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Sample GSM543847 Query DataSets for GSM543847
Status Public on Dec 06, 2010
Title Mdh1 IP (1) B
Sample type RNA
 
Channel 1
Source name Extract tot. RNA Mdh1-TAP (1)
Organism Saccharomyces cerevisiae
Characteristics experiment: Extract tot. RNA Mdh1-TAP (1)
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, Mdh1-TAP (1)
Organism Saccharomyces cerevisiae
Characteristics experiment: Affinity isolated RNA, Mdh1-TAP (1)
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/2007-04/73671.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
1 713 368 79 117 634 251 785 377 79 118 706 260 0 0 199 107 16 24 100 96 100 96 885 966 2.526 .396 .368 .371 .398 1.48 32 236 .4 .93 70 2040 7090 33 40 44 51 0 2188 696 1492 2.354 2242 1546 .425 2.19 1.235 1.131
2 199 127 74 118 125 9 191 128 74 118 117 10 0 0 39 28 16 23 100 28 96 9 134 127 13.889 .072 .085 .195 .204 2.769 32 176 .096 .19 60 2260 7090 34 40 67 73 0 755 702 54 .428 761 59 2.336 .508 -1.224 -.977
3 565 249 74 117 491 132 613 251 76 118 539 134 0 0 170 73 15 26 100 96 100 93 623 673 3.72 .269 .249 .257 .266 1.424 32 236 .279 .87 70 2480 7090 33 40 88 95 0 1481 696 785 1.599 1492 797 .626 1.478 .677 .564
4 170 142 79 113 91 29 158 145 80 117 79 32 0 0 43 32 17 26 100 50 91 16 120 111 3.138 .319 .405 .378 .536 3.072 12 104 .107 .1 50 2710 7090 34 39 112 117 0 844 672 172 1.895 862 190 .528 2.408 .922 1.268
5 144 128 82 118 62 10 138 124 92 118 56 6 0 0 58 35 38 26 61 22 35 12 72 62 6.2 .161 .107 .438 .482 5.413 80 560 .259 .28 100 2910 7080 31 41 130 140 -50 761 702 59 .959 737 36 1.043 .637 -.06 -.65
6 153 122 78 112 75 10 154 128 79 119 76 16 0 0 42 29 19 26 91 41 75 8 85 92 7.5 .133 .211 .289 .311 2.179 12 68 .136 .06 40 3150 7080 34 38 157 161 0 725 666 59 .793 761 95 1.261 1.252 -.335 .324
7 407 154 77 116 330 38 376 150 79 119 299 34 0 0 89 50 18 27 100 50 100 25 368 333 8.684 .115 .114 .11 .145 2.472 12 104 .091 .34 50 3360 7080 33 38 177 182 0 916 690 226 .685 892 202 1.461 .676 -.546 -.565
8 172 143 73 115 99 28 166 139 73 117 93 24 0 0 50 29 15 26 96 43 87 15 127 117 3.536 .283 .258 .292 .324 3.018 32 176 .239 .36 60 3580 7080 33 39 199 205 0 850 684 166 1.682 826 143 .595 1.534 .75 .618
9 184 126 76 117 108 9 177 125 75 117 101 8 0 0 53 29 16 24 96 31 93 3 117 109 12 .083 .079 .17 .182 2.492 32 176 .167 .31 60 3800 7100 35 41 221 227 0 749 696 54 .495 743 48 2.018 .471 -1.013 -1.086
10 208 130 71 114 137 16 208 123 73 116 137 9 0 0 48 31 15 25 100 28 100 18 153 146 8.563 .117 .066 .128 .134 3.345 32 176 .1 .2 60 4020 7090 34 40 243 249 0 773 678 95 .694 731 54 1.44 .391 -.526 -1.356
11 2073 345 74 113 1999 232 2304 378 75 116 2230 265 0 0 679 111 16 25 100 100 100 90 2231 2495 8.616 .116 .119 .108 .118 1.648 32 176 .115 .93 60 4240 7080 33 39 265 271 0 2051 672 1379 .69 2248 1576 1.449 .707 -.535 -.501
12 143 130 72 114 71 16 140 128 73 116 68 14 0 0 37 27 15 24 93 37 84 15 87 82 4.438 .225 .206 .381 .364 2.96 32 236 .31 .27 70 4460 7080 32 39 286 293 0 773 678 95 1.34 761 83 .746 1.224 .422 .292
13 363 203 74 115 289 88 384 198 75 116 310 83 0 0 62 35 17 24 100 96 100 87 377 393 3.284 .304 .268 .281 .314 1.598 32 236 .325 .81 70 4680 7090 33 40 308 315 0 1207 684 523 1.811 1177 494 .552 1.592 .856 .671
14 183 133 70 114 113 19 181 133 72 114 111 19 0 0 39 27 15 24 100 34 96 9 132 130 5.947 .168 .171 .207 .232 2.404 32 236 .19 .3 70 4890 7090 33 40 329 336 0 791 678 113 1 791 113 1 1.018 0 .025
15 202 150 77 113 125 37 203 152 78 115 126 39 0 0 44 30 18 30 100 58 100 16 162 165 3.378 .296 .31 .267 .261 3.181 12 104 .108 .17 50 5120 7080 33 38 353 358 0 892 672 220 1.76 904 232 .568 1.84 .816 .88
16 439 153 73 114 366 39 434 158 77 115 361 44 0 0 75 31 23 24 100 68 100 34 405 405 9.385 .107 .122 .1 .136 2.175 32 176 .11 .59 60 5340 7080 33 39 375 381 0 910 678 232 .634 939 262 1.578 .725 -.658 -.465
17 158 134 73 115 85 19 154 137 73 117 81 22 0 0 49 28 15 26 90 46 88 13 104 103 4.474 .224 .272 .346 .273 3.377 52 340 .27 .31 80 5550 7090 33 41 395 403 0 797 684 113 1.329 815 131 .752 1.615 .41 .691
18 172 134 75 113 97 21 170 127 76 115 95 14 0 0 38 32 17 25 100 37 96 15 118 109 4.619 .216 .147 .226 .268 2.93 32 236 .215 .25 70 5780 7090 33 40 418 425 0 797 672 125 1.287 755 83 .777 .876 .364 -.191
19 188 130 75 115 113 15 187 121 76 116 112 6 0 0 46 32 15 24 96 31 96 15 128 118 7.533 .133 .054 .227 .219 3.552 32 176 .15 .24 60 5990 7080 33 39 440 446 0 773 684 89 .789 719 36 1.267 .319 -.341 -1.65
20 143 126 76 112 67 14 140 128 77 115 64 16 0 0 29 27 15 24 96 31 90 9 81 80 4.786 .209 .25 .428 .352 2.555 32 176 .191 .13 60 2040 7320 57 63 45 51 0 749 666 83 1.242 761 95 .805 1.486 .313 .572

Total number of rows: 10944

Table truncated, full table size 2338 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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