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Sample GSM73570 Query DataSets for GSM73570
Status Public on Sep 09, 2005
Title 4' 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 4' post rif
Organism Escherichia coli
Characteristics MG1655 4' post rif
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA decay, Rifampicin
Image: http://smd.stanford.edu/MicroArray/gifs/2000-08/8378.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

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1B_MEAN CH2B_MEAN PERGTBCH1I_1SD PERGTBCH2I_1SD PIX_RAT2_MEDIAN TOT_SPIX TOT_BPIX REGR CORR TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN RAT1N_MEAN VALUE
1 988 572 57 104 931 468 58 109 73 66 .528 112 1435 .499 .932 86 98 77 89 0 1122 204 918 .986 1.015 -.021
2 95 120 62 107 33 13 68 113 20 16 .721 112 1230 .551 .663 86 98 99 111 0 235 210 25 .772 1.295 -.373
3 1309 705 65 109 1244 596 74 116 86 75 .488 112 1241 .467 .935 86 98 115 127 0 1382 214 1169 .939 1.064 -.09
4 244 188 64 108 180 80 76 116 62 43 .554 112 1241 .394 .747 85 97 137 149 0 369 212 157 .871 1.148 -.198
5 82 114 65 109 17 5 79 118 15 16 .602 112 1174 .344 .501 85 97 155 167 0 224 214 10 .577 1.734 -.794
6 284 194 68 114 216 80 82 122 62 39 .539 112 1099 .309 .769 85 97 173 185 0 380 224 157 .726 1.377 -.462
7 12692 7037 68 113 12624 6924 83 123 98 93 .529 208 1024 .547 .974 82 98 187 203 0 13798 222 13576 1.075 .93 .105
8 3519 2014 64 112 3455 1902 85 124 85 85 .528 208 1038 .541 .951 82 98 205 221 0 3949 220 3729 1.079 .926 .11
9 2582 1573 60 110 2522 1463 78 122 100 99 .563 156 1076 .582 .962 83 97 226 240 0 3084 216 2869 1.137 .879 .186
10 1668 1091 61 111 1607 980 69 119 95 92 .586 156 1109 .614 .955 82 96 245 259 0 2139 218 1922 1.196 .836 .258
11 706 497 62 111 644 386 67 118 100 91 .575 156 1108 .598 .908 82 96 263 277 0 975 218 757 1.175 .851 .233
12 878 669 63 113 815 556 75 121 90 89 .646 156 1115 .684 .94 82 96 281 295 0 1312 222 1090 1.338 .748 .42
13 63 111 65 115 -2 -4 82 123 2 7 2.111 112 1145 .272 .337 83 95 300 312 0 218 225 -8 null null null
14 65 119 65 115 null 4 76 121 2 10 2.389 112 1164 .181 .179 82 94 314 326 0 233 225 8 null null null
15 66 117 68 113 -2 4 82 120 2 14 2.818 112 1191 .198 .235 82 94 329 341 0 229 222 8 null null null
16 72 120 71 113 1 7 81 120 3 10 2.875 112 1208 .285 .269 82 94 347 359 0 235 222 14 13.725 .073 3.779
17 74 117 77 119 -3 -2 83 125 1 11 2.762 112 1215 .29 .183 81 93 365 377 0 229 233 -4 null null null
18 88 138 83 122 5 16 94 127 6 20 3.083 112 1184 .283 .27 81 93 383 395 0 271 239 31 6.275 .159 2.65
19 90 121 95 126 -5 -5 106 132 0 7 4.333 112 1176 .179 .198 81 93 402 414 0 237 247 -10 null null null
20 113 145 113 138 null 7 134 148 3 15 2.167 112 1179 .339 .314 81 93 420 432 0 284 271 14 null null null

Total number of rows: 7040

Table truncated, full table size 777 Kbytes.




Supplementary data files not provided
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