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Sample GSM402961 Query DataSets for GSM402961
Status Public on Jul 15, 2009
Title Trf4 delta (1)
Sample type RNA
 
Channel 1
Source name total RNA WT
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
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/2008-12/82458.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 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 5316 2415 51 35 5265 2380 5826 2630 52 35 5775 2595 0 0 1653 731 13 4 100 100 100 100 7645 8370 2.212 .452 .449 .454 .451 1.084 32 236 .452 1 70 2010 7190 47 54 29 36 0 4098 59 4039 .767 4463 4404 1.304 .763 -.383 -.391
2 468 210 48 34 420 176 538 244 48 34 490 210 0 0 194 91 6 4 100 96 100 93 596 700 2.386 .419 .429 .372 .405 1.445 32 176 .425 .98 60 2230 7180 47 53 52 58 0 356 58 299 .711 414 356 1.406 .727 -.492 -.459
3 2485 1035 48 35 2437 1000 3059 1226 48 34 3011 1191 0 0 1135 415 6 4 100 100 100 100 3437 4202 2.437 .41 .396 .448 .405 1.341 32 176 .4 .99 60 2450 7190 48 54 74 80 0 1756 59 1697 .696 2080 2021 1.436 .671 -.522 -.575
4 164 213 48 35 116 178 174 230 48 34 126 195 0 0 47 59 7 4 100 100 100 100 294 321 .652 1.534 1.548 1.618 1.571 1.318 32 176 1.496 .97 60 2670 7190 48 54 96 102 0 361 59 302 2.604 390 331 .384 2.626 1.381 1.393
5 98 60 46 35 52 25 110 60 47 34 64 25 0 0 25 11 6 4 96 93 87 93 77 89 2.08 .481 .391 .503 .473 1.602 32 176 .458 .89 60 2890 7200 49 55 118 124 0 102 59 42 .816 102 42 1.226 .663 -.294 -.593
6 132 328 47 35 85 293 125 331 47 35 78 296 0 0 30 43 6 4 100 100 100 100 378 374 .29 3.447 3.795 3.623 3.629 1.355 12 104 3.36 .95 50 3100 7180 47 52 139 144 0 557 59 497 5.85 562 502 .171 6.44 2.548 2.687
7 1536 790 48 34 1488 756 1911 958 49 34 1863 924 0 0 684 358 8 4 100 100 100 100 2244 2787 1.968 .508 .496 .488 .506 1.249 32 176 .51 .99 60 3340 7190 48 54 163 169 0 1341 58 1283 .862 1626 1568 1.16 .842 -.214 -.249
8 476 212 48 34 428 178 511 227 48 34 463 193 0 0 141 48 7 4 100 100 100 100 606 656 2.404 .416 .417 .428 .416 1.226 32 176 .4 .98 60 3550 7190 48 54 184 190 0 360 58 302 .706 385 328 1.417 .707 -.503 -.499
9 350 185 46 35 304 150 388 190 50 36 342 155 0 0 96 39 18 8 100 100 100 100 454 497 2.027 .493 .453 .508 .484 1.274 12 104 .473 .98 50 3770 7180 47 52 206 211 0 314 59 255 .837 322 263 1.194 .769 -.256 -.379
10 525 225 46 34 479 191 629 269 46 34 583 235 0 0 237 103 7 4 100 93 96 93 670 818 2.508 .399 .403 .369 .386 1.35 32 176 .401 .98 60 4000 7200 49 55 229 235 0 382 58 324 .677 456 399 1.478 .684 -.564 -.548
11 4911 2572 49 35 4862 2537 6272 3219 50 36 6223 3184 0 0 2317 1192 9 5 100 100 100 100 7399 9407 1.916 .522 .512 .531 .525 1.173 32 236 .52 1 70 4210 7190 47 54 249 256 0 4365 59 4305 .885 5463 5403 1.129 .868 -.175 -.204
12 127 63 47 35 80 28 120 61 48 35 73 26 0 0 19 8 7 5 100 100 100 100 108 99 2.857 .35 .356 .353 .365 1.319 12 104 .372 .88 50 4430 7170 46 51 272 277 0 107 59 48 .594 104 44 1.684 .604 -.752 -.726
13 272 135 46 35 226 100 269 139 46 35 223 104 0 0 96 48 6 4 100 100 100 98 326 327 2.26 .442 .466 .423 .425 1.236 52 340 .45 .98 80 4660 7190 47 55 294 302 0 229 59 170 .751 236 176 1.332 .791 -.413 -.338
14 569 230 46 35 523 195 577 236 47 34 531 201 0 0 162 66 6 4 100 100 100 100 718 732 2.682 .373 .379 .368 .368 1.138 52 340 .376 .99 80 4870 7190 47 55 315 323 0 390 59 331 .633 400 341 1.581 .642 -.66 -.639
15 335 174 48 35 287 139 337 170 48 34 289 135 0 0 50 26 8 4 100 100 100 100 426 424 2.065 .484 .467 .486 .483 1.159 32 236 .489 .98 70 5090 7180 46 53 337 344 0 295 59 236 .822 288 229 1.217 .793 -.283 -.335
16 1791 1040 47 34 1744 1006 1881 1101 47 34 1834 1067 0 0 873 506 7 4 100 100 100 100 2750 2901 1.734 .577 .582 .573 .573 1.207 52 340 .576 1 80 5310 7190 47 55 359 367 0 1765 58 1707 .979 1868 1811 1.022 .987 -.031 -.018
17 608 389 46 35 562 354 579 381 46 34 533 346 0 0 131 72 7 4 100 100 100 100 916 879 1.588 .63 .649 .635 .625 1.135 32 236 .615 .99 70 5530 7190 47 54 381 388 0 660 59 601 1.069 647 587 .936 1.102 .096 .14
18 250 133 46 34 204 99 255 136 46 34 209 102 0 0 68 31 6 4 100 100 100 100 303 311 2.061 .485 .488 .487 .476 1.304 52 340 .47 .97 80 5750 7180 46 54 403 411 0 226 58 168 .824 231 173 1.214 .828 -.28 -.272
19 386 206 46 35 340 171 401 211 46 34 355 176 0 0 112 60 6 4 100 100 100 100 511 531 1.988 .503 .496 .499 .497 1.189 32 176 .502 .98 60 5970 7180 47 53 426 432 0 350 59 290 .853 358 299 1.172 .841 -.229 -.249
20 91 59 49 35 42 24 91 59 50 35 42 24 0 0 17 9 7 3 96 96 90 96 66 66 1.75 .571 .571 .597 .605 1.538 32 236 .508 .83 70 2010 7400 68 75 29 36 0 100 59 41 .97 100 41 1.031 .97 -.044 -.044

Total number of rows: 10944

Table truncated, full table size 2322 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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