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Sample GSM75944 Query DataSets for GSM75944
Status Public on Sep 24, 2005
Title wt_plus_gamma_10_min
Sample type RNA
 
Channel 1
Source name asynchronous_wild_type
Organism Saccharomyces cerevisiae
Characteristics asynchronous_wild_type
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name DES460-wild_type-_plus_170_Gy_gamma_10_min
Organism Saccharomyces cerevisiae
Characteristics DES460-wild_type-_plus_170_Gy_gamma_10_min
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: DNA damage, Gamma radiation
Image: http://smd.stanford.edu/MicroArray/gifs/1999-10/977.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 23, 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 GPL55
Series (1)
GSE3358 DNA damage responses and Mec1p

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 values 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 value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value 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 1151 1855 97 69 1054 1786 102 77 64 69 1.777 225 1041 1.444 .863 109 126 108 125 0 1432 53 1379 1.308 .765 .387
2 105 93 98 73 7 20 123 105 8 15 1.118 225 760 1.011 .812 109 126 126 143 0 72 56 15 2.205 .453 1.141
3 1331 1556 98 72 1233 1484 134 110 68 69 1.128 225 702 1.109 .805 110 127 143 160 0 1201 56 1145 .929 1.076 -.106
4 110 95 95 69 15 26 114 84 10 13 1.031 225 710 1.071 .745 110 127 161 178 0 73 53 20 1.338 .747 .42
5 231 280 96 71 135 209 105 82 21 39 1.017 225 745 1.205 .841 110 127 178 195 0 216 55 161 1.195 .837 .257
6 104 91 97 72 7 19 100 78 8 13 1.788 225 756 1.219 .764 110 127 196 213 0 70 56 15 2.095 .477 1.067
7 105 87 104 80 1 7 136 92 8 9 .837 225 756 .262 .091 110 127 213 230 0 67 62 5 5.403 .185 2.434
8 107 73 105 81 2 null 137 92 9 5 .8 225 756 .044 .069 110 127 231 248 0 56 63 -6 null null null
9 99 82 100 73 null 9 104 81 2 17 1.917 225 756 .282 .139 110 127 248 265 0 63 56 7 null null null
10 101 84 97 73 4 11 103 81 7 17 1.067 225 720 .038 .021 111 128 266 283 0 65 56 8 2.123 .471 1.086
11 100 73 98 72 2 1 107 80 6 12 1.266 225 751 .157 .194 111 128 283 300 0 56 56 1 .386 2.591 -1.374
12 97 73 95 69 2 4 277 269 8 16 .729 225 804 .179 .17 111 128 301 318 0 56 53 3 1.544 .648 .626
13 99 75 92 68 7 7 271 269 11 16 .87 225 796 .083 .051 111 128 318 335 0 58 52 5 .772 1.296 -.374
14 98 78 92 71 6 7 96 76 6 14 1.167 225 765 .595 .385 111 128 336 353 0 60 55 5 .901 1.11 -.151
15 139 85 98 77 41 8 154 97 22 18 .807 225 756 .105 .31 111 128 353 370 0 66 59 6 .151 6.639 -2.731
16 158 112 111 86 47 26 204 148 20 19 .81 225 743 .452 .728 112 129 371 388 0 86 66 20 .427 2.342 -1.228
17 101 88 109 84 null 4 201 145 4 8 1.375 225 725 -.025 -.011 112 129 388 405 0 68 65 3 null null null
18 96 83 101 75 null 8 141 147 4 11 1.667 225 714 .108 .036 112 129 406 423 0 64 58 6 null null null
19 121 127 98 72 23 55 125 142 6 16 1.429 225 745 1.998 .924 112 129 423 440 0 98 56 42 1.846 .542 .884
20 87 69 95 68 null 1 117 107 2 11 1.533 225 756 -.145 -.112 112 129 441 458 0 53 52 1 null null null

Total number of rows: 8448

Table truncated, full table size 924 Kbytes.




Supplementary data files not provided
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