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Sample GSM543856 Query DataSets for GSM543856
Status Public on Dec 06, 2010
Title Pfk2 IP (1) A
Sample type RNA
 
Channel 1
Source name Extract tot. RNA Pfk2 (1)
Organism Saccharomyces cerevisiae
Characteristics experiment: Extract tot. RNA Pfk2 (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, Pfk2 (1)
Organism Saccharomyces cerevisiae
Characteristics experiment: Affinity isolated RNA, Pfk2 (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/2007-03/72827.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) andre.gerber@pharma.ethz.ch
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
1 703 269 124 208 579 61 736 255 129 211 612 47 0 0 248 69 32 50 100 50 93 28 640 659 9.492 .105 .077 .1 .131 2.811 32 176 .116 .51 60 1950 7080 65 71 68 74 0 2287 1768 519 .896 2168 400 1.117 .653 -.159 -.615
2 342 231 118 191 224 40 342 236 122 199 224 45 0 0 122 57 32 52 93 43 84 12 264 269 5.6 .179 .201 .257 .232 3.118 32 176 .075 .13 60 2170 7080 65 71 90 96 0 1964 1624 340 1.518 2006 383 .659 1.708 .602 .772
3 507 257 119 200 388 57 542 261 125 202 423 61 0 0 195 63 31 50 93 56 87 18 445 484 6.807 .147 .144 .19 .175 3.341 32 176 .156 .5 60 2380 7080 65 71 111 117 0 2185 1700 485 1.249 2219 519 .801 1.226 .321 .294
4 297 230 122 196 175 34 290 217 126 201 168 21 0 0 118 60 33 49 93 31 87 9 209 189 5.147 .194 .125 .171 .165 3.605 32 176 .189 .28 60 2610 7080 65 71 134 140 0 1955 1666 289 1.652 1845 179 .605 1.063 .724 .088
5 378 206 124 212 254 -6 367 207 126 215 243 -5 0 0 82 36 32 44 100 8 100 0 248 238 null null null .075 .116 2.871 12 68 .055 .13 40 2830 7080 66 70 157 161 0 1751 1802 -51 null 1760 -43 null null null null
6 308 254 122 202 186 52 310 252 122 205 188 50 0 0 56 50 29 49 100 50 100 16 238 238 3.577 .28 .266 .232 .346 3.44 12 104 .158 .23 50 3050 7080 65 70 178 183 0 2159 1717 442 2.377 2142 425 .421 2.261 1.249 1.177
7 505 278 124 199 381 79 498 283 128 206 374 84 0 0 89 56 34 49 100 75 100 41 460 458 4.823 .207 .225 .204 .321 2.304 12 104 .121 .27 50 3270 7070 64 69 200 205 0 2363 1692 672 1.763 2406 714 .567 1.909 .818 .933
8 351 218 118 202 233 16 357 235 123 210 239 33 0 0 59 55 41 51 100 25 100 0 249 272 14.563 .069 .138 .176 .22 1.806 12 104 .015 .03 50 3480 7080 65 70 221 226 0 1853 1717 136 .584 1998 281 1.713 1.174 -.777 .231
9 370 247 122 201 248 46 365 241 126 203 243 40 0 0 69 67 40 45 100 41 100 16 294 283 5.391 .185 .165 .212 .299 2.564 12 104 .091 .22 50 3700 7070 64 69 243 248 0 2100 1709 391 1.577 2049 340 .634 1.399 .657 .485
10 471 221 125 199 346 22 424 224 131 202 299 25 0 0 145 42 37 49 100 16 100 8 368 324 15.727 .064 .084 .085 .095 3.204 12 104 .118 .28 50 3920 7070 64 69 265 270 0 1879 1692 187 .541 1904 213 1.85 .711 -.888 -.492
11 793 256 124 202 669 54 867 244 126 207 743 42 0 0 237 68 32 50 100 46 100 15 723 785 12.389 .081 .057 .071 .086 2.76 32 176 .065 .35 60 4150 7070 64 70 288 294 0 2176 1717 459 .686 2074 357 1.457 .481 -.543 -1.057
12 282 219 119 192 163 27 288 212 122 198 169 20 0 0 76 47 32 48 96 28 93 12 190 189 6.037 .166 .118 .167 .207 4.26 32 236 .132 .14 70 4370 7070 63 70 309 316 0 1862 1632 230 1.408 1802 170 .71 1.006 .494 .009
13 369 224 122 200 247 24 343 216 123 205 221 16 0 0 78 52 29 49 100 28 100 9 271 237 10.292 .097 .072 .134 .165 4.09 32 236 .086 .15 70 4580 7080 64 71 330 337 0 1904 1700 204 .826 1836 136 1.211 .615 -.276 -.7
14 319 236 125 201 194 35 318 241 128 206 193 40 0 0 63 44 36 48 100 43 100 6 229 233 5.543 .18 .207 .213 .28 2.943 32 236 .101 .14 70 4800 7070 63 70 352 359 0 2006 1709 298 1.534 2049 340 .652 1.762 .617 .817
15 332 224 124 208 208 16 343 214 129 204 219 6 0 0 74 51 56 47 96 21 87 9 224 225 13 .077 .027 .156 .186 4.272 32 236 .068 .12 70 5020 7080 64 71 374 381 0 1904 1768 136 .654 1819 51 1.529 .233 -.613 -2.102
16 604 233 121 207 483 26 596 241 123 206 475 34 0 0 95 52 32 47 100 28 100 9 509 509 18.577 .054 .072 .087 .091 1.921 32 236 .052 .2 70 5250 7070 63 70 397 404 0 1981 1760 221 .458 2049 289 2.185 .609 -1.128 -.717
17 376 236 122 198 254 38 365 228 124 199 243 30 0 0 78 63 32 44 100 40 100 15 292 273 6.684 .15 .123 .151 .164 3.487 32 236 .166 .3 70 5470 7070 63 70 419 426 0 2006 1683 323 1.272 1938 255 .786 1.05 .347 .07
18 332 216 126 203 206 13 332 217 130 206 206 14 0 0 76 41 36 49 100 18 100 3 219 220 15.846 .063 .068 .161 .149 2.959 32 176 -.058 -.08 60 5690 7070 64 70 442 448 0 1836 1726 111 .536 1845 119 1.864 .578 -.898 -.791
19 361 232 122 197 239 35 365 228 125 201 243 31 0 0 132 44 32 49 93 34 93 6 274 274 6.829 .146 .128 .207 .197 2.92 32 236 .118 .25 70 5920 7070 63 70 464 471 0 1972 1675 298 1.245 1938 264 .803 1.085 .316 .117
20 316 216 129 206 187 10 326 220 131 205 197 14 0 0 76 48 32 48 100 21 93 3 197 211 18.7 .053 .071 .21 .256 2.496 32 176 .057 .08 60 1950 7300 87 93 68 74 0 1836 1751 85 .455 1870 119 2.2 .604 -1.137 -.727

Total number of rows: 10944

Table truncated, full table size 2376 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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