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Sample GSM75952 Query DataSets for GSM75952
Status Public on Sep 24, 2005
Title mec1_plus_gamma_30_min
Sample type RNA
 
Channel 1
Source name asynchronous_mec5
Organism Saccharomyces cerevisiae
Characteristics asynchronous_mec5
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name DES459-mec1-_plus_170_Gy_gamma_30_min
Organism Saccharomyces cerevisiae
Characteristics DES459-mec1-_plus_170_Gy_gamma_30_min
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: DNA damage, Gamma radiation
Image: http://smd.stanford.edu/MicroArray/gifs/1999-11/1252.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
1 528 666 112 65 416 601 120 67 49 54 1.462 225 1016 1.248 .877 131 148 83 100 0 601 59 543 1.304 .767 .383
2 109 66 113 64 null 2 114 66 8 11 1.218 225 710 .375 .466 131 148 100 117 0 60 58 2 null null null
3 417 476 112 64 305 412 115 66 42 49 1.313 205 734 1.061 .856 131 148 118 135 0 430 58 372 1.22 .82 .287
4 133 87 113 66 20 21 117 67 11 14 .947 156 896 .821 .885 132 146 136 150 0 79 60 19 .948 1.055 -.077
5 260 279 112 66 148 213 118 67 23 32 1 156 958 1.018 .794 132 146 155 169 0 252 60 192 1.3 .77 .378
6 111 68 113 66 null 2 115 67 4 7 .75 225 795 .743 .628 131 148 171 188 0 61 60 2 null null null
7 112 64 112 66 null null 113 67 3 0 .368 225 731 .072 .152 131 148 188 205 0 58 60 -2 null null null
8 118 69 112 66 6 3 114 66 7 4 .5 225 720 -.019 -.034 131 148 206 223 0 62 60 3 .451 2.215 -1.147
9 266 257 115 67 151 190 118 68 10 17 .767 225 694 .237 .195 131 148 223 240 0 232 60 172 1.136 .88 .184
10 145 80 116 67 29 13 120 68 12 12 .6 225 694 .035 .285 131 148 240 257 0 72 60 12 .405 2.471 -1.305
11 118 71 118 69 null 2 122 72 2 2 .5 222 693 .03 .054 131 148 257 274 0 64 62 2 null null null
12 120 65 116 69 4 null 120 71 5 0 .5 225 770 .03 .06 129 146 273 290 0 59 62 -4 null null null
13 115 68 115 68 null null 119 71 2 2 .5 225 741 .052 .075 129 146 290 307 0 61 61 0 null null null
14 126 66 116 68 10 null 188 84 6 1 .364 225 735 .054 .177 129 146 307 324 0 60 61 -2 null null null
15 124 68 122 70 2 null 194 89 4 3 .583 225 720 .093 .121 129 146 325 342 0 61 63 -2 null null null
16 141 75 128 72 13 3 196 89 4 4 .407 225 752 .096 .365 128 145 342 359 0 68 65 3 .208 4.799 -2.263
17 135 77 128 71 7 6 131 72 3 7 .695 225 784 .129 .223 128 145 359 376 0 70 64 5 .774 1.292 -.37
18 124 69 125 70 null null 127 72 4 2 .529 225 836 .052 .091 128 145 378 395 0 62 63 -1 null null null
19 124 69 121 67 3 2 122 68 5 3 .588 225 766 .03 .06 130 147 397 414 0 62 60 2 .602 1.661 -.732
20 124 66 118 65 6 1 119 66 4 4 .5 225 746 -.031 -.062 130 147 414 431 0 60 59 1 .15 6.645 -2.732

Total number of rows: 8448

Table truncated, full table size 906 Kbytes.




Supplementary data files not provided
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