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Sample GSM259463 Query DataSets for GSM259463
Status Public on Aug 26, 2008
Title BY4741 mock (3)
Sample type RNA
 
Channel 1
Source name BY4741 tot. RNA extract (3)
Organism Saccharomyces cerevisiae
Characteristics BY4741 tot. RNA extract (3)
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name BY4741 RNA-IP (3)
Organism Saccharomyces cerevisiae
Characteristics BY4741 RNA-IP (3)
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol Gerber et al. (2004) PLoS Biology; The protocol can be found in the Series supplementary file
 
 
Hybridization protocol not provided
Scan protocol Scanner Make = Axon Instruments (V1.00); Scanner Model = GenePix 4000B [81971]; Scanning software = AxImageIO
Description Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/37361.gif
Strain Name: not tagged
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Jan 25, 2008
Last update date Aug 26, 2008
Contact name Andre Gerber
E-mail(s) andre.gerber@pharma.ethz.ch
Phone +41 44 6337378
Fax +41 44 6337364
Organization name Swiss Federal Institute of Technology
Department Institute of Pharmaceutical Science
Street address Wolfgang Pauli Str. 10, HCI H396
City ETH Hoenggerberg, Zuerich
ZIP/Postal code ZH
Country Switzerland
 
Platform ID GPL6419
Series (1)
GSE10279 Khd1p associated mRNAs

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEAN Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEDIAN The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_MEDIAN The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH1D_MEAN The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN .The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1I_MEDIAN Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEDIAN Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEAN The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background
CH1D_MEDIAN The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH2D_MEDIAN The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH1_PER_SAT The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale
CH2_PER_SAT The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale
CH1I_SD The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_SD The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_SD The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_SD The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; 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
PERGTBCH1I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
SUM_MEAN The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
SUM_MEDIAN The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
RAT1_MEAN Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio.; Type: float; Scale: linear_scale
RAT2_MEAN The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_MEDIAN The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEAN The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEDIAN The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_SD The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale
TOT_SPIX The total number of feature pixels.; Type: integer; Scale: linear_scale
TOT_BPIX The total 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
DIAMETER The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale
X_COORD X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
Y_COORD Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; 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 The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; 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
CH2IN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; 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
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale
LOG_RAT2N_MEAN 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
VALUE Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1I_MEDIAN CH2I_MEDIAN CH1B_MEAN CH2B_MEAN CH1D_MEDIAN CH2D_MEDIAN CH1_PER_SAT CH2_PER_SAT CH1I_SD CH2I_SD CH1B_SD CH2B_SD PERGTBCH1I_1SD PERGTBCH2I_1SD PERGTBCH1I_2SD PERGTBCH2I_2SD SUM_MEAN SUM_MEDIAN RAT1_MEAN RAT2_MEAN RAT2_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN RAT2_SD TOT_SPIX TOT_BPIX REGR CORR DIAMETER X_COORD Y_COORD TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN LOG_RAT2N_MEAN VALUE
1 109 36 99 31 10 5 99 32 103 32 0 1 0 0 30 17 25 5 23 25 8 16 15 1 2 .5 null .505 .462 3.427 80 442 .277 .5 100 2680 17720 31 41 51 61 -50 328 282 46 4.55 291 9 .22 null 2.186 null
2 115 35 108 32 7 3 110 32 112 33 2 0 0 0 30 13 27 5 16 18 7 10 10 2 2.333 .429 null .291 .333 3.305 80 430 .182 .52 100 2850 17720 31 41 68 78 -50 319 291 27 3.9 291 0 .256 null 1.964 null
3 119 40 110 32 9 8 110 35 115 32 0 3 0 0 36 17 27 5 21 31 10 18 17 3 1.125 .889 null .302 .32 3.282 80 432 .193 .47 100 3030 17730 32 42 86 96 -50 364 291 73 8.089 319 27 .124 null 3.016 null
4 117 33 112 31 5 2 111 30 115 31 -1 -1 0 0 30 12 24 5 18 17 10 11 7 -2 2.5 .4 null .24 .224 3.119 80 420 .133 .43 100 3200 17730 32 42 103 113 -50 300 282 18 3.64 273 -9 .275 null 1.864 null
5 117 44 113 33 4 11 108 35 117 34 -5 2 0 0 34 25 27 5 17 27 8 21 15 -3 .364 2.75 null .447 .38 2.929 80 432 .337 .53 100 3370 17730 32 42 120 130 -50 400 300 100 25.027 319 18 .04 null 4.645 null
6 155 40 125 33 30 7 141 35 142 35 16 2 0 0 71 21 53 8 22 17 5 12 37 18 4.286 .233 .125 .183 .179 3.122 80 357 .155 .69 100 3540 17730 32 42 137 147 -50 364 300 64 2.123 319 18 .471 1.138 1.086 .186
7 223 52 127 38 96 14 218 48 143 40 91 10 0 0 61 16 47 11 82 46 46 15 110 101 6.857 .146 .11 .135 .133 2.619 156 672 .102 .48 140 3690 17740 31 45 150 164 -100 473 346 127 1.327 437 91 .753 1 .408 0
8 225 53 144 41 81 12 196 46 153 42 52 5 0 0 97 25 43 10 60 30 20 17 93 57 6.75 .148 .096 .17 .157 3.365 80 441 .178 .76 100 3880 17730 32 42 171 181 -50 482 373 109 1.348 419 46 .742 .875 .431 -.193
9 231 53 123 39 108 14 218 46 136 40 95 7 0 0 72 20 42 9 93 32 58 20 122 102 7.714 .13 .074 .099 .102 2.314 80 507 .114 .53 110 4080 17740 32 43 190 201 -100 482 355 127 1.18 419 64 .848 .671 .238 -.577
10 656 90 116 40 540 50 679 87 127 42 563 47 0 0 154 25 36 9 100 97 97 92 590 610 10.8 .093 .083 .087 .084 1.542 80 426 .086 .82 110 4250 17750 33 44 207 218 0 819 364 455 .843 792 428 1.187 .76 -.247 -.396
11 207 47 131 39 76 8 197 44 143 40 66 5 0 0 54 13 41 10 77 31 35 11 84 71 9.5 .105 .076 .142 .133 2.836 80 388 .152 .59 100 4390 17730 32 42 222 232 -50 428 355 73 .958 400 46 1.044 .689 -.062 -.537
12 239 54 129 40 110 14 229 50 145 42 100 10 0 0 102 19 48 9 87 55 55 20 124 110 7.857 .127 .1 .101 .109 2.09 120 592 .092 .53 130 4580 17750 32 45 239 252 -100 491 364 127 1.158 455 91 .863 .91 .212 -.136
13 2015 249 131 36 1884 213 2194 264 194 43 2063 228 0 0 832 72 219 24 95 98 92 96 2097 2291 8.845 .113 .111 .123 .108 1.828 120 415 .102 .94 120 4750 17750 33 45 257 269 0 2266 328 1938 1.029 2403 2075 .972 1.006 .041 .008
14 14219 1038 136 38 14083 1000 4043 653 188 44 3907 615 0 0 15417 1016 177 23 83 80 74 71 15083 4522 14.083 .071 .157 .091 .072 2.232 208 906 .065 .96 160 4900 17760 32 48 270 286 0 9446 346 9101 .646 5943 5597 1.547 1.433 -.63 .519
15 53585 5806 144 45 53441 5761 56922 6095 184 49 56778 6050 2 0 12104 1134 95 22 100 100 100 100 59202 62828 9.276 .108 .107 .11 .107 1.328 80 483 .106 .98 110 5080 17750 33 44 290 301 0 52838 410 52428 .981 55468 55058 1.019 .97 -.028 -.044
16 2475 243 138 35 2337 208 2570 249 164 40 2432 214 0 0 762 47 82 21 100 100 100 100 2545 2646 11.236 .089 .088 .093 .086 1.39 80 496 .082 .95 110 5260 17750 33 44 308 319 0 2211 319 1893 .81 2266 1948 1.235 .801 -.304 -.321
17 1084 120 139 36 945 84 1084 120 149 38 945 84 0 0 276 26 55 8 100 100 100 100 1029 1029 11.25 .089 .089 .089 .084 1.541 80 420 .078 .86 100 5430 17750 34 44 326 336 0 1092 328 764 .809 1092 764 1.236 .809 -.306 -.306
18 11965 1218 148 36 11817 1182 12414 1231 154 37 12266 1195 0 0 2996 295 51 8 100 100 100 100 12999 13461 9.997 .1 .097 .101 .099 1.198 80 483 .098 .96 110 5600 17750 33 44 342 353 0 11085 328 10757 .91 11203 10875 1.099 .887 -.136 -.174
19 1629 154 176 41 1453 113 1635 154 197 43 1459 113 0 0 444 29 76 12 100 100 100 100 1566 1572 12.858 .078 .077 .079 .074 1.389 80 468 .073 .91 110 5770 17760 34 45 359 370 0 1401 373 1028 .708 1401 1028 1.413 .705 -.499 -.505
20 1396 160 161 39 1235 121 1393 159 181 40 1232 120 0 0 415 37 71 10 100 100 100 100 1356 1352 10.207 .098 .097 .101 .094 1.544 80 479 .09 .93 110 5940 17750 33 44 376 387 0 1456 355 1101 .892 1447 1092 1.122 .886 -.165 -.174

Total number of rows: 9984

Table truncated, full table size 2135 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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