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Sample GSM402959 Query DataSets for GSM402959
Status Public on Jul 15, 2009
Title Trf4-DADA (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 from trf4-DADA cells (2)
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/2008-12/82465.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 7190 4828 48 55 7142 4773 3484 2143 50 59 3436 2088 0 0 7288 5048 14 16 100 100 100 98 11915 5524 1.496 .668 .608 .601 .663 1.412 80 554 .681 1 100 2220 6790 42 52 77 87 0 7749 88 7660 1.073 3439 3351 .932 .975 .101 -.036
2 1099 607 42 52 1057 555 1299 686 44 53 1257 634 0 0 625 333 10 10 100 100 100 96 1612 1891 1.905 .525 .504 .475 .527 1.457 52 340 .525 .99 80 2450 6780 42 50 101 109 0 974 83 891 .843 1101 1018 1.187 .809 -.247 -.305
3 8220 4171 44 52 8176 4119 9421 4669 45 53 9377 4617 0 0 4102 2048 11 10 100 100 100 100 12295 13994 1.985 .504 .492 .511 .504 1.148 52 420 .501 1 90 2660 6780 41 50 121 130 0 6694 83 6611 .809 7494 7410 1.237 .79 -.307 -.34
4 428 377 40 50 388 327 415 394 41 50 375 344 0 0 126 106 8 8 100 100 100 100 715 719 1.187 .843 .917 .84 .826 1.226 32 236 .837 .98 70 2890 6790 43 50 145 152 0 605 80 525 1.353 632 552 .739 1.472 .436 .558
5 307 279 42 50 265 229 307 273 43 51 265 223 0 0 95 86 9 9 100 100 100 100 494 488 1.157 .864 .842 .83 .852 1.336 32 236 .864 .97 70 3110 6780 42 49 167 174 0 448 80 368 1.387 438 358 .721 1.351 .472 .434
6 559 551 45 53 514 498 594 576 46 54 549 523 0 0 198 212 9 8 100 100 100 100 1012 1072 1.032 .969 .953 .948 .939 1.152 32 236 .989 .99 70 3330 6780 42 49 189 196 0 884 85 799 1.555 924 839 .643 1.529 .637 .613
7 3319 2163 49 54 3270 2109 3335 2157 53 57 3286 2103 0 0 1164 757 33 26 100 100 100 100 5379 5389 1.55 .645 .64 .64 .65 1.114 32 236 .653 .99 70 3550 6780 42 49 211 218 0 3472 87 3385 1.035 3462 3375 .966 1.027 .05 .039
8 1132 575 53 58 1079 517 1089 540 53 59 1036 482 0 0 298 157 10 11 100 100 100 100 1596 1518 2.087 .479 .465 .476 .488 1.121 32 236 .481 .99 70 3770 6780 42 49 233 240 0 923 93 830 .769 867 774 1.3 .747 -.379 -.421
9 796 506 67 73 729 433 764 500 69 74 697 427 0 0 209 124 16 13 100 100 100 100 1162 1124 1.684 .594 .613 .601 .598 1.189 32 236 .571 .98 70 3990 6790 43 50 255 262 0 812 117 695 .953 802 685 1.049 .983 -.069 -.024
10 769 460 101 100 668 360 474 347 128 120 373 247 0 0 593 280 74 58 88 90 80 76 1028 620 1.856 .539 .662 .612 .565 1.424 80 560 .499 .98 100 4220 6780 41 51 277 287 0 738 160 578 .865 557 396 1.156 1.063 -.209 .088
11 8806 6150 68 72 8738 6078 9915 6387 70 75 9847 6315 0 0 5640 3967 20 19 100 100 100 100 14816 16162 1.438 .696 .641 .68 .692 1.215 52 340 .698 .99 80 4430 6780 42 50 299 307 0 9870 116 9755 1.116 10251 10135 .896 1.029 .159 .042
12 459 304 71 76 388 228 458 302 109 106 387 226 0 0 84 73 125 103 100 96 96 59 616 613 1.702 .588 .584 .571 .568 1.234 32 236 .625 .96 70 4660 6780 42 49 322 329 0 488 122 366 .943 485 363 1.06 .937 -.084 -.093
13 972 647 56 62 916 585 888 607 56 62 832 545 0 0 460 274 10 10 100 100 100 100 1501 1377 1.566 .639 .655 .649 .644 1.175 52 420 .623 .99 90 4870 6790 42 51 342 351 0 1038 100 939 1.025 974 875 .976 1.051 .036 .072
14 3551 2255 53 58 3498 2197 3231 2142 54 60 3178 2084 0 0 1804 1226 10 10 100 100 100 100 5695 5262 1.592 .628 .656 .584 .637 1.329 52 420 .644 .99 90 5100 6780 41 50 365 374 0 3619 93 3526 1.008 3438 3345 .992 1.052 .012 .074
15 1200 733 49 54 1151 679 1146 718 49 55 1097 664 0 0 473 299 10 10 100 100 100 100 1830 1761 1.695 .59 .605 .569 .58 1.201 52 340 .599 .98 80 5320 6780 42 50 388 396 0 1176 87 1090 .947 1152 1066 1.056 .971 -.079 -.042
16 7482 5921 48 54 7434 5867 6702 5126 49 56 6654 5072 0 0 6582 5236 10 10 100 100 100 100 13301 11726 1.267 .789 .762 .748 .793 1.347 80 560 .792 1 100 5540 6790 42 52 409 419 0 9503 87 9416 1.267 8227 8140 .789 1.223 .341 .291
17 2125 1659 48 55 2077 1604 1937 1584 49 55 1889 1529 0 0 849 638 9 9 100 100 100 100 3681 3418 1.295 .772 .809 .781 .759 1.216 52 340 .768 .99 80 5760 6790 43 51 432 440 0 2663 88 2574 1.239 2542 2454 .807 1.299 .31 .377
18 1032 778 44 51 988 727 954 718 45 52 910 667 0 0 409 274 10 10 100 100 100 100 1715 1577 1.359 .736 .733 .756 .734 1.228 52 340 .723 .99 80 5980 6790 43 51 454 462 0 1249 82 1167 1.181 1152 1071 .847 1.176 .24 .234
19 1527 1019 45 51 1482 968 1551 1095 45 52 1506 1044 0 0 810 513 10 9 100 100 100 100 2450 2550 1.531 .653 .693 .659 .643 1.341 52 340 .646 .99 80 6210 6790 43 51 477 485 0 1635 82 1554 1.048 1757 1676 .954 1.113 .068 .154
20 196 203 87 108 109 95 202 203 97 122 115 95 0 0 49 39 37 51 90 88 71 41 204 210 1.147 .872 .826 .919 .812 1.553 80 554 .996 .82 100 2230 7000 63 73 78 88 0 326 173 152 1.399 326 152 .715 1.326 .484 .407

Total number of rows: 10944

Table truncated, full table size 2314 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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