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Sample GSM75946 Query DataSets for GSM75946
Status Public on Sep 24, 2005
Title wt_plus_gamma_20_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_20_min
Organism Saccharomyces cerevisiae
Characteristics DES460-wild_type-_plus_170_Gy_gamma_20_min
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: DNA damage, Gamma radiation
Image: http://smd.stanford.edu/MicroArray/gifs/1999-10/978.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 1080 1109 97 122 983 987 103 130 58 62 1.103 225 1005 .82 .771 55 72 122 139 0 1098 121 977 .994 1.006 -.009
2 106 127 109 142 null null 146 196 7 7 1.037 225 723 1.025 .741 55 72 140 157 0 126 141 null null null null
3 1207 1298 110 143 1097 1155 150 198 70 62 .968 225 720 .881 .798 55 72 157 174 0 1285 142 1143 1.042 .96 .059
4 105 133 95 124 10 9 103 142 11 9 1.751 225 732 .928 .748 55 72 175 192 0 132 123 9 .9 1.111 -.152
5 241 323 92 119 149 204 95 124 28 24 1.133 225 756 .706 .565 55 72 192 209 -100 320 118 202 1.356 .738 .439
6 105 127 92 114 13 13 96 120 10 12 1.507 225 756 .954 .768 55 72 210 227 0 126 113 13 1 1 0
7 93 127 93 116 null 11 102 129 5 7 1.4 225 766 -.017 -.012 55 72 227 244 0 126 115 11 null null null
8 87 117 93 126 null null 104 144 4 4 2.333 225 756 .196 .133 55 72 245 262 0 116 125 null null null null
9 137 451 94 131 43 320 104 147 10 11 1.75 225 756 5.782 .519 55 72 262 279 0 447 130 317 7.372 .136 2.882
10 98 139 96 133 2 6 100 141 6 8 2.574 225 756 .037 .024 55 72 280 297 0 138 132 6 3 .333 1.585
11 98 140 96 129 2 11 98 135 7 7 2 225 787 -.015 -.011 55 72 297 314 0 139 128 11 5.5 .182 2.459
12 99 121 96 120 3 1 100 125 5 8 1.64 225 846 .14 .127 55 72 315 332 0 120 119 1 .333 3 -1.585
13 102 119 96 118 6 1 101 135 8 5 1.229 225 767 .034 .027 56 73 333 350 0 118 117 1 .167 6 -2.585
14 91 123 95 122 null 1 100 141 4 8 2.071 225 726 .024 .016 56 73 350 367 0 122 121 1 null null null
15 98 137 94 128 4 9 100 140 9 8 1.143 225 720 .249 .112 56 73 368 385 0 136 127 9 2.25 .444 1.17
16 97 142 95 131 2 11 116 156 7 10 2.1 225 752 .257 .156 56 73 385 402 0 141 130 11 5.5 .182 2.459
17 102 136 95 125 7 11 119 151 10 10 1.231 225 751 .351 .222 56 73 403 420 0 135 124 11 1.571 .636 .652
18 98 128 97 122 1 6 116 150 6 8 1.333 225 741 -.004 -.003 56 73 420 437 0 127 121 6 6 .167 2.585
19 119 132 96 117 23 15 101 131 16 11 1.048 225 756 .187 .217 56 73 438 455 0 131 116 15 .652 1.533 -.617
20 102 119 95 112 7 7 100 121 9 5 1.152 225 766 -.014 -.013 56 73 455 472 0 118 111 7 1 1 0

Total number of rows: 8448

Table truncated, full table size 932 Kbytes.




Supplementary data files not provided
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