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Sample GSM402962 Query DataSets for GSM402962
Status Public on Jul 15, 2009
Title Trf4-DADA (3)
Sample type RNA
 
Channel 1
Source name total RNA WT (3)
Organism Saccharomyces cerevisiae
Characteristics strain: WT
Extracted molecule total RNA
Extraction protocol Total RNA was isolated by hot phenol extraction from exponentially growing cells,
Label Cy3
Label protocol not provided
 
Channel 2
Source name total RNA from trf4-DADA cells (3)
Organism Saccharomyces cerevisiae
Characteristics strain: from trf4-DADA cells
Extracted molecule total RNA
Extraction protocol Total RNA was isolated by hot phenol extraction from exponentially growing cells,
Label Cy5
Label protocol not provided
 
 
Hybridization protocol cDNAs were hybridized on yeast oligo microarrays over night at 42 degrees in formamide-based hybridization buffer
Scan protocol GenePix 4200A
Description Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82466.gif
mutated gene: trf4 (DADA) mutant
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 14, 2009
Last update date Jul 15, 2009
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 GPL8546
Series (2)
GSE16103 Wild-type versus trf4, trf5, and trf4-DADA mutant cells
GSE16107 trf4, trf5, and trf4-DADA mutant cells gene expression; Trf4p X-RIP-Chip

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 1404 657 31 64 1373 593 1428 638 31 66 1397 574 0 0 318 156 5 14 100 100 100 100 1966 1971 2.315 .432 .411 .428 .428 1.112 32 236 .432 .99 70 2160 6940 58 65 72 79 0 1169 114 1055 .768 1135 1021 1.301 .731 -.38 -.452
2 127 118 30 66 97 52 124 114 31 67 94 48 0 0 25 25 5 13 100 96 100 87 149 142 1.865 .536 .511 .511 .512 1.599 32 176 .562 .82 60 2380 6940 59 65 95 101 0 210 117 93 .954 203 85 1.049 .908 -.068 -.139
3 708 210 30 67 678 143 745 210 30 67 715 143 0 0 148 48 5 13 100 100 100 100 821 858 4.741 .211 .2 .202 .2 1.353 32 236 .211 .95 70 2600 6940 58 65 116 123 0 374 119 254 .375 374 254 2.665 .356 -1.414 -1.491
4 52 79 30 69 22 10 51 79 30 68 21 10 0 0 10 15 5 15 100 37 87 6 32 31 2.2 .455 .476 .713 .924 2.266 32 176 1.92 .41 60 2830 6940 59 65 140 146 0 141 123 18 .809 141 18 1.237 .847 -.306 -.239
5 35 70 30 67 5 3 34 68 30 68 4 1 0 0 8 13 4 13 45 20 27 1 8 5 1.667 .6 .25 1.273 1.383 3.677 80 560 22.897 .08 100 3050 6940 57 67 160 170 -50 125 119 5 1.067 121 2 .937 .445 .094 -1.169
6 56 89 30 67 26 22 56 88 30 68 26 21 0 0 11 14 4 14 96 75 93 28 48 47 1.182 .846 .808 .681 .924 2.752 32 176 1.433 .5 60 3270 6940 59 65 184 190 0 158 119 39 1.505 157 37 .664 1.437 .59 .523
7 330 254 30 69 300 185 337 262 30 69 307 193 0 0 70 55 5 15 100 100 100 100 485 500 1.622 .617 .629 .603 .617 1.253 32 176 .634 .96 60 3490 6940 59 65 206 212 0 452 123 329 1.097 466 343 .912 1.118 .134 .161
8 119 111 29 69 90 42 116 109 30 70 87 40 0 0 24 20 4 14 100 93 100 75 132 127 2.143 .467 .46 .431 .44 1.747 32 176 .503 .74 60 3710 6940 59 65 228 234 0 197 123 75 .83 194 71 1.205 .818 -.268 -.29
9 91 97 30 68 61 29 95 96 30 69 65 28 0 0 20 20 4 14 100 78 100 50 90 93 2.103 .475 .431 .484 .534 1.785 32 236 .614 .6 70 3920 6940 58 65 248 255 0 173 121 52 .846 171 50 1.182 .766 -.242 -.384
10 148 135 31 67 117 68 154 132 30 68 123 65 0 0 34 33 4 14 100 93 100 87 185 188 1.721 .581 .528 .538 .529 1.589 32 176 .611 .84 60 4150 6940 59 65 272 278 0 240 119 121 1.034 235 116 .967 .94 .048 -.089
11 1283 537 30 66 1253 471 1311 520 31 69 1281 454 0 0 371 155 5 15 100 100 100 100 1724 1735 2.66 .376 .354 .368 .362 1.214 32 236 .375 .98 70 4370 6940 58 65 293 300 0 955 117 838 .669 925 808 1.495 .631 -.58 -.665
12 50 71 29 68 21 3 51 70 30 69 22 2 0 0 7 15 5 14 100 28 96 0 24 24 7 .143 .091 .521 .68 2.636 32 236 9.25 .08 70 4580 6940 58 65 314 321 0 126 121 5 .254 125 4 3.935 .162 -1.976 -2.628
13 163 116 30 65 133 51 169 114 30 66 139 49 0 0 60 24 5 13 100 92 98 86 184 188 2.608 .383 .353 .38 .379 1.707 52 340 .366 .83 80 4800 6940 58 66 336 344 0 206 116 91 .682 203 87 1.466 .627 -.552 -.673
14 373 188 32 70 341 118 380 183 62 81 348 113 0 0 117 46 109 46 94 94 82 71 459 461 2.89 .346 .325 .336 .334 1.371 52 340 .341 .94 80 5020 6940 58 66 358 366 0 334 125 210 .616 326 201 1.624 .578 -.7 -.792
15 146 107 30 67 116 40 148 105 54 74 118 38 0 0 40 20 179 60 5 15 0 0 156 156 2.9 .345 .322 .315 .349 1.861 52 420 .31 .96 90 5240 6950 58 67 379 388 0 190 119 71 .613 187 68 1.63 .573 -.705 -.804
16 930 386 30 67 900 319 1041 421 31 67 1011 354 0 0 406 159 6 13 100 98 98 94 1219 1365 2.821 .354 .35 .358 .355 1.318 52 340 .357 .98 80 5460 6940 58 66 402 410 0 687 119 568 .631 749 630 1.586 .623 -.665 -.683
17 239 148 29 66 210 82 258 146 30 67 229 80 0 0 102 47 6 13 100 92 100 88 292 309 2.561 .39 .349 .385 .379 1.604 52 340 .391 .91 80 5680 6940 58 66 424 432 0 263 117 146 .695 260 142 1.44 .621 -.526 -.686
18 142 134 30 67 112 67 148 131 30 67 118 64 0 0 32 32 5 14 100 100 100 90 179 182 1.672 .598 .542 .559 .554 1.529 52 340 .623 .85 80 5900 6950 59 67 446 454 0 238 119 119 1.064 233 114 .94 .965 .09 -.052
19 150 117 30 67 120 50 152 114 30 67 122 47 0 0 36 23 5 13 100 96 100 90 170 169 2.4 .417 .385 .393 .418 1.459 32 236 .429 .8 70 6130 6950 59 66 469 476 0 208 119 89 .741 203 84 1.349 .685 -.432 -.545
20 36 67 31 67 5 0 37 66 33 67 6 -1 0 0 7 11 14 14 8 8 0 1 5 5 null null null 1.181 1.143 3.627 80 560 -1 -1 100 2170 7160 79 89 72 82 -50 119 119 0 null 117 -2 null null null null

Total number of rows: 10944

Table truncated, full table size 2306 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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