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Sample GSM543844 Query DataSets for GSM543844
Status Public on Dec 06, 2010
Title Mock IP (3) A
Sample type RNA
 
Channel 1
Source name Extract tot. RNA BY4741
Organism Saccharomyces cerevisiae
Characteristics test: Extract total RNA BY4741
Growth protocol yeast cells expressing TAP-tagged RBP or the wild-type strain BY4741 (mock control) were grown to mid-log phase in rich medium and harvested by centrifugation.
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name Affinity isolated RNA, BY4741
Organism Saccharomyces cerevisiae
Characteristics control: Affinity isolated RNA, BY4741
Growth protocol yeast cells expressing TAP-tagged RBP or the wild-type strain BY4741 (mock control) were grown to mid-log phase in rich medium and harvested by centrifugation.
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol GenePix 4200A
Description Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/72573.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 May 17, 2010
Last update date Dec 06, 2010
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 (3)
GSE21864 RNA-affinity isolations 13 RBPs
GSE24003 Gis2 affinity isolations
GSE24005 Gis2 studies

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
1 743 430 130 309 613 121 791 408 130 314 661 99 0 0 191 108 33 76 100 62 100 37 734 760 5.066 .197 .15 .211 .235 1.867 32 176 .22 .61 60 2030 7300 59 65 60 66 0 2993 2151 842 1.374 2840 689 .728 1.042 .458 .06
2 465 351 129 300 336 51 424 364 132 303 295 64 0 0 137 66 29 66 100 33 100 8 387 359 6.588 .152 .217 .255 .215 1.738 12 104 .079 .1 50 2230 7290 58 63 80 85 0 2443 2088 355 1.056 2533 445 .947 1.51 .079 .594
3 621 389 131 304 490 85 632 383 133 320 501 79 0 0 103 90 30 84 100 50 100 25 575 580 5.765 .173 .158 .125 .198 4.737 12 104 .13 .31 50 2470 7290 58 63 104 109 0 2707 2116 592 1.207 2666 550 .828 1.097 .272 .134
4 318 369 133 300 185 69 314 341 134 310 181 41 0 0 71 118 31 71 100 33 91 25 254 222 2.681 .373 .227 .356 .543 5.997 12 104 .843 .1 50 2680 7300 59 64 125 130 0 2568 2088 480 2.596 2373 285 .385 1.576 1.376 .657
5 388 410 129 319 259 91 364 416 132 319 235 97 0 0 87 44 30 83 100 66 100 0 350 332 2.846 .351 .413 .298 .335 2.451 12 68 .461 .4 40 2900 7290 59 63 148 152 0 2853 2220 633 2.445 2895 675 .409 2.873 1.29 1.522
6 178 331 125 296 53 35 150 329 130 302 25 33 0 0 81 88 34 77 46 27 26 10 88 58 1.514 .66 1.32 1.484 1.5 4.117 80 560 4.986 .17 100 3120 7290 56 66 167 177 -50 2304 2060 244 4.596 2290 230 .218 9.187 2.2 3.2
7 385 356 127 299 258 57 394 348 125 304 267 49 0 0 163 83 32 86 90 34 84 6 315 316 4.526 .221 .184 .38 .353 3.279 32 176 .231 .28 60 3360 7300 59 65 193 199 0 2478 2081 397 1.538 2422 341 .65 1.277 .621 .353
8 364 339 126 292 238 47 364 316 127 310 238 24 0 0 61 96 35 76 100 25 100 8 285 262 5.064 .197 .101 .226 .297 4.156 12 104 .192 .13 50 3560 7290 58 63 213 218 0 2359 2032 327 1.374 2199 167 .728 .702 .459 -.511
9 393 328 128 324 265 4 378 315 129 317 250 -9 0 0 78 119 30 82 100 16 100 8 269 241 66.25 .015 null .288 .287 2.501 12 104 .185 .1 50 3790 7290 58 63 236 241 0 2283 2255 28 .105 2192 -63 9.519 null -3.251 null
10 424 389 132 309 292 80 419 388 136 303 287 79 0 0 116 45 38 69 100 66 100 8 372 366 3.65 .274 .275 .261 .225 1.893 12 104 .347 .43 50 3990 7290 58 63 256 261 0 2707 2151 557 1.907 2700 550 .524 1.916 .931 .938
11 1064 370 128 320 936 50 1127 375 130 321 999 55 0 0 378 65 32 84 100 31 100 0 986 1054 18.72 .053 .055 .053 .069 3.548 32 176 .059 .33 60 4230 7300 59 65 280 286 0 2575 2227 348 .372 2610 383 2.69 .383 -1.427 -1.384
12 369 341 120 303 249 38 318 345 123 312 198 42 0 0 121 101 31 77 100 25 100 16 287 240 6.553 .153 .212 .277 .267 2.198 12 104 .173 .1 50 4450 7290 58 63 302 307 0 2373 2109 264 1.062 2401 292 .942 1.476 .087 .562
13 353 349 130 299 223 50 360 346 133 306 230 47 0 0 96 83 39 84 96 34 93 9 273 277 4.46 .224 .204 .339 .332 3.329 32 176 .072 .06 60 4660 7290 58 64 323 329 0 2429 2081 348 1.56 2408 327 .641 1.422 .642 .508
14 379 388 130 305 249 83 410 398 132 310 280 93 0 0 68 64 34 85 100 58 100 8 332 373 3 .333 .332 .383 .413 2.066 12 104 .406 .33 50 4880 7290 58 63 345 350 0 2700 2123 578 2.32 2770 647 .431 2.312 1.214 1.209
15 382 299 106 309 276 -10 382 288 102 313 276 -21 0 0 93 78 40 64 100 16 100 8 266 255 null null null .133 .158 4.732 12 68 -.025 -.04 40 5100 7300 60 64 368 372 0 2081 2151 -70 null 2004 -146 null null null null
16 974 352 134 314 840 38 959 349 135 320 825 35 0 0 185 73 31 80 100 31 100 3 878 860 22.105 .045 .042 .069 .089 2.459 32 176 .049 .23 60 5330 7290 58 64 390 396 0 2450 2185 264 .315 2429 244 3.176 .295 -1.667 -1.76
17 467 442 117 300 350 142 449 410 116 297 332 110 0 0 84 139 59 74 100 58 100 33 492 442 2.465 .406 .331 .425 .349 1.778 12 104 .367 .41 50 5550 7280 57 62 412 417 0 3076 2088 988 2.824 2853 766 .354 2.306 1.498 1.205
18 391 333 137 309 254 24 379 339 141 310 242 30 0 0 106 93 31 75 100 31 96 6 278 272 10.583 .094 .124 .317 .333 1.871 32 176 .134 .13 60 5770 7300 59 65 434 440 0 2318 2151 167 .658 2359 209 1.521 .863 -.605 -.213
19 357 349 130 301 227 48 341 328 132 305 211 27 0 0 146 93 35 77 84 28 81 12 275 238 4.729 .211 .128 .327 .31 3.681 32 236 .29 .25 70 5970 7300 58 65 453 460 0 2429 2095 334 1.472 2283 188 .68 .891 .557 -.167
20 342 329 136 320 206 9 355 332 139 325 219 12 0 0 101 79 34 83 91 16 91 0 215 231 22.889 .044 .055 .152 .217 10.361 12 104 -.375 -.22 50 2030 7510 80 85 60 65 0 2290 2227 63 .304 2311 84 3.289 .381 -1.718 -1.391

Total number of rows: 10944

Table truncated, full table size 2402 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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