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Sample GSM402958 Query DataSets for GSM402958
Status Public on Jul 15, 2009
Title Trf5 delta (2)
Sample type RNA
 
Channel 1
Source name total RNA WT (2)
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 trf5 delta (2)
Organism Saccharomyces cerevisiae
Characteristics strain: trf5 delta
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/2008-12/82461.gif
mutated gene: trf5 deltion
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) 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 (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 4038 2372 63 42 3975 2330 4337 2539 64 41 4274 2497 0 0 1108 625 10 6 100 100 100 100 6305 6771 1.706 .586 .584 .593 .585 1.108 32 236 .582 1 70 2030 7030 39 46 39 46 0 4119 73 4046 1.018 4409 4336 .982 1.015 .026 .021
2 394 246 62 41 332 205 400 249 64 42 338 208 0 0 69 47 18 8 100 100 100 100 537 546 1.62 .617 .615 .62 .626 1.299 32 176 .601 .96 60 2250 7040 41 47 62 68 0 427 71 356 1.072 432 361 .933 1.069 .101 .096
3 1229 645 62 40 1167 605 1263 702 62 40 1201 662 0 0 243 135 11 6 100 100 100 100 1772 1863 1.929 .518 .551 .517 .516 1.159 32 176 .516 .99 60 2470 7030 40 46 84 90 0 1120 69 1051 .9 1219 1150 1.111 .957 -.152 -.063
4 128 75 61 40 67 35 126 73 61 40 65 33 0 0 20 16 10 5 100 100 100 96 102 98 1.914 .522 .508 .487 .521 1.812 32 176 .433 .79 60 2690 7030 40 46 106 112 0 130 69 61 .907 127 57 1.102 .882 -.141 -.182
5 109 49 61 40 48 9 108 50 60 40 47 10 0 0 23 6 8 4 100 75 100 75 57 57 5.333 .188 .213 .231 .247 1.923 12 68 .138 .41 40 2920 7020 40 44 130 134 0 85 69 16 .326 87 17 3.071 .369 -1.619 -1.436
6 109 51 60 40 49 11 110 48 60 41 50 8 0 0 25 10 9 5 96 71 93 40 60 58 4.455 .224 .16 .22 .25 2.562 32 176 .184 .53 60 3140 7030 40 46 151 157 0 89 69 19 .39 83 14 2.565 .278 -1.359 -1.848
7 755 535 61 40 694 495 818 566 61 41 757 526 0 0 202 168 9 6 100 100 100 100 1189 1283 1.402 .713 .695 .674 .723 1.284 32 176 .723 .99 60 3360 7030 40 46 173 179 0 929 69 860 1.239 983 913 .807 1.207 .309 .271
8 312 195 61 41 251 154 303 192 61 41 242 151 0 0 64 40 9 6 100 100 100 100 405 393 1.63 .614 .624 .614 .596 1.347 32 176 .593 .93 60 3580 7020 39 45 195 201 0 339 71 267 1.065 333 262 .939 1.084 .091 .116
9 206 116 59 40 147 76 217 119 60 40 158 79 0 0 55 35 8 6 100 96 96 96 223 237 1.934 .517 .5 .507 .558 1.563 32 176 .491 .87 60 3800 7030 40 46 217 223 0 201 69 132 .898 207 137 1.114 .868 -.156 -.204
10 323 194 60 40 263 154 333 181 60 41 273 141 0 0 76 50 9 6 100 100 100 100 417 414 1.708 .586 .516 .584 .548 1.296 32 176 .576 .95 60 4020 7040 41 47 239 245 0 337 69 267 1.017 314 245 .983 .897 .024 -.157
11 2617 1802 60 40 2557 1762 2746 1849 59 41 2686 1809 0 0 506 340 9 6 100 100 100 100 4319 4495 1.451 .689 .673 .69 .697 1.087 32 176 .685 1 60 4240 7030 40 46 261 267 0 3129 69 3060 1.197 3211 3141 .836 1.17 .259 .226
12 101 88 59 40 42 48 103 90 60 40 44 50 0 0 22 20 9 6 90 96 87 93 90 94 .875 1.143 1.136 1.145 1.02 2.243 32 236 1.045 .82 70 4470 7020 38 45 283 290 0 153 69 83 1.985 156 87 .504 1.973 .989 .981
13 335 211 59 41 276 170 316 209 61 41 257 168 0 0 69 49 15 7 100 100 100 100 446 425 1.624 .616 .654 .606 .604 1.312 32 236 .608 .96 70 4670 7030 39 46 303 310 0 366 71 295 1.07 363 292 .935 1.135 .097 .183
14 708 361 58 41 650 320 707 350 59 41 649 309 0 0 114 58 9 6 100 100 100 100 970 958 2.031 .492 .476 .492 .49 1.195 52 340 .489 .98 80 4900 7030 39 47 326 334 0 627 71 556 .855 608 537 1.17 .827 -.226 -.274
15 250 162 60 43 190 119 265 168 102 78 205 125 0 0 76 49 177 154 67 28 0 0 309 330 1.597 .626 .61 .641 .673 1.444 52 340 .657 .94 80 5110 7030 39 47 347 355 0 281 75 207 1.088 292 217 .919 1.059 .121 .083
16 1857 1020 60 43 1797 977 2100 1112 107 81 2040 1069 0 0 740 408 204 171 96 94 94 90 2774 3109 1.839 .544 .524 .545 .542 1.142 52 340 .542 .99 80 5340 7020 38 46 370 378 0 1771 75 1697 .944 1931 1856 1.059 .91 -.083 -.136
17 392 247 60 41 332 206 420 257 60 42 360 216 0 0 129 86 9 6 100 100 100 100 538 576 1.612 .62 .6 .617 .586 1.204 52 340 .621 .98 80 5550 7030 39 47 391 399 0 429 71 358 1.077 446 375 .928 1.042 .108 .059
18 209 121 58 41 151 80 206 123 59 41 148 82 0 0 46 31 9 6 100 100 100 100 231 230 1.888 .53 .554 .517 .524 1.658 52 340 .516 .89 80 5780 7030 39 47 414 422 0 210 71 139 .92 214 142 1.087 .962 -.12 -.056
19 308 198 60 42 248 156 311 202 61 42 251 160 0 0 73 44 9 6 100 100 100 100 404 411 1.59 .629 .637 .637 .634 1.386 32 236 .606 .94 70 5990 7030 39 46 435 442 0 344 73 271 1.092 351 278 .915 1.107 .127 .147
20 105 50 62 39 43 11 106 51 64 41 44 12 0 0 22 8 23 8 78 62 37 21 54 56 3.909 .256 .273 .253 .283 2.805 32 176 .212 .68 60 2030 7250 62 68 40 46 0 87 68 19 .444 89 21 2.251 .474 -1.171 -1.078

Total number of rows: 10944

Table truncated, full table size 2340 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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