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Sample GSM402965 Query DataSets for GSM402965
Status Public on Jul 15, 2009
Title Trf4 delta (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 trf4 delta (3)
Organism Saccharomyces cerevisiae
Characteristics strain: trf4 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/2008-12/82463.gif
mutated gene: trf4 deletion
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 1254 763 26 37 1228 726 1347 812 28 38 1321 775 0 0 531 314 12 15 100 100 100 96 1954 2096 1.691 .591 .587 .584 .593 1.173 32 176 .582 .98 60 2240 7100 35 41 65 71 0 3157 153 3004 2.446 3360 3207 .409 2.428 1.291 1.28
2 118 84 27 38 91 46 108 77 28 38 81 39 0 0 53 35 6 7 100 96 100 90 137 120 1.978 .505 .481 .459 .546 1.606 32 176 .559 .93 60 2470 7090 34 40 88 94 0 348 157 190 2.092 319 161 .478 1.992 1.065 .995
3 357 174 28 39 329 135 415 204 54 71 387 165 0 0 207 89 437 531 44 0 0 0 464 552 2.437 .41 .426 .424 .423 1.546 52 340 .412 .98 80 2690 7090 33 41 109 117 0 720 161 559 1.698 844 683 .589 1.764 .764 .819
4 70 79 26 38 44 41 72 80 27 38 46 42 0 0 19 20 4 7 100 93 96 90 85 88 1.073 .932 .913 .981 1.009 1.533 32 176 .797 .71 60 2920 7090 34 40 133 139 0 327 157 170 3.856 331 174 .259 3.778 1.947 1.918
5 143 72 27 38 116 34 93 65 28 39 66 27 0 0 122 30 10 7 87 82 80 71 150 93 3.412 .293 .409 .382 .406 2.395 80 556 .225 .81 100 3110 7110 34 44 150 160 0 298 157 141 1.213 269 112 .824 1.693 .278 .759
6 164 120 28 40 136 80 156 119 33 41 128 79 0 0 60 20 49 19 100 100 62 100 216 207 1.7 .588 .617 .629 .586 1.496 32 176 .522 .9 60 3350 7090 34 40 176 182 0 497 166 331 2.434 492 327 .411 2.554 1.283 1.353
7 281 188 27 38 254 150 293 197 28 39 266 159 0 0 56 40 3 10 100 100 100 100 404 425 1.693 .591 .598 .584 .585 1.176 32 176 .595 .98 60 3570 7100 35 41 198 204 0 778 157 621 2.444 815 658 .409 2.473 1.289 1.307
8 99 69 27 37 72 32 98 68 27 37 71 31 0 0 20 11 3 6 100 100 100 93 104 102 2.25 .444 .437 .422 .429 1.477 32 176 .404 .81 60 3790 7100 35 41 220 226 0 286 153 132 1.839 281 128 .544 1.807 .879 .853
9 63 55 27 37 36 18 62 54 27 38 35 17 0 0 12 11 3 6 100 87 100 68 54 52 2 .5 .486 .452 .455 1.946 32 176 .536 .64 60 4010 7090 34 40 242 248 0 228 153 74 2.069 223 70 .483 2.01 1.049 1.007
10 106 77 26 37 80 40 112 79 27 37 86 42 0 0 29 18 3 6 100 96 100 93 120 128 2 .5 .488 .489 .479 1.442 32 176 .53 .88 60 4230 7100 35 41 264 270 0 319 153 166 2.069 327 174 .483 2.021 1.049 1.015
11 953 612 27 38 926 574 1014 644 27 38 987 606 0 0 238 142 3 6 100 100 100 100 1500 1593 1.613 .62 .614 .627 .616 1.152 32 176 .618 .99 60 4450 7100 35 41 286 292 0 2532 157 2375 2.565 2665 2508 .39 2.541 1.359 1.345
12 50 44 27 37 23 7 49 44 27 37 22 7 0 0 10 6 4 6 100 53 100 25 30 29 3.286 .304 .318 .365 .417 1.993 32 176 .364 .47 60 4670 7100 35 41 308 314 0 182 153 29 1.259 182 29 .794 1.317 .333 .397
13 145 85 27 37 118 48 151 86 27 37 124 49 0 0 50 21 4 7 100 98 100 94 166 173 2.458 .407 .395 .408 .401 1.497 52 340 .391 .92 80 4890 7100 34 42 329 337 0 352 153 199 1.683 356 203 .594 1.635 .751 .709
14 225 112 28 38 197 74 238 115 33 38 210 77 0 0 65 25 20 7 100 100 100 100 271 287 2.662 .376 .367 .372 .376 1.317 52 340 .367 .95 80 5110 7100 34 42 351 359 0 463 157 306 1.554 476 319 .643 1.517 .636 .601
15 108 68 28 38 80 30 116 69 30 39 88 31 0 0 30 14 9 6 100 98 100 90 110 119 2.667 .375 .352 .367 .389 1.586 52 340 .365 .86 80 5330 7100 34 42 373 381 0 281 157 124 1.552 286 128 .644 1.458 .634 .544
16 665 423 28 38 637 385 776 512 39 40 748 474 0 0 330 196 49 11 94 96 88 96 1022 1222 1.655 .604 .634 .619 .626 1.28 52 340 .597 .99 80 5550 7100 34 42 395 403 0 1750 157 1593 2.501 2119 1961 .4 2.622 1.323 1.391
17 182 117 27 38 155 79 182 121 27 37 155 83 0 0 33 17 3 6 100 100 100 100 234 238 1.962 .51 .535 .509 .513 1.206 32 236 .505 .96 70 5770 7100 34 41 417 424 0 484 157 327 2.109 501 343 .474 2.216 1.077 1.148
18 85 65 27 39 58 26 85 66 52 65 58 27 0 0 21 14 188 203 0 0 0 0 84 85 2.231 .448 .466 .425 .439 1.583 52 340 .468 .83 80 5990 7100 34 42 439 447 0 269 161 108 1.855 273 112 .539 1.926 .891 .946
19 118 80 27 38 91 42 114 80 28 38 87 42 0 0 27 16 9 6 100 100 100 100 133 129 2.167 .462 .483 .446 .444 1.369 32 236 .449 .91 70 6210 7100 34 41 461 468 0 331 157 174 1.91 331 174 .524 1.998 .933 .998
20 32 46 26 37 6 9 31 46 26 37 5 9 0 0 5 9 4 5 62 65 18 37 15 14 .667 1.5 1.8 1.767 2 2.767 32 236 2.804 .45 70 2250 7310 55 62 65 72 0 190 153 37 6.207 190 37 .161 7.448 2.634 2.897

Total number of rows: 10944

Table truncated, full table size 2292 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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