|
| Status |
Public on Oct 14, 2011 |
| Title |
FUR- mutant vs. WT (dye swap-2) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
FUR null mutant
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium |
| Characteristics |
strain: ATCC14028s
|
| Growth protocol |
OD600=0.3, anaerobic, LB medium, 20 mM Xylose
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with the RNeasy RNA extraction kit (QIAGEN), and the samples were treated with RNase-free DNase (Invitrogen, Carlsbad, CA). The absence of contaminating DNA and the quality of the RNA was confirmed by using agarose gel electrophoresis.
|
| Label |
Cy5
|
| Label protocol |
The labelling of the total RNA was performed using indirect labelling with AA-dUTP and subsequent coupling.
|
| |
|
| Channel 2 |
| Source name |
WT
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium |
| Characteristics |
strain: ATCC14028s
|
| Growth protocol |
OD600=0.3, anaerobic, LB medium, 20 mM Xylose
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with the RNeasy RNA extraction kit (QIAGEN), and the samples were treated with RNase-free DNase (Invitrogen, Carlsbad, CA). The absence of contaminating DNA and the quality of the RNA was confirmed by using agarose gel electrophoresis.
|
| Label |
Cy3
|
| Label protocol |
The labelling of the total RNA was performed using indirect labelling with AA-dUTP and subsequent coupling.
|
| |
|
| |
| Hybridization protocol |
The slides were washed at increasing stringencies (2x SSC [1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate], 0.1% sodium dodecyl sulfate [SDS], 42°C; 0.1% SSC, 0.1% SDS, room temperature; 0.1% SSC, room temperature).
|
| Scan protocol |
the microarrays were scanned for the Cy3 and Cy5 fluorescent signals with a ScanArray 4000 microarray scanner from GSI Lumonics (Watertown, MA). The intensity of every spot was codified as the sum of the intensities of all the pixels within a circle positioned over the spot itself and the background as the sum of the intensities of an identical number of pixels in the immediate surroundings of the circled spot.
|
| Description |
no additional information
|
| Data processing |
The signal intensity at each spot from the FNR mutant and the WT were background subtracted, normalized, and used to calculate the ratio of gene expression between the two strains. All replicas were combined, and the median expression ratios and standard deviations were calculated for open reading frames (ORFs) showing 2.5-fold change.
VALUE column reports log2 (mutant/wt) ratios.
|
| |
|
| Submission date |
Oct 06, 2009 |
| Last update date |
Oct 15, 2011 |
| Contact name |
Ryan Cristiano Fink |
| E-mail(s) |
rcfink@stcloudstate.edu
|
| Organization name |
St. Cloud State University
|
| Department |
Biology
|
| Lab |
Ryan C. Fink
|
| Street address |
720 4th Ave S
|
| City |
St. Cloud |
| State/province |
MN |
| ZIP/Postal code |
56301 |
| Country |
USA |
| |
|
| Platform ID |
GPL1835 |
| Series (1) |
|
| Data table header descriptions |
| ID_REF |
identifier reference column |
| VALUE |
log ratio (log2 of RATIO Median) |
| Ch1 Median |
median of the raw signal output for channel 1 |
| Ch1 Mean |
mean of the raw signal output for channel 1 |
| Ch1 SD |
standard deviation calculated for the mean signal for channel 1 |
| Ch1 B Median |
Median of the background signal output for channel 1 |
| Ch1 B Mean |
Median of the background signal output for channel 1 |
| Ch1 B SD |
standard deviation for the mean background signal for channel 1 |
| Ch1 Median-B |
background subtracted median of the raw signal output for channel 1 |
| Ch1 Mean - B |
Background subtracted mean of the raw signal output for channel 1 |
| Ch1 SignalNoiseRatio |
Ratio of the raw signal over the background |
| Ch2 Median |
median of the raw signal output for channel 2 |
| Ch2 Mean |
mean of the raw signal output for channel 2 |
| Ch2 SD |
standard deviation calculated for the mean signal for channel 2 |
| Ch2 B Median |
Median of the background signal output for channel 2 |
| Ch2 B Mean |
Median of the background signal output for channel 2 |
| Ch2 B SD |
standard deviation for the mean background signal for channel 2 |
| Ch2 Median - B |
background subtracted median of the raw signal output for channel 2 |
| Ch2 Mean - B |
Background subtracted mean of the raw signal output for channel 2 |
| RATIO Median |
(Cy5 median-Backgroung)/(Cy3 median-Background) |
| RATIO Mean |
(Cy5 mean-Backgroung)/(Cy3 mean-Background) |
| INV VALUE Median |
log ratio (log2 of RATIO Median) |
| INV VALUE Mean |
log ratio (log2 of RATIO Mean) |
