submission date |
Aug 09, 2005 |
Last update date |
Jan 10, 2006 |
Contact name |
Sébastien P Faucher |
E-mail(s) |
[email protected]
|
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 |
GPL1835 |
Series (1) |
GSE3096 |
Expression profiles of Salmonella typhi inside human macrophages (THP-1) compared to supernatant |
|
Data table header descriptions |
ID_REF |
Number |
X_LOCATION |
X-coordinate of spot |
Y_LOCATION |
Y-coordinate of spot |
CH1_MEAN |
Channel 1 mean |
CH1_BKD_MEAN |
Channel 1 mean background |
CH1_MEAN_SD |
|
CH1_BKD_SD |
Channel 1 background standard deviation |
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_BKD_UNIFORMITY |
Channel 1 background uniformity |
CH1_SIGNAL_NOISE_RATIO |
Channel 1 signal to noise ratio |
CH1_CONFIDENCE |
Channel 1 confidence |
CH2_MEAN |
Channel 2 mean |
CH2_BKD_MEAN |
Channel 2 mean background |
CH2_SD |
Channel 2 standard deviation |
CH2_BKD_SD |
Channel 2 background standard deviation |
CH2_DIAMETER |
Channel 2 diameter |
CH2_AREA |
Channel 2 area |
CH2_FOOTPRINT |
Channel 2 footprint |
C2_CIRCULARITY |
|
CH2_SPOT_UNIFORMITY |
Channel 2 spot uniformity |
CH2_BKD_UNIFORMITY |
Channel 2 background uniformity |
CH2_SIGNAL_NOISE_RATIO |
Channel 2 signal to noise ratio |
CH2_CONFIDENCE |
Channel 2 confidence |
CH1_DIAMETER_FILTER |
Channel 1 diameter filter |
CH1_AREA_FILTER |
Channel 1 area filter |
CH1_CIRCULARITY_FILTER |
Channel 1 circularity filter |
CH1_SPOT_UNIFORMITY_FILTER |
Channel 1 spot uniformity filter |
CH1_BKD_UNIFORMITY_FILTER |
Channel 1 background uniformity filter |
CH1_SIGNAL_NOISE_RATIO_FILTER |
Channel 1 signal to noise ratio filter |
CH2_DIAMETER_FILTER |
Channel 2 diameter filter |
CH2_AREA_FILTER |
Channel 2 area filter |
CH2_CIRCULARITY_FILTER |
Channel 2 circularity filter |
CH2_SPOT_UNIFORMITY_FILTER |
Channel 2 spot uniformity filter |
CH2_BKD_UNIFORMITY_FILTER |
Channel 2 background uniformity filter |
CH2_SIGNAL_NOISE_RATIO_FILTER |
Channel 2 signal to noise ratio filter |
IGNORE_FILTER |
Ignore filter |
CH1_BKD_CORR |
Channel 1 background correlation |
CH2_BKD_CORR |
Channel 2 background correlation |
CH1%_OF_TOTAL |
Channel 1 % of total |
CH2%_OF_TOTAL |
Channel 2 % of total |
PRE-VALUE |
ch1 % of total / ch2 % of total |
VALUE |
log base 2 of ch1 % of total / ch2 % of total |