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Sample GSM75968 Query DataSets for GSM75968
Status Public on Sep 24, 2005
Title wt_plus_gamma_120_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_120_min
Organism Saccharomyces cerevisiae
Characteristics DES460-wild_type-_plus_170_Gy_gamma_120_min
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: DNA damage, Gamma radiation
Image: http://smd.stanford.edu/MicroArray/gifs/1999-10/983.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
1 856 1513 361 137 495 1376 364 141 45 60 2.497 225 990 2.524 .916 58 75 71 88 0 968 88 880 1.778 .562 .83
2 346 149 326 137 20 12 326 141 2 10 1.036 225 696 .499 .342 58 75 88 105 0 95 88 8 .384 2.605 -1.381
3 664 1116 283 133 381 983 285 137 39 53 2.353 205 725 2.385 .897 58 75 106 123 0 714 85 629 1.65 .606 .723
4 287 177 244 126 43 51 246 128 8 11 1.176 156 863 1.709 .712 59 73 124 138 0 113 81 33 .759 1.318 -.398
5 446 733 208 124 238 609 210 125 19 38 1.727 156 934 1.524 .729 59 73 142 156 0 469 79 390 1.637 .611 .711
6 160 137 157 119 3 18 161 122 8 10 1.634 225 841 .969 .466 58 75 158 175 0 88 76 12 3.838 .261 1.94
7 113 116 125 118 null null 127 121 0 5 1.103 225 756 -.003 -.002 58 75 176 193 0 74 75 -1 null null null
8 150 128 149 122 1 6 157 124 2 7 1.25 225 756 .079 .037 58 75 193 210 0 82 78 4 3.838 .261 1.94
9 218 124 175 124 43 null 176 127 13 4 .5 225 720 -.003 -.003 59 76 211 228 0 79 79 0 null null null
10 140 122 165 122 null null 170 130 0 5 1.263 225 730 .051 .039 59 76 228 245 0 78 78 0 null null null
11 202 123 181 122 21 1 182 128 5 5 .85 222 734 .021 .023 59 76 246 263 0 79 78 1 .03 32.827 -5.037
12 235 129 214 123 21 6 216 128 1 8 1 225 810 -.009 -.006 57 74 262 279 0 83 79 4 .183 5.471 -2.452
13 216 126 210 121 6 5 209 129 0 10 .667 225 804 -.035 -.034 57 74 279 296 0 81 77 3 .533 1.876 -.908
14 138 128 150 120 null 8 157 128 3 8 1.5 225 770 .065 .064 57 74 297 314 0 82 77 5 null null null
15 106 125 104 119 2 6 111 125 6 9 1.81 225 720 .013 .015 58 75 314 331 0 80 76 4 1.919 .521 .94
16 93 121 92 115 1 6 95 125 4 8 1.615 225 752 .498 .371 58 75 332 349 0 77 74 4 3.838 .261 1.94
17 96 118 89 113 7 5 92 121 4 11 2.067 225 784 .189 .247 58 75 349 366 0 75 72 3 .457 2.188 -1.13
18 97 111 87 109 10 2 92 116 9 9 1.59 225 853 .057 .12 58 75 368 385 0 71 70 1 .128 7.816 -2.966
19 87 114 83 101 4 13 89 109 10 12 2 225 796 .039 .025 60 77 388 405 0 73 65 8 2.079 .481 1.056
20 83 103 77 95 6 8 81 100 9 12 1.286 225 756 .071 .053 60 77 405 422 0 66 61 5 .853 1.172 -.229

Total number of rows: 8448

Table truncated, full table size 915 Kbytes.




Supplementary data files not provided
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