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Sample GSM543825 Query DataSets for GSM543825
Status Public on Dec 06, 2010
Title Pre10 IP (2) A
Sample type RNA
 
Channel 1
Source name Extract tot. RNA Pre10-TAP (2)
Organism Saccharomyces cerevisiae
Characteristics experiment: Extract tot. RNA Pre10-TAP (2)
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 (2)
Organism Saccharomyces cerevisiae
Characteristics experiment: Affinity isolated RNA, Pre10-TAP (2)
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/2007-04/73889.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
1 654 131 64 121 590 10 727 131 65 121 663 10 0 0 204 34 17 26 100 34 100 9 600 673 59 .017 .015 .036 .043 3.288 32 176 .01 .1 60 1990 7010 22 28 56 62 0 3235 2988 247 .419 3235 247 2.389 .373 -1.256 -1.425
2 230 128 65 120 165 8 237 124 67 122 172 4 0 0 75 23 15 25 93 25 93 0 173 176 20.625 .048 .023 .097 .104 3.821 32 176 .035 .12 60 2210 7010 22 28 78 84 0 3161 2964 198 1.197 3062 99 .835 .574 .26 -.8
3 383 129 63 120 320 9 419 125 66 124 356 5 0 0 121 29 14 28 100 31 100 6 329 361 35.556 .028 .014 .063 .1 3.941 32 176 -1 -1 60 2430 7010 22 28 100 106 0 3186 2964 222 .695 3087 123 1.44 .347 -.526 -1.528
4 193 129 73 121 120 8 186 133 75 121 113 12 0 0 40 21 18 23 100 16 100 0 128 125 15 .067 .106 .134 .113 2.273 12 104 .03 .06 50 2650 7000 21 26 122 127 0 3186 2988 198 1.646 3285 296 .607 2.623 .719 1.391
5 212 131 79 121 133 10 220 126 80 123 141 5 0 0 58 32 18 25 93 21 93 12 143 146 13.3 .075 .035 .114 .153 4.021 32 176 .057 .12 60 2880 7010 22 28 145 151 0 3235 2988 247 1.857 3112 123 .539 .876 .893 -.191
6 177 135 74 118 103 17 179 130 73 122 105 12 0 0 39 27 14 29 96 31 96 6 120 117 6.059 .165 .114 .179 .239 3.27 32 176 .175 .24 60 3090 7010 22 28 166 172 0 3334 2914 420 4.076 3211 296 .245 2.822 2.027 1.497
7 251 134 71 123 180 11 259 136 73 125 188 13 0 0 33 22 23 28 100 25 100 0 191 201 16.364 .061 .069 .137 .121 2.169 12 104 .041 .17 50 3310 6990 20 25 188 193 0 3309 3038 272 1.509 3359 321 .663 1.708 .594 .772
8 182 122 68 120 114 2 171 125 67 121 103 5 0 0 46 28 14 26 100 25 100 0 116 108 57 .018 .049 .184 .234 3.338 32 176 -1 -1 60 3540 7010 22 28 211 217 0 3013 2964 49 .433 3087 123 2.308 1.199 -1.207 .262
9 189 130 63 118 126 12 197 131 65 122 134 13 0 0 50 26 15 25 100 31 100 6 138 147 10.5 .095 .097 .192 .312 2.974 32 176 .049 .1 60 3760 7010 22 28 233 239 0 3211 2914 296 2.352 3235 321 .425 2.396 1.234 1.261
10 256 133 65 120 191 13 255 137 114 122 190 17 0 0 31 26 374 28 0 33 0 0 204 207 14.692 .068 .089 .128 .152 1.773 12 104 .017 .29 50 3970 7010 22 27 254 259 0 3285 2964 321 1.681 3383 420 .595 2.21 .749 1.144
11 540 128 63 116 477 12 576 121 66 116 513 5 0 0 133 22 22 22 100 28 100 12 489 518 39.75 .025 .01 .034 .048 3.766 32 176 .018 .16 60 4190 7010 22 28 276 282 0 3161 2865 296 .621 2988 123 1.61 .241 -.687 -2.055
12 154 126 62 114 92 12 155 119 65 116 93 5 0 0 41 25 15 24 93 28 90 9 104 98 7.667 .13 .054 .253 .248 2.302 32 176 .143 .21 60 4420 7020 23 29 299 305 0 3112 2815 296 3.221 2939 123 .31 1.328 1.688 .409
13 173 123 64 115 109 8 189 121 66 117 125 6 0 0 52 24 17 26 90 17 88 3 117 131 13.625 .073 .048 .149 .175 3.13 52 340 .062 .11 80 4630 7000 20 28 319 327 0 3038 2840 198 1.813 2988 148 .552 1.185 .858 .245
14 156 126 65 112 91 14 158 123 65 115 93 11 0 0 38 28 15 24 96 28 93 18 105 104 6.5 .154 .118 .196 .251 2.822 32 176 .196 .29 60 4840 7000 21 27 341 347 0 3112 2766 346 3.8 3038 272 .263 2.921 1.926 1.547
15 195 128 63 117 132 11 192 128 67 118 129 11 0 0 35 31 19 27 100 31 100 12 143 140 12 .083 .085 .199 .262 2.466 32 236 .015 .37 70 5080 7010 21 28 364 371 0 3161 2890 272 2.058 3161 272 .486 2.106 1.041 1.074
16 324 118 65 115 259 3 346 121 67 116 281 6 0 0 94 26 21 24 100 23 98 1 262 287 86.333 .012 .021 .077 .087 2.626 52 340 .005 .03 80 5290 7010 21 29 385 393 0 2914 2840 74 .286 2988 148 3.496 .527 -1.806 -.923
17 207 125 64 118 143 7 213 122 65 118 149 4 0 0 43 34 16 26 100 18 100 12 150 153 20.429 .049 .027 .118 .145 3.828 32 236 .016 .03 70 5510 7020 22 29 407 414 0 3087 2914 173 1.209 3013 99 .827 .663 .274 -.593
18 166 125 67 118 99 7 164 126 66 116 97 8 0 0 32 22 15 25 100 15 100 0 106 105 14.143 .071 .082 .135 .194 2.948 32 236 .09 .14 70 5720 7010 21 28 428 435 0 3087 2914 173 1.746 3112 198 .573 2.037 .804 1.026
19 186 128 67 113 119 15 187 129 67 114 120 16 0 0 50 25 14 23 100 37 93 6 134 136 7.933 .126 .133 .177 .2 3.041 32 236 .101 .21 70 5950 7020 22 29 451 458 0 3161 2791 370 3.113 3186 395 .321 3.293 1.638 1.719
20 156 125 65 123 91 2 160 121 69 125 95 -2 0 0 32 17 18 28 100 16 91 0 93 93 45.5 .022 null .162 .103 4.021 12 104 -.03 -.03 50 1990 7230 44 49 56 61 0 3087 3038 49 .543 2988 -49 1.842 null -.882 null

Total number of rows: 10944

Table truncated, full table size 2309 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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