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Sample GSM543835 Query DataSets for GSM543835
Status Public on Dec 06, 2010
Title Lap3 IP (3) A
Sample type RNA
 
Channel 1
Source name Extract tot. RNA Lap3 (3)
Organism Saccharomyces cerevisiae
Characteristics experiment: Extract tot. RNA Lap3 (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, Lap3 (3)
Organism Saccharomyces cerevisiae
Characteristics experiment: Affinity isolated RNA, Lap3 (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/2007-03/72828.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
1 384 195 63 156 321 39 387 185 64 159 324 29 0 0 58 46 12 33 100 43 100 21 360 353 8.231 .121 .09 .105 .103 2.771 32 176 .114 .36 60 1960 7050 62 68 69 75 0 3468 2774 694 2.161 3290 516 .463 1.592 1.111 .671
2 136 170 55 153 81 17 139 155 56 155 84 2 0 0 25 45 18 34 96 28 90 12 98 86 4.765 .21 .024 .328 .514 4.569 32 176 .064 .09 60 2180 7050 62 68 91 97 0 3023 2721 302 3.732 2757 36 .268 .423 1.9 -1.24
3 165 168 53 151 112 17 169 162 54 154 116 11 0 0 41 39 10 34 100 34 100 6 129 127 6.588 .152 .095 .303 .396 3.179 32 236 .221 .16 70 2400 7050 61 68 112 119 0 2988 2685 302 2.699 2881 196 .37 1.686 1.433 .754
4 143 169 57 148 86 21 139 163 60 149 82 15 0 0 57 40 19 36 93 28 87 15 107 97 4.095 .244 .183 .325 .4 3.717 32 176 .154 .09 60 2630 7060 63 69 136 142 0 3005 2632 373 4.343 2899 267 .23 3.253 2.119 1.702
5 75 157 55 148 20 9 66 153 56 151 11 5 0 0 30 40 12 34 48 31 41 7 29 16 2.222 .45 .455 1.268 1.548 4.767 80 554 23.135 .04 100 2840 7050 60 70 155 165 -50 2792 2632 160 8.003 2721 89 .125 8.084 3.001 3.015
6 148 158 52 148 96 10 138 153 52 147 86 5 0 0 33 39 10 31 100 25 100 8 106 91 9.6 .104 .058 .253 .26 3.222 12 104 .473 .11 50 3070 7060 63 68 180 185 0 2810 2632 178 1.852 2721 89 .54 1.034 .889 .048
7 164 179 54 154 110 25 161 171 55 154 107 17 0 0 44 49 14 33 96 31 96 18 135 124 4.4 .227 .159 .3 .314 3.475 32 176 .311 .19 60 3290 7040 61 67 202 208 0 3183 2739 445 4.042 3041 302 .247 2.825 2.015 1.499
8 148 169 53 155 95 14 147 165 59 154 94 10 0 0 40 34 28 32 96 28 81 15 109 104 6.786 .147 .106 .315 .354 2.428 32 176 .2 .16 60 3510 7040 61 67 224 230 0 3005 2757 249 2.621 2934 178 .382 1.892 1.39 .92
9 170 165 50 151 120 14 166 148 50 155 116 -3 0 0 39 41 10 33 100 25 96 12 134 113 8.571 .117 null .282 .312 3.212 32 176 .144 .15 60 3730 7040 61 67 246 252 0 2934 2685 249 2.075 2632 -53 .482 null 1.053 null
10 219 166 50 151 169 15 213 160 51 153 163 9 0 0 48 37 11 34 100 21 100 9 184 172 11.267 .089 .055 .142 .159 2.71 32 176 .066 .12 60 3950 7050 62 68 268 274 0 2952 2685 267 1.578 2845 160 .634 .982 .659 -.026
11 1365 167 49 149 1316 18 1465 161 51 150 1416 12 0 0 378 47 10 35 100 21 100 15 1334 1428 73.111 .014 .008 .022 .02 3.111 32 176 .013 .21 60 4170 7040 61 67 290 296 0 2970 2650 320 .243 2863 213 4.111 .151 -2.04 -2.73
12 111 168 49 158 62 10 115 169 49 157 66 11 0 0 21 33 10 38 96 18 96 0 72 77 6.2 .161 .167 .396 .479 2.386 32 176 2.344 .12 60 4380 7040 61 67 311 317 0 2988 2810 178 2.868 3005 196 .349 2.964 1.52 1.568
13 169 167 50 157 119 10 168 168 50 157 118 11 0 0 35 34 10 37 100 21 100 3 129 129 11.9 .084 .093 .25 .238 2.233 32 236 .093 .07 70 4600 7040 60 67 332 339 0 2970 2792 178 1.494 2988 196 .669 1.658 .58 .729
14 146 152 49 152 97 0 140 151 50 160 91 -1 0 0 28 39 10 34 100 21 100 3 97 90 null null null .234 .371 3.35 32 176 -.278 -.15 60 4820 7040 61 67 355 361 0 2703 2703 0 null 2685 -18 null null null null
15 172 165 48 156 124 9 178 160 49 159 130 4 0 0 46 44 9 34 98 19 96 11 133 134 13.778 .073 .031 .182 .196 3.795 52 340 .062 .06 80 5040 7040 60 68 376 384 0 2934 2774 160 1.291 2845 71 .775 .547 .368 -.87
16 789 174 50 156 739 18 783 167 51 156 733 11 0 0 92 34 10 33 100 28 100 12 757 744 41.056 .024 .015 .028 .03 3.122 32 236 .018 .17 70 5260 7040 60 67 398 405 0 3094 2774 320 .433 2970 196 2.309 .267 -1.207 -1.906
17 264 165 48 153 216 12 260 164 49 154 212 11 0 0 40 32 10 34 100 15 100 9 228 223 18 .056 .052 .102 .111 2.099 32 236 .03 .07 70 5480 7040 60 67 420 427 0 2934 2721 213 .988 2917 196 1.012 .923 -.017 -.116
18 158 170 50 154 108 16 162 168 52 157 112 14 0 0 47 38 17 36 94 17 90 7 124 126 6.75 .148 .125 .229 .258 3.03 52 340 .197 .14 80 5700 7050 61 69 442 450 0 3023 2739 285 2.635 2988 249 .38 2.223 1.398 1.153
19 226 170 50 155 176 15 231 166 50 155 181 11 0 0 45 39 9 35 100 25 100 9 191 192 11.733 .085 .061 .11 .12 3.195 32 176 .084 .17 60 5920 7030 60 66 465 471 0 3023 2757 267 1.516 2952 196 .66 1.081 .6 .112
20 188 174 63 148 125 26 162 177 66 151 99 29 0 0 114 36 14 32 98 48 94 13 151 128 4.808 .208 .293 .328 .399 2.749 52 340 .134 .25 80 1950 7280 84 92 67 75 0 3094 2632 462 3.699 3148 516 .27 5.209 1.887 2.381

Total number of rows: 10944

Table truncated, full table size 2317 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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