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Sample GSM75964 Query DataSets for GSM75964
Status Public on Sep 24, 2005
Title wt_plus_gamma_45_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_45_min
Organism Saccharomyces cerevisiae
Characteristics DES460-wild_type-_plus_170_Gy_gamma_45_min
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: DNA damage, Gamma radiation
Image: http://smd.stanford.edu/MicroArray/gifs/1999-10/980.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
1 671 1244 75 118 596 1126 77 123 57 63 1.837 225 1016 1.687 .871 84 101 94 111 0 776 74 703 1.179 .848 .237
2 76 131 75 120 1 11 80 126 10 10 1.71 225 760 1.286 .652 84 101 111 128 0 82 75 7 6.864 .146 2.779
3 776 1194 78 123 698 1071 88 134 68 61 1.726 225 774 1.079 .705 85 102 129 146 0 745 77 668 .957 1.044 -.063
4 82 129 79 122 3 7 87 133 14 11 2.2 156 889 1.174 .675 86 100 148 162 0 80 76 4 1.456 .687 .542
5 196 362 76 121 120 241 81 129 22 22 1.719 156 935 1.703 .768 86 100 165 179 0 226 76 150 1.253 .798 .326
6 93 169 76 121 17 48 81 130 18 23 1.739 225 830 .896 .497 85 102 182 199 0 105 76 30 1.762 .568 .817
7 85 165 77 120 8 45 79 126 11 22 2.324 225 741 4.022 .471 86 103 199 216 0 103 75 28 3.51 .285 1.811
8 82 155 79 125 3 30 81 133 8 14 1.839 225 761 .683 .158 86 103 217 234 0 97 78 19 6.24 .16 2.641
9 80 131 79 125 1 6 81 131 5 10 1.944 225 756 .343 .172 86 103 235 252 0 82 78 4 3.744 .267 1.905
10 78 125 78 122 null 3 80 127 6 6 1.722 225 756 .21 .132 86 103 252 269 0 78 76 2 null null null
11 83 128 77 122 6 6 81 127 9 7 1.326 225 762 .746 .497 87 104 270 287 0 80 76 4 .624 1.603 -.68
12 81 121 78 124 3 null 80 127 10 3 2.176 225 804 .261 .175 87 104 287 304 0 76 77 -2 null null null
13 82 169 79 125 3 44 81 128 8 10 2 225 786 7.313 .423 87 104 305 322 0 105 78 27 9.152 .109 3.194
14 81 126 80 126 1 null 83 132 4 3 1.636 225 775 .122 .09 87 104 322 339 0 79 79 0 null null null
15 80 122 80 127 null null 83 133 5 4 1.444 225 746 .01 .007 88 105 340 357 0 76 79 -3 null null null
16 84 128 82 124 2 4 90 138 6 6 1.038 225 767 .202 .122 88 105 358 375 0 80 77 2 1.248 .801 .32
17 80 127 85 123 null 4 92 136 2 6 2.364 225 766 -.167 -.087 88 105 375 392 0 79 77 2 null null null
18 115 175 87 122 28 53 89 132 23 34 2.25 225 746 1.06 .744 88 105 393 410 0 109 76 33 1.181 .847 .24
19 89 133 86 123 3 10 90 133 8 8 1.25 225 741 .124 .051 89 106 410 427 0 83 77 6 2.08 .481 1.057
20 84 123 82 120 2 3 86 126 4 5 1.522 225 761 .094 .057 89 106 428 445 0 77 75 2 .936 1.068 -.095

Total number of rows: 8448

Table truncated, full table size 922 Kbytes.




Supplementary data files not provided
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