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Sample GSM675159 Query DataSets for GSM675159
Status Public on Feb 08, 2012
Title Fpr1 2
Sample type RNA
 
Channel 1
Source name total RNA Fpr1-TAP
Organism Saccharomyces cerevisiae
Characteristics reference: total RNA Fpr1-TAP
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name IP RNA Fpr1-TAP
Organism Saccharomyces cerevisiae
Characteristics experiment: IP RNA Fpr1-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/2008-02/78762.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
1 499 213 56 87 443 126 528 219 68 89 472 132 0 0 111 51 92 24 100 93 100 93 569 604 3.516 .284 .28 .261 .274 1.6 32 236 .277 .87 70 2100 7040 28 35 42 49 0 1021 417 604 1.363 1050 633 .734 1.34 .447 .423
2 197 106 57 89 140 17 127 101 63 91 70 12 0 0 314 57 31 20 73 26 53 11 157 82 8.235 .121 .171 .232 .196 3.042 52 340 .167 .83 80 2290 7020 26 34 61 69 -100 508 427 81 .582 484 58 1.718 .822 -.781 -.283
3 430 232 56 89 374 143 448 241 73 93 392 152 0 0 131 70 95 28 93 93 87 87 517 544 2.615 .382 .388 .364 .379 1.422 32 236 .393 .9 70 2540 7030 27 34 86 93 0 1112 427 685 1.833 1155 729 .546 1.858 .874 .894
4 69 92 57 89 12 3 67 92 62 91 10 3 0 0 22 21 31 21 18 13 2 3 15 13 4 .25 .3 .915 1.083 3.727 80 560 .927 .12 100 2760 7030 26 36 107 117 -50 441 427 14 1.198 441 14 .835 1.438 .261 .524
5 137 92 59 92 78 0 130 85 63 92 71 -7 0 0 25 26 28 21 100 16 75 8 78 64 null null null .165 .125 4.674 12 104 .028 .03 50 2980 7040 29 34 131 136 0 441 441 0 null 407 -34 null null null null
6 79 90 56 91 23 -1 65 87 156 114 9 -4 0 0 54 22 1110 311 0 0 0 0 22 5 null null null .974 .915 3.833 80 560 .281 .99 100 3200 7030 26 36 151 161 -50 431 436 -5 null 417 -19 null null null null
7 229 116 57 88 172 28 233 119 62 90 176 31 0 0 58 20 39 21 96 68 90 18 200 207 6.143 .163 .176 .164 .171 1.681 32 236 .17 .53 70 3430 7040 28 35 175 182 0 556 422 134 .78 570 149 1.282 .844 -.358 -.244
8 178 115 52 83 126 32 180 117 54 84 128 34 0 0 55 27 13 16 100 62 100 53 158 162 3.938 .254 .266 .243 .378 2.537 32 176 .229 .56 60 3650 7040 29 35 198 204 0 551 398 153 1.217 561 163 .822 1.273 .284 .348
9 93 96 55 89 38 7 93 91 72 93 38 2 0 0 22 20 122 29 0 16 0 0 45 40 5.429 .184 .053 .568 .451 4.121 12 68 .898 .28 40 3870 7030 29 33 221 225 0 460 427 34 .883 436 10 1.133 .252 -.18 -1.987
10 105 100 53 86 52 14 104 112 55 86 51 26 0 0 21 28 14 19 100 58 83 33 66 77 3.714 .269 .51 .842 .833 1.701 12 68 .336 .1 40 4100 7030 29 33 244 248 0 479 412 67 1.29 537 125 .775 2.443 .368 1.289
11 243 165 54 85 189 80 243 174 56 88 189 89 0 0 47 36 13 19 100 100 100 84 269 278 2.363 .423 .471 .389 .42 1.61 32 176 .41 .82 60 4320 7040 29 35 265 271 0 791 407 383 2.029 834 427 .493 2.257 1.021 1.174
12 78 93 56 89 22 4 72 90 469 899 16 1 0 0 28 17 2919 5682 0 0 0 0 26 17 5.5 .182 .063 .772 1 6.221 80 560 .39 .05 100 4530 7030 26 36 284 294 -50 446 427 19 .871 431 5 1.148 .3 -.199 -1.739
13 123 101 52 83 71 18 126 98 53 86 74 15 0 0 29 22 11 20 100 46 96 19 89 89 3.944 .254 .203 .304 .358 2.881 52 340 .217 .21 80 4750 7040 28 36 307 315 0 484 398 86 1.215 470 72 .823 .972 .281 -.042
14 116 95 51 89 65 6 120 93 61 91 69 4 0 0 36 23 82 35 32 9 0 0 71 73 10.833 .092 .058 .269 .269 3.363 52 340 .223 .27 80 4980 7030 27 35 330 338 0 455 427 29 .442 446 19 2.26 .278 -1.176 -1.848
15 111 101 53 92 58 9 114 101 55 92 61 9 0 0 25 22 15 20 100 25 84 9 67 70 6.444 .155 .148 .25 .195 3.132 32 236 .097 .07 70 5200 7030 27 34 352 359 0 484 441 43 .744 484 43 1.345 .707 -.427 -.5
16 342 198 56 91 286 107 329 192 59 92 273 101 0 0 83 47 22 21 100 96 100 90 393 374 2.673 .374 .37 .348 .375 1.637 32 236 .353 .85 70 5400 7040 28 35 372 379 0 949 436 513 1.793 920 484 .558 1.773 .843 .826
17 169 117 55 89 114 28 172 119 55 89 117 30 0 0 38 26 13 18 100 62 100 34 142 147 4.071 .246 .256 .252 .309 2.389 32 236 .295 .5 70 5640 7040 28 35 396 403 0 561 427 134 1.177 570 144 .849 1.229 .235 .297
18 98 100 54 84 44 16 100 99 55 86 46 15 0 0 29 18 14 20 83 41 66 8 60 61 2.75 .364 .326 .396 .41 2.616 12 68 6.825 .07 40 5870 7040 30 34 421 425 0 479 403 77 1.743 475 72 .574 1.563 .801 .644
19 129 102 53 89 76 13 129 95 55 89 76 6 0 0 27 26 15 21 100 40 100 12 89 82 5.846 .171 .079 .272 .343 2.86 32 176 .194 .2 60 6080 7040 29 35 441 447 0 489 427 62 .82 455 29 1.22 .378 -.287 -1.402
20 110 99 61 91 49 8 86 94 71 93 25 3 0 0 64 28 41 24 43 18 21 6 57 28 6.125 .163 .12 .408 .438 4.164 32 236 .3 .49 70 2090 7250 49 56 41 48 0 475 436 38 .783 451 14 1.278 .575 -.354 -.798

Total number of rows: 10944

Table truncated, full table size 2274 Kbytes.




Supplementary data files not provided
Processed data provided as supplementary file
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