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Sample GSM68757 Query DataSets for GSM68757
Status Public on Jan 10, 2006
Title 2h post-infection of THP-1 treated with 1 rounds of SCOTS, replicate 4
Sample type mixed
 
Channel 1
Source name 1XSCOTS cDNA obtained 2h post-infection
Organism Salmonella enterica subsp. enterica serovar Typhi
Characteristics Salmonella typhi infection of THP-1 cells, recovered 2 h post-infection
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, cells were washed with PBS and fresh RPMI containing 100 ug ml-1 was added to the wells. After 2 hours, cells were washed with PBS and recovered in 5 ml PBS. After centrifuation, the pellet was lysed with 2 ml TRIzol (Invitrogen).
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 1 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 effect of SCOTS on transcript population.
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 GPL548
Series (1)
GSE3095 Analysis of SCOTS effect on transcript population

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

Data table
ID_REF X_LOCATION Y_LOCATION CH1_MEAN CH1_BKD_MEAN CH1_MEAN_SD CH1_BKD_SD CH1_DIAMETER CH1_AREA CH1_FOOTPRINT CH1_CIRCULARITY CH1_SPOT_UNIFORMITY CH1_BKD_UNIFORMITY CH1_SIGNAL_NOISE_RATIO CH1_CONFIDENCE CH2_MEAN CH2_BKD_MEAN CH2_SD CH2_BKD_SD CH2_DIAMETER CH2_AREA CH2_FOOTPRINT C2_CIRCULARITY CH2_SPOT_UNIFORMITY CH2_BKD_UNIFORMITY CH2_SIGNAL_NOISE_RATIO CH2_CONFIDENCE CH1_DIAMETER_FILTER CH1_AREA_FILTER CH1_CIRCULARITY_FILTER CH1_SPOT_UNIFORMITY_FILTER CH1_BKD_UNIFORMITY_FILTER CH1_SIGNAL_NOISE_RATIO_FILTER CH2_DIAMETER_FILTER CH2_AREA_FILTER CH2_CIRCULARITY_FILTER CH2_SPOT_UNIFORMITY_FILTER CH2_BKD_UNIFORMITY_FILTER CH2_SIGNAL_NOISE_RATIO_FILTER IGNORE_FILTER CH1_BKD_CORR CH2_BKD_CORR CH1%_OF_TOTAL CH2%_OF_TOTAL PRE-VALUE VALUE
1 1120 50 0 0 0 0 0 0 22.036673 0 0 0 3.40282E+38 0 0 0 0 0 0 0 22.036673 0 0 0 3.40282E+38 0 0 0 0 0 0 1 0 0 0 0 0 1 1 0 0 0 0
2 1340 50 0 0 0 0 0 0 15.726459 0 0 0 3.40282E+38 0 0 0 0 0 0 0 15.726459 0 0 0 3.40282E+38 0 0 0 0 0 0 1 0 0 0 0 0 1 1 0 0 0 0
3 1580 50 0 0 0 0 0 0 16.635885 0 0 0 3.40282E+38 0 0 0 0 0 0 0 16.635885 0 0 0 3.40282E+38 0 0 0 0 0 0 1 0 0 0 0 0 1 1 0 0 0 0
4 1840 50 0 0 0 0 0 0 34.262348 0 0 0 3.40282E+38 0 0 0 0 0 0 0 34.262348 0 0 0 3.40282E+38 0 0 0 0 0 0 1 0 0 0 0 0 1 1 0 0 0 0
5 2060 50 0 0 0 0 0 0 22.036673 0 0 0 3.40282E+38 0 0 0 0 0 0 0 22.036673 0 0 0 3.40282E+38 0 0 0 0 0 0 1 0 0 0 0 0 1 1 0 0 0 0
6 2290 60 0 0 0 0 0 0 11.907121 0 0 0 3.40282E+38 0 0 0 0 0 0 0 11.907121 0 0 0 3.40282E+38 0 0 0 0 0 0 1 0 0 0 0 0 1 1 0 0 0 0
7 2520 50 0 0 0 0 0 0 16.635885 0 0 0 3.40282E+38 0 0 0 0 0 0 0 16.635885 0 0 0 3.40282E+38 0 0 0 0 0 0 1 0 0 0 0 0 1 1 0 0 0 0
8 2750 60 0 0 0 0 0 0 5.737352 0 0 0 3.40282E+38 0 0 0 0 0 0 0 5.737352 0 0 0 3.40282E+38 0 0 0 0 0 0 1 0 0 0 0 0 1 1 0 0 0 0
9 2980 70 0 0 0 0 0 0 6.251541 0 0 0 3.40282E+38 0 0 0 0 0 0 0 6.251541 0 0 0 3.40282E+38 0 0 0 0 0 0 1 0 0 0 0 0 1 1 0 0 0 0
10 3220 70 0 0 0 0 0 0 4.302663 0 0 0 3.40282E+38 0 0 0 0 0 0 0 4.302663 0 0 0 3.40282E+38 0 0 0 0 0 0 1 0 0 0 0 0 1 1 0 0 0 0
11 3450 60 0 0 0 0 0 0 7.313416 0 0 0 3.40282E+38 0 0 0 0 0 0 0 7.313416 0 0 0 3.40282E+38 0 0 0 0 0 0 1 0 0 0 0 0 1 1 0 0 0 0
12 3740 60 0 0 0 0 0 0 50.766415 0 0 0 3.40282E+38 0 0 0 0 0 0 0 50.766415 0 0 0 3.40282E+38 0 0 0 0 0 0 1 0 0 0 0 0 1 1 0 0 0 0
13 3920 60 0 0 0 0 0 0 7.313416 0 0 0 3.40282E+38 0 0 0 0 0 0 0 7.313416 0 0 0 3.40282E+38 0 0 0 0 0 0 1 0 0 0 0 0 1 1 0 0 0 0
14 4160 60 0 0 0 0 0 0 5.737352 0 0 0 3.40282E+38 0 0 0 0 0 0 0 5.737352 0 0 0 3.40282E+38 0 0 0 0 0 0 1 0 0 0 0 0 1 1 0 0 0 0
15 4400 60 0 0 0 0 0 0 7.896098 0 0 0 3.40282E+38 0 0 0 0 0 0 0 7.896098 0 0 0 3.40282E+38 0 0 0 0 0 0 1 0 0 0 0 0 1 1 0 0 0 0
16 4640 60 0 0 0 0 0 0 11.907121 0 0 0 3.40282E+38 0 0 0 0 0 0 0 11.907121 0 0 0 3.40282E+38 0 0 0 0 0 0 1 0 0 0 0 0 1 1 0 0 0 0
17 4870 80 0 0 0 0 0 0 15.282008 0 0 0 3.40282E+38 0 0 0 0 0 0 0 15.282008 0 0 0 3.40282E+38 0 0 0 0 0 0 1 0 0 0 0 0 1 1 0 0 0 0
18 5120 70 0 0 0 0 0 0 20.886299 0 0 0 3.40282E+38 0 0 0 0 0 0 0 20.886299 0 0 0 3.40282E+38 0 0 0 0 0 0 1 0 0 0 0 0 1 1 0 0 0 0
19 5350 70 0 0 0 0 0 0 16.025179 0 0 0 3.40282E+38 0 0 0 0 0 0 0 16.025179 0 0 0 3.40282E+38 0 0 0 0 0 0 1 0 0 0 0 0 1 1 0 0 0 0
20 1120 280 254.235291 50.838234 234.347504 105.331261 176.077789 6800 25.842157 0.930901 0.992752 0.996849 2.413674 0.643646 253.793808 53.632355 260.574799 192.986969 186.950348 9700 25.842157 0.966722 0.99189 0.995674 1.315083 0.350689 1 1 1 1 1 0 1 1 1 1 1 0 1 203.397057 200.161453 0.011774947 0.00391068 3.010971465 1.590229035

Total number of rows: 5776

Table truncated, full table size 1900 Kbytes.




Supplementary data files not provided
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