|
| Status |
Public on Nov 21, 2012 |
| Title |
RR2_nsrR_Cy3_ch1_wt_Cy5_ch2_7DS13315878_rep1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
14028s nsrR mutant
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S |
| Characteristics |
genotype/variation: nsrR mutant
|
| Growth protocol |
aerobically in LB to mid-log phase (OD600~0.5) at 37°C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
1Vol culture was mixed with 2Vol RNAprotect reagent (Qiagen, Valencia, CA, USA) and RNA immediately purified using the Qiagen RNeasy midi kit (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
Standard labeling using Cy3-dUTP with reverse transcriptase and random hexamers
|
| |
|
| Channel 2 |
| Source name |
14028s wild type
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S |
| Characteristics |
genotype/variation: wild type
|
| Growth protocol |
aerobically in LB to mid-log phase (OD600~0.5) at 37°C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
1Vol culture was mixed with 2Vol RNAprotect reagent (Qiagen, Valencia, CA, USA) and RNA immediately purified using the Qiagen RNeasy midi kit (Qiagen).
|
| Label |
Cy5
|
| Label protocol |
Standard labeling using Cy5-dUTP with reverse transcriptase and random hexamers
|
| |
|
| |
| Hybridization protocol |
overnight hyb on Corning UltraGAPS slides at 42°C in 25% formamide / 5xSSC / 0.1% BSA
|
| Scan protocol |
Perkin Elmer ScanArray 5000 scanner at 10?m resolution, 95% laser power, PMT for low scan set to where maximal intensity of spots was 75% of saturation; PMT for high scan was 20% higher than low scan PMT. Image acquisition with ScanArray Express 3.0.1 software, spot quantification using MolecularWare AnalyzerDG Pro version 2.50.
|
| Description |
biological replicate
|
| Data processing |
used values for median measurements for spot and background in high PMT setting; normalized based on total signal for each channel, background subtracted VALUE data obtained from log of normalized background subtracted ch1/ch2 signal.
|
| |
|
| Submission date |
Oct 03, 2011 |
| Last update date |
Nov 21, 2012 |
| Contact name |
Michael McClelland |
| E-mail(s) |
mcclelland.michael@gmail.com
|
| Phone |
858-336-9554
|
| Organization name |
University of California, Irvine
|
| Department |
Microbiology & Molecular Genetics
|
| Street address |
132 Med Surge I
|
| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92697 |
| Country |
USA |
| |
|
| Platform ID |
GPL6868 |
| Series (1) |
| GSE32585 |
The nsrR regulon in Salmonella Typhimurium 14028s |
|
| Data table header descriptions |
| ID_REF |
Number |
| Spot_Confidence_(Cy3H) |
Spot Confidence Cy3 high scan |
| Spot_Confidence_(Cy3L) |
Spot Confidence Cy3 low scan |
| Spot_Confidence_(Cy5H) |
Spot Confidence Cy5 high scan |
| Spot_Confidence_(Cy5L) |
Spot Confidence Cy5 low scan |
| Spot_Mean_Intensity_(Cy3H) |
Spot Mean Intensity Cy3 high scan |
| Spot_Mean_Intensity_(Cy3L) |
Spot Mean Intensity Cy3 low scan |
| Spot_Mean_Intensity_(Cy5H) |
Spot Mean Intensity Cy5 high scan |
| Spot_Mean_Intensity_(Cy5L) |
Spot Mean Intensity Cy5 low scan |
| Spot_Median_Intensity_(Cy3H) |
Spot Median Intensity Cy3 high scan |
| Spot_Median_Intensity_(Cy3L) |
Spot Median Intensity Cy3 low scan |
| Spot_Median_Intensity_(Cy5H) |
Spot Median Intensity Cy5 high scan |
| Spot_Median_Intensity_(Cy5L) |
Spot Median Intensity Cy5 low scan |
| Spot_Standard_Deviation_(Cy3H) |
Spot Standard Deviation Cy3 high scan |
| Spot_Standard_Deviation_(Cy3L) |
Spot Standard Deviation Cy3 low scan |
| Spot_Standard_Deviation_(Cy5H) |
Spot Standard Deviation Cy5 high scan |
| Spot_Standard_Deviation_(Cy5L) |
Spot Standard Deviation Cy5 low scan |
| Spot_Number_of_Pixels_(Cy3H) |
Spot Number of Pixels Cy3 high scan |
| Spot_Number_of_Pixels_(Cy3L) |
Spot Number of Pixels Cy3 low scan |
| Spot_Number_of_Pixels_(Cy5H) |
Spot Number of Pixels Cy5 high scan |
| Spot_Number_of_Pixels_(Cy5L) |
Spot Number of Pixels Cy5 low scan |
| Spot_Total_Intensity_(Cy3H) |
Spot Total Intensity Cy3 high scan |
| Spot_Total_Intensity_(Cy3L) |
Spot Total Intensity Cy3 low scan |
| Spot_Total_Intensity_(Cy5H) |
Spot Total Intensity Cy5 high scan |
| Spot_Total_Intensity_(Cy5L) |
Spot Total Intensity Cy5 low scan |
| Spot_Peak_Intensity_(Cy3H) |
Spot Peak Intensity Cy3 high scan |
| Spot_Peak_Intensity_(Cy3L) |
Spot Peak Intensity Cy3 low scan |
| Spot_Peak_Intensity_(Cy5H) |
Spot Peak Intensity Cy5 high scan |
| Spot_Peak_Intensity_(Cy5L) |
Spot Peak Intensity Cy5 low scan |
| Background_Mean_Intensity_(Cy3H) |
Background Mean Intensity Cy3 high scan |
| Background_Mean_Intensity_(Cy3L) |
Background Mean Intensity Cy3 low scan |
| Background_Mean_Intensity_(Cy5H) |
Background Mean Intensity Cy5 high scan |
| Background_Mean_Intensity_(Cy5L) |
Background Mean Intensity Cy5 low scan |
| Background_Median_Intensity_(Cy3H) |
Background Median Intensity Cy3 high scan |
| Background_Median_Intensity_(Cy3L) |
Background Median Intensity Cy3 low scan |
| Background_Median_Intensity_(Cy5H) |
Background Median Intensity Cy5 high scan |
| Background_Median_Intensity_(Cy5L) |
Background Median Intensity Cy5 low scan |
| Background_Standard_Deviation_(Cy3H) |
Background Standard Deviation Cy3 high scan |
| Background_Standard_Deviation_(Cy3L) |
Background Standard Deviation Cy3 low scan |
| Background_Standard_Deviation_(Cy5H) |
Background Standard Deviation Cy5 high scan |
| Background_Standard_Deviation_(Cy5L) |
Background Standard Deviation Cy5 low scan |
| Background_Number_of_Pixels_(Cy3H) |
Background Number of Pixels Cy3 high scan |
| Background_Number_of_Pixels_(Cy3L) |
Background Number of Pixels Cy3 low scan |
| Background_Number_of_Pixels_(Cy5H) |
Background Number of Pixels Cy5 high scan |
| Background_Number_of_Pixels_(Cy5L) |
Background Number of Pixels Cy5 low scan |
| CH1_BKD_CORR |
Channel 1 median values of high scan background corrected |
| CH2_BKD_CORR |
Channel 2 median values of high scan background corrected |
| CH1%_OF_TOTAL |
Channel 1 median values of high scan % of total |
| CH2%_OF_TOTAL |
Channel 2 median values of high scan % of total |
| PRE-VALUE |
ch1 median values of high scan % of total / ch2 median values of high scan % of total |
| VALUE |
log of ch1 median values of high scan % of total / ch2 median values of high scan % of total |
