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Sample GSM675162 Query DataSets for GSM675162
Status Public on Feb 08, 2012
Title Sro9 3
Sample type RNA
 
Channel 1
Source name total RNA SRO9-TAP
Organism Saccharomyces cerevisiae
Characteristics reference: total RNA SRO9-TAP
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name IP RNA SRO9-TAP
Organism Saccharomyces cerevisiae
Characteristics experiment: IP RNA SRO9-TAP
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol GenePix 4200A
Description Simple annotation: RNA coimmunoprecipitation, Copper
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77143.gif
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 Feb 14, 2011
Last update date Feb 08, 2012
Contact name Andre Gerber
E-mail(s) [email protected]
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 GPL8306
Series (2)
GSE27310 Slf1p and Sro9p affinity isolations
GSE27312 Slf1p and Sro9p affinity isolations; SLF1 overexpression

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
1 324 850 35 49 289 801 320 861 35 49 285 812 0 0 72 189 6 9 100 100 100 100 1090 1097 .361 2.772 2.849 2.787 2.794 1.156 32 236 2.873 .98 70 1890 7080 56 63 53 60 0 708 41 667 2.308 717 676 .433 2.372 1.206 1.246
2 82 142 34 47 48 95 82 142 35 48 48 95 0 0 17 22 7 9 100 100 100 100 143 143 .505 1.979 1.979 2.022 1.969 1.465 32 176 1.966 .89 60 2100 7090 58 64 75 81 0 118 39 79 1.648 118 79 .607 1.648 .721 .721
3 259 630 33 47 226 583 264 665 34 47 231 618 0 0 55 114 6 7 100 100 100 100 809 849 .388 2.58 2.675 2.609 2.627 1.152 32 176 2.606 .98 60 2320 7080 57 63 97 103 0 525 39 485 2.148 554 515 .466 2.227 1.103 1.155
4 41 52 36 49 5 3 38 50 37 50 2 1 0 0 12 13 6 10 37 23 23 8 8 3 1.667 .6 .5 1.056 .854 2.784 80 560 2.122 .3 100 2530 7080 55 65 116 126 -50 43 41 2 .5 42 1 2.002 .416 -1.001 -1.264
5 108 75 36 52 72 23 111 77 36 54 75 25 0 0 27 13 7 11 96 78 93 59 95 100 3.13 .319 .333 .307 .324 1.936 32 176 .292 .66 60 2760 7070 56 62 141 147 0 62 43 19 .266 64 21 3.76 .278 -1.911 -1.849
6 103 83 37 50 66 33 104 78 37 51 67 28 0 0 12 22 5 9 100 91 100 66 99 95 2 .5 .418 .424 .477 2.016 12 68 .825 .64 40 2980 7090 59 63 164 168 0 69 42 27 .416 65 23 2.402 .348 -1.264 -1.523
7 193 387 44 67 149 320 187 402 48 71 143 335 0 0 45 91 14 21 100 100 100 100 469 478 .466 2.148 2.343 2.147 2.149 1.239 32 236 2.25 .96 70 3200 7080 56 63 184 191 0 322 56 266 1.788 335 279 .559 1.95 .838 .964
8 279 445 43 62 236 383 273 429 49 70 230 367 0 0 53 95 20 31 100 100 100 100 619 597 .616 1.623 1.596 1.612 1.601 1.206 32 236 1.658 .97 70 3420 7080 56 63 206 213 0 371 52 319 1.351 357 306 .74 1.329 .434 .41
9 125 153 42 60 83 93 133 150 47 67 91 90 0 0 31 45 22 30 100 96 90 71 176 181 .892 1.12 .989 1.061 1.016 1.47 32 236 1.349 .91 70 3640 7090 57 64 228 235 0 127 50 77 .933 125 75 1.072 .823 -.1 -.28
10 123 134 38 54 85 80 118 130 45 64 80 76 0 0 27 36 25 37 100 90 93 53 165 156 1.063 .941 .95 .889 .899 1.512 32 236 1.131 .85 70 3860 7090 57 64 250 257 0 112 45 67 .784 108 63 1.276 .791 -.352 -.338
11 425 999 37 53 388 946 439 1087 40 57 402 1034 0 0 126 323 13 19 100 100 100 100 1334 1436 .41 2.438 2.572 2.374 2.48 1.18 32 236 2.474 .99 70 4080 7090 57 64 272 279 0 832 44 788 2.03 905 861 .493 2.142 1.021 1.099
12 151 204 34 46 117 158 152 206 36 47 118 160 0 0 30 44 22 8 100 100 100 100 275 278 .741 1.35 1.356 1.343 1.382 1.371 32 176 1.396 .94 60 4310 7080 57 63 296 302 0 170 38 132 1.124 172 133 .889 1.129 .169 .175
13 109 116 33 45 76 71 112 117 34 45 79 72 0 0 26 28 6 8 100 98 100 96 147 151 1.07 .934 .911 .906 .876 1.455 52 340 .975 .91 80 4520 7080 56 64 316 324 0 97 37 59 .778 97 60 1.286 .759 -.362 -.398
14 92 157 33 45 59 112 93 159 33 45 60 114 0 0 16 34 5 8 100 100 100 100 171 174 .527 1.898 1.9 1.852 1.918 1.38 52 340 1.989 .92 80 4740 7080 56 64 338 346 0 131 37 93 1.581 132 95 .633 1.582 .66 .662
15 163 249 34 46 129 203 168 244 36 50 134 198 0 0 40 75 11 16 100 100 98 100 332 332 .635 1.574 1.478 1.536 1.553 1.294 52 340 1.628 .96 80 4960 7080 56 64 360 368 0 207 38 169 1.31 203 165 .763 1.23 .39 .299
16 312 731 34 46 278 685 333 773 37 49 299 727 0 0 115 309 11 15 100 98 100 98 963 1026 .406 2.464 2.431 2.3 2.499 1.393 52 420 2.545 .98 90 5190 7090 56 65 382 391 0 609 38 570 2.052 644 605 .487 2.024 1.037 1.018
17 220 467 34 46 186 421 234 497 35 47 200 451 0 0 61 165 11 14 100 100 98 98 607 651 .442 2.263 2.255 2.152 2.192 1.414 52 340 2.37 .97 80 5400 7090 57 65 404 412 0 389 38 351 1.885 414 376 .531 1.878 .914 .909
18 130 159 35 47 95 112 130 155 37 52 95 108 0 0 30 34 14 29 98 98 98 96 207 203 .848 1.179 1.137 1.202 1.154 1.352 52 340 1.233 .91 80 5620 7090 57 65 426 434 0 132 39 93 .982 129 90 1.019 .947 -.027 -.079
19 244 448 34 46 210 402 253 468 34 46 219 422 0 0 49 99 6 7 100 100 100 100 612 641 .522 1.914 1.927 1.901 1.909 1.149 32 236 1.943 .98 70 5850 7080 56 63 449 456 0 373 38 335 1.594 390 351 .627 1.604 .673 .682
20 63 118 40 54 23 64 61 117 41 55 21 63 0 0 12 21 8 12 96 100 71 96 87 84 .359 2.783 3 2.945 2.739 1.62 32 236 2.989 .68 70 1880 7310 79 86 52 59 0 98 45 53 2.317 97 52 .432 2.498 1.212 1.321

Total number of rows: 10944

Table truncated, full table size 2299 Kbytes.




Supplementary data files not provided
Processed data provided as supplementary file
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