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Sample GSM543818 Query DataSets for GSM543818
Status Public on Dec 06, 2010
Title Pre10 IP (3) A
Sample type RNA
 
Channel 1
Source name Extract tot. RNA Pre10-TAP (3)
Organism Saccharomyces cerevisiae
Characteristics experiment: Extract tot. RNA Pre10-TAP (3)
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, Pre10-TAP (3)
Organism Saccharomyces cerevisiae
Characteristics experiment: Affinity isolated RNA, Pre10-TAP (3)
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 Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-04/73887.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 (1)
GSE21864 RNA-affinity isolations 13 RBPs

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
1 464 135 86 109 378 26 504 131 88 113 418 22 0 0 123 33 22 24 100 43 100 25 404 440 14.538 .069 .053 .07 .08 3.041 32 176 .043 .28 60 1970 7030 24 30 54 60 0 2624 2118 505 1.337 2546 428 .748 1.023 .419 .033
2 207 120 87 111 120 9 214 120 89 112 127 9 0 0 55 30 23 23 96 28 87 9 129 136 13.333 .075 .071 .238 .214 2.267 32 176 .09 .18 60 2190 7030 24 30 76 82 0 2332 2157 175 1.458 2332 175 .686 1.377 .544 .462
3 376 130 88 109 288 21 376 127 87 113 288 18 0 0 45 16 19 23 100 33 100 8 309 306 13.714 .073 .063 .063 .068 2.237 12 104 .061 .32 50 2410 7030 24 29 98 103 0 2526 2118 408 1.417 2468 350 .706 1.215 .503 .281
4 232 120 86 113 146 7 238 116 87 112 152 3 0 0 42 28 20 23 100 25 100 16 153 155 20.857 .048 .02 .144 .193 2.232 12 104 .052 .1 50 2630 7020 23 28 120 125 0 2332 2196 136 .932 2254 58 1.073 .384 -.102 -1.382
5 208 114 83 109 125 5 212 119 85 111 129 10 0 0 51 27 19 24 100 18 96 6 130 139 25 .04 .078 .196 .189 2.212 32 176 .034 .07 60 2850 7020 23 29 142 148 0 2215 2118 97 .777 2313 194 1.286 1.507 -.363 .591
6 199 129 79 113 120 16 193 122 80 113 114 9 0 0 26 39 17 29 100 16 100 16 136 123 7.5 .133 .079 .13 .199 4.488 12 68 .195 .34 40 3080 7020 24 28 166 170 0 2507 2196 311 2.591 2371 175 .386 1.534 1.374 .618
7 266 149 84 108 182 41 267 151 85 111 183 43 0 0 35 26 20 24 100 83 100 33 223 226 4.439 .225 .235 .203 .258 2.25 12 104 .182 .39 50 3290 7020 23 28 186 191 0 2896 2099 797 4.378 2935 836 .228 4.566 2.13 2.191
8 197 119 101 115 96 4 197 113 101 115 96 -2 0 0 30 18 23 24 100 16 100 0 100 94 24 .042 null .22 .271 2.45 12 104 .03 .04 50 3500 7020 23 28 207 212 0 2313 2235 78 .81 2196 -39 1.235 null -.304 null
9 207 131 89 111 118 20 216 133 91 111 127 22 0 0 49 27 20 23 100 41 91 16 138 149 5.9 .169 .173 .255 .367 2.694 12 104 .104 .19 50 3730 7020 23 28 230 235 0 2546 2157 389 3.294 2585 428 .304 3.367 1.72 1.751
10 204 124 87 108 117 16 201 121 89 112 114 13 0 0 68 25 20 24 96 28 90 9 133 127 7.313 .137 .114 .246 .185 3.196 32 176 .096 .23 60 3950 7020 23 29 252 258 0 2410 2099 311 2.658 2352 253 .376 2.216 1.41 1.148
11 342 124 87 108 255 16 356 120 89 107 269 12 0 0 97 30 20 25 100 28 100 12 271 281 15.938 .063 .045 .085 .094 2.951 32 176 .058 .26 60 4170 7020 23 29 274 280 0 2410 2099 311 1.219 2332 233 .82 .867 .286 -.206
12 202 114 90 113 112 1 200 120 90 114 110 7 0 0 39 23 22 27 100 0 91 0 113 117 112 .009 .064 .111 .14 2.733 12 104 .071 .09 50 4400 7030 24 29 297 302 0 2215 2196 19 .174 2332 136 5.763 1.237 -2.527 .307
13 188 116 88 112 100 4 184 113 90 113 96 1 0 0 48 22 22 27 100 18 90 0 104 97 25 .04 .01 .141 .152 4.627 32 176 -.017 -.03 60 4600 7020 23 29 317 323 0 2254 2177 78 .777 2196 19 1.286 .202 -.363 -2.304
14 190 120 87 108 103 12 184 117 89 109 97 9 0 0 36 24 21 24 100 25 100 6 115 106 8.583 .117 .093 .189 .186 2.398 32 176 .146 .22 60 4830 7020 23 29 340 346 0 2332 2099 233 2.264 2274 175 .442 1.803 1.179 .851
15 198 120 83 110 115 10 199 117 86 109 116 7 0 0 45 32 21 24 100 31 93 9 125 123 11.5 .087 .06 .193 .193 2.834 32 176 .04 .06 60 5050 7020 23 29 362 368 0 2332 2138 194 1.69 2274 136 .592 1.173 .757 .23
16 260 122 82 111 178 11 262 127 84 111 180 16 0 0 49 23 20 23 100 34 100 6 189 196 16.182 .062 .089 .111 .102 1.992 32 236 .076 .22 70 5270 7020 22 29 383 390 0 2371 2157 214 1.201 2468 311 .833 1.727 .264 .789
17 210 122 87 106 123 16 204 122 89 110 117 16 0 0 50 20 26 25 100 31 93 6 139 133 7.688 .13 .137 .129 .145 3.032 32 176 .094 .22 60 5490 7020 23 29 406 412 0 2371 2060 311 2.528 2371 311 .396 2.658 1.338 1.41
18 182 122 86 111 96 11 177 125 87 111 91 14 0 0 43 27 19 25 96 31 93 9 107 105 8.727 .115 .154 .319 .256 2.46 32 236 .116 .18 70 5710 7010 21 28 427 434 0 2371 2157 214 2.227 2429 272 .449 2.99 1.155 1.58
19 184 116 83 110 101 6 178 116 86 110 95 6 0 0 45 26 22 25 96 18 90 6 107 101 16.833 .059 .063 .176 .164 2.769 32 176 .099 .13 60 5930 7020 23 29 450 456 0 2254 2138 117 1.154 2254 117 .866 1.227 .207 .296
20 170 127 88 113 82 14 165 124 93 114 77 11 0 0 53 27 38 25 81 21 50 9 96 88 5.857 .171 .143 .22 .225 3.257 32 236 .137 .21 70 1970 7240 44 51 53 60 0 2468 2196 272 3.318 2410 214 .301 2.776 1.73 1.473

Total number of rows: 10944

Table truncated, full table size 2310 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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