|
| Status |
Public on Sep 09, 2005 |
| Title |
6' RNA Decay of MG1655 (Repaired NCM 3416) in LB at 30 C |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
MG1655 at 30 Degrees
|
| Organism |
Escherichia coli |
| Characteristics |
MG1655 at 30 Degrees
|
| Extracted molecule |
total RNA |
| Label |
Cy3
|
| |
|
| Channel 2 |
| Source name |
MG1655 6' post rif
|
| Organism |
Escherichia coli |
| Characteristics |
MG1655 6' post rif
|
| Extracted molecule |
total RNA |
| Label |
Cy5
|
| |
|
| |
| Description |
Simple annotation: RNA decay, Rifampicin
Image: http://smd.stanford.edu/MicroArray/gifs/2000-08/8379.gif
|
| Data processing |
VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
|
| |
|
| Submission date |
Sep 08, 2005 |
| Last update date |
Sep 22, 2006 |
| Organization |
Stanford Microarray Database (SMD) |
| E-mail(s) |
array@genome.stanford.edu
|
| Phone |
650-498-6012
|
| URL |
http://genome-www5.stanford.edu/
|
| Department |
Stanford University, School of Medicine
|
| Street address |
300 Pasteur Drive
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL2820 |
| Series (2) |
| GSE3267 |
mRNA decay in E. coli |
| GSE4344 |
Global analysis of mRNA decay and abundance in Escherichia coli |
|
| Data table header descriptions |
| ID_REF |
ID_REF |
| CH1I_MEAN |
Uncorrected Cy3 mean pixel intensity.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel |
| CH2I_MEAN |
Uncorrected Cy3 mean pixel intensity.; Type: integer; Scale: linear_scale; Channel: Cy5 channel |
| CH1B_MEDIAN |
Median intensities of background pixels of Cy3.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel |
| CH2B_MEDIAN |
Median intensities of background pixels of Cy3.; Type: integer; Scale: linear_scale; Channel: Cy5 channel |
| CH1D_MEAN |
The mean feature pixel intensity with the median background subtracted (channel 1).; Type: integer; Scale: linear_scale; Channel: Cy3 Channel |
| CH2D_MEAN |
The mean feature pixel intensity with the median background subtracted (channel 2).; Type: integer; Scale: linear_scale; Channel: Cy5 channel |
| CH1B_MEAN |
Mean intensities of background pixels of Cy3.; Type: integer; Scale: linear_scale; Background |
| CH2B_MEAN |
Mean intensities of background pixels of Cy5.; Type: integer; Scale: linear_scale; Background |
| PERGTBCH1I_1SD |
The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale |
| PERGTBCH2I_1SD |
The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale |
| PIX_RAT2_MEDIAN |
Contains median of Ch2PI-CH2B/Ch1PI-CH1B where Ch1PI & Ch2PI represent single pixel intensities.; Type: float; Scale: linear_scale |
| TOT_SPIX |
Count of the number of pixels in the spot.; Type: integer; Scale: linear_scale |
| TOT_BPIX |
Number of background pixels.; Type: integer; Scale: linear_scale |
| REGR |
The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale |
| CORR |
The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high LOG_RAT2N_MEDIANs imply better fit & good spot quality.; Type: float; Scale: linear_scale |
| TOP |
Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale |
| BOT |
Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale |
| LEFT |
Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale |
| RIGHT |
Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale |
| FLAG |
User defined spot flag (default 0).; Type: integer; Scale: linear_scale |
| CH2IN_MEAN |
Normalized LOG_RAT2N_MEDIAN of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel |
| CH2BN_MEDIAN |
Normalized LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background |
| CH2DN_MEAN |
Normalized LOG_RAT2N_MEDIAN of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel |
| RAT2N_MEAN |
Type: float; Scale: linear_scale |
| RAT1N_MEAN |
Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale |
| VALUE |
Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2 |
