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Sample GSM73161 Query DataSets for GSM73161
Status Public on Jul 03, 2006
Title CLIP80459 - replicate #4
Sample type RNA
 
Source name CLIP80459
Organism Listeria monocytogenes
Characteristics CLIP80459
Growth protocol All strains were grown until late exponential phase (OD600 0.9) in the defined rich medium MCDB 202 (CryoBioSystem), at 37oC. Pulsed Field Gel Electrophoresis was performed for molecular characterization of the strains. Bacterial cells were grown overnight in BHI medium (Difco) and inoculated (10%) in 10 ml MCDB 202 medium for total RNA extraction. For each strain, two overnight cultures were used.
Extracted molecule total RNA
Extraction protocol Cells were harvested by centrifugation at 12000 g for 4 min at 4oC, and immediately frozen. Pellets were resuspended in 400 ul of buffer (10% glucose, 12.5 mM Tris pH 7.6, 5 mM EDTA) and 60 ul of EDTA 0.5 M, and cells were mechanically disrupted in a FastPrep apparatus after the addition of 500 ul of acid phenol (pH 4.5) and 0.4 g of glass beads (Sigma). After a centrifugation step, the aqueous phase was transferred to new tubes, 1 ml of Trizol (Invitrogen) was added and samples were incubated for 5 min at room temperature. 200 ul of chlorophorm/isoamylic alcohol were added to each sample, followed by centrifugation for 5 min. This step was repeated twice and to the final aqueous supernatant 500 ul of 2-propanol were added for total RNA precipitation. The mixture was left at -20oC for 15 min and centrifuged for 30 min at 4oC. Pellets were then washed with 70% ethanol and dried at room temperature prior to being dissolved in 50 ul of diethylpyocarbonate (DEPC)-treated water. The RNA concentration was estimated using a spectrophotometer and RNA quality was checked on agarose gel containing ethidium bromide.
Label 33P
Label protocol Total RNA (1ug) was mixed with 6 ul of 5X AMV reverse transcriptase buffer (Roche), 3 ul of a mixture of dATP, dGTP, dTTP (10 mM), 5 ug of random hexamers (Primer Random p(dN)6, Roche) and DEPC-treated water to a final volume of 21 ul. The mixture was heated at 90oC for 2 min and cooled to 42oC before addition of 3 ul of alpha-33P dCTP (20 uCi) and 2 ul (50U/ul) of AMV reverse transcriptase (Roche). The mixture was incubated for 2 h at 42oC. A column was used for the removal of unincorporated nucleotides according to the manufacturer’s instructions (QIAquick Nucleotide Removal Kit, QIAgen). The obtained cDNA was denaturated by heating at 99oC for 5 min just before hybridization.
 
Hybridization protocol Macroarrays were pre-hybridized in roller bottles with 10 ml of a hybridization solution containing 5X SSPE (1X SSPE is 0.18 M NaCl, 10 mM NaH2PO4 and 1 mM EDTA pH7.7), 2% SDS, 1X Denhardt’s reagent (Sigma), 100 ug/ml of sonicated salmon sperm DNA for 1h at 65oC. Hybridizations were performed overnight at 65oC with 5 ml of fresh hybridization solution containing the labeled cDNA. After hybridization macroarrays were washed twice for 5 min at room temperature and twice for 20 min at 65oC with a washing solution (0.5X SSPE, 0.2% SDS).
Scan protocol The macroarrays were then exposed to a phosphoimager screen and scanned with the Typhoon phosphoimager (Pharmacia-Amersham). Two hybridizations for each independent RNA extraction were performed. In total, a set of 4 macroarrays was used for each strain. Hybridized arrays were scanned using the Typhoon 9400 phosphoimager (Amersham Biosciences). The signal intensity was quantified using the ArrayVision software (Imaging Research). The intensity was measured in arbitrary units using the ARMdens measure.
Description see above.
Data processing Normalized by a multiplicative constant. The correction factor is obtained setting arbitrarily the median of log10(intensities) to ZERO.
 
Submission date Sep 03, 2005
Last update date Oct 28, 2005
Contact name Ricardo Z.N. Vêncio
Organization name Universidade de São Paulo
Department Computing and Mathematics Department
Lab http://labpib.fmrp.usp.br
Street address Av. Bandeirantes, 3900
City Ribeirao Preto
State/province SP
ZIP/Postal code 14049-900
Country Brazil
 
Platform ID GPL2811
Series (1)
GSE3247 Expression profile comparison among Listeria monocytogenes strains

Data table header descriptions
ID_REF
VALUE Normalized intensity
Intensity Intensity

Data table
ID_REF VALUE Intensity
1 0.918769637836944 4611.314
2 1.07812516811084 5411.121
3 0.835401802347475 4192.89
4 1.12840321099181 5663.467
5 0.612043410951563 3071.852
6 0.981966961611952 4928.502
7 0.599918908310604 3010.999
8 0.543771181966165 2729.193
9 0.250170252699238 1255.607
10 0.576411483539583 2893.015
11 0.893423404217167 4484.101
12 0.224158150710997 1125.052
13 0.167352724939779 839.945
14 0.275685643184612 1383.669
15 0.110981647775159 557.018
16 0.138909864694432 697.19
17 0.223135638303172 1119.92
18 0.237230051344787 1190.66
19 0.18248997312219 915.919
20 0.213165544599433 1069.88

Total number of rows: 2995

Table truncated, full table size 91 Kbytes.




Supplementary data files not provided

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