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Sample GSM73577 Query DataSets for GSM73577
Status Public on Sep 09, 2005
Title 8' 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 8' post rif
Organism Escherichia coli
Characteristics MG1655 8' post rif
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA decay, Rifampicin
Image: http://smd.stanford.edu/MicroArray/gifs/2000-08/8380.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
1 568 290 55 106 513 184 59 113 83 68 .345 112 1437 .347 .915 66 78 62 74 0 259 95 164 .32 3.123 -1.643
2 58 113 54 108 4 5 62 115 7 15 2.655 112 1195 .562 .446 66 78 85 97 0 101 96 4 1.116 .896 .158
3 1421 681 55 111 1366 570 64 119 83 83 .433 112 1225 .401 .952 64 76 100 112 0 608 99 509 .373 2.684 -1.424
4 227 184 57 115 170 69 68 121 58 37 .522 112 1277 .419 .84 64 76 120 132 0 164 103 62 .362 2.759 -1.464
5 101 149 59 117 42 32 68 123 16 21 1.333 112 1209 .366 .473 64 76 140 152 0 133 104 29 .68 1.47 -.556
6 404 250 65 126 339 124 84 135 74 43 .444 112 1134 .378 .906 64 76 156 168 0 223 113 111 .327 3.062 -1.614
7 13743 16917 67 131 13676 16786 106 159 99 100 1.197 208 1015 1.253 .982 64 80 171 187 0 15104 117 14988 1.096 .912 .132
8 4345 5148 64 128 4281 5020 128 183 96 100 1.14 156 1106 1.159 .964 63 77 190 204 0 4596 114 4482 1.047 .955 .066
9 2409 2891 60 123 2349 2768 117 179 96 94 1.178 156 1106 1.176 .96 63 77 210 224 0 2581 110 2471 1.052 .95 .073
10 1529 1867 59 120 1470 1747 96 156 98 96 1.171 156 1120 1.225 .97 63 77 228 242 0 1667 107 1560 1.061 .942 .086
11 719 964 61 119 658 845 74 135 87 90 1.245 156 1121 1.341 .955 63 77 248 262 0 861 106 754 1.147 .872 .197
12 989 1397 61 119 928 1278 71 129 92 91 1.387 156 1139 1.405 .959 63 77 266 280 0 1247 106 1141 1.23 .813 .298
13 62 123 61 116 1 7 76 125 4 11 4.2 112 1140 .401 .365 65 77 287 299 0 110 104 6 6.25 .16 2.644
14 56 109 61 118 -5 -9 73 125 0 7 9 112 1099 .305 .263 65 77 302 314 0 97 105 -8 null null null
15 60 117 64 116 -4 1 75 122 0 10 2.167 112 1177 .197 .171 65 77 316 328 0 104 104 1 null null null
16 64 121 67 121 -3 null 87 132 2 11 2.053 112 1207 .537 .487 65 77 335 347 0 108 108 0 null null null
17 63 124 67 123 -4 1 95 136 0 11 2.219 112 1187 .35 .428 65 77 353 365 0 111 110 1 null null null
18 64 130 66 124 -2 6 86 132 0 11 4.286 112 1181 .153 .216 65 77 371 383 0 116 111 5 null null null
19 68 122 67 126 1 -4 88 132 1 8 2.25 112 1167 .142 .218 65 77 389 401 0 109 113 -4 null null null
20 61 125 66 127 -5 -2 87 134 0 10 3.286 112 1177 .272 .306 65 77 407 419 0 112 113 -2 null null null

Total number of rows: 7040

Table truncated, full table size 776 Kbytes.




Supplementary data files not provided
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