NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM402963 Query DataSets for GSM402963
Status Public on Jul 15, 2009
Title Trf5 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 trf5 delta (3)
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/2008-12/82462.gif
mutated gene: trf5 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 1578 1020 34 68 1544 952 1724 1076 56 73 1690 1008 0 0 664 410 197 52 96 96 90 96 2496 2698 1.622 .617 .596 .608 .607 1.203 52 340 .6 .97 80 2140 6990 55 63 70 78 0 1992 133 1859 1.204 2101 1968 .831 1.165 .268 .22
2 142 165 32 67 110 98 148 152 33 67 116 85 0 0 42 79 7 16 96 90 93 90 208 201 1.122 .891 .733 .825 .82 1.963 32 236 1.123 .77 70 2360 6980 54 61 92 99 0 322 131 191 1.74 297 166 .575 1.431 .799 .517
3 468 195 34 70 434 125 517 190 109 74 483 120 0 0 164 61 215 20 88 98 59 90 559 603 3.472 .288 .248 .285 .272 1.502 52 340 .29 .92 80 2590 6990 55 63 115 123 0 381 137 244 .562 371 234 1.778 .485 -.83 -1.044
4 510 173 106 82 404 91 382 128 119 84 276 46 0 0 218 191 67 19 100 78 100 59 495 322 4.44 .225 .167 .132 .136 2.524 32 176 .317 .5 60 2810 6990 56 62 138 144 0 338 160 178 .44 250 90 2.274 .325 -1.185 -1.62
5 131 88 36 70 95 18 120 86 37 71 84 16 0 0 33 27 7 15 100 50 100 15 113 100 5.278 .189 .19 .177 .167 2.616 32 236 .238 .42 70 3030 6990 55 62 159 166 0 172 137 35 .37 168 31 2.703 .372 -1.435 -1.427
6 47 69 34 68 13 1 46 69 36 70 12 1 0 0 15 15 16 16 36 11 11 5 14 13 13 .077 .083 .813 .767 3.7 80 560 5.539 .13 100 3250 6990 54 64 180 190 -50 135 133 2 .15 135 2 6.658 .163 -2.735 -2.62
7 366 208 37 70 329 138 364 199 39 72 327 129 0 0 79 50 15 30 100 100 100 93 467 456 2.384 .419 .394 .405 .393 1.376 32 236 .421 .91 70 3480 7000 56 63 204 211 0 406 137 269 .819 389 252 1.221 .77 -.288 -.377
8 111 101 35 68 76 33 103 99 46 73 68 31 0 0 25 13 121 45 3 21 0 0 109 99 2.303 .434 .456 .416 .435 1.72 32 236 .355 .73 70 3700 7000 56 63 226 233 0 197 133 64 .848 193 61 1.18 .89 -.238 -.168
9 62 82 33 68 29 14 60 80 34 69 27 12 0 0 15 16 7 14 93 43 84 9 43 39 2.071 .483 .444 .579 .675 3.28 32 236 1.31 .29 70 3920 6990 55 62 248 255 0 160 133 27 .943 156 23 1.061 .868 -.085 -.205
10 137 150 32 67 105 83 139 144 35 68 107 77 0 0 28 37 13 15 100 100 100 93 188 184 1.265 .79 .72 .744 .779 1.532 32 176 .833 .83 60 4140 6990 56 62 271 277 0 293 131 162 1.543 281 150 .648 1.405 .626 .491
11 596 481 35 70 561 411 636 524 40 71 601 454 0 0 250 183 32 18 93 93 93 93 972 1055 1.365 .733 .755 .756 .775 1.238 32 236 .729 .98 70 4350 6980 54 61 291 298 0 939 137 802 1.43 1023 886 .699 1.475 .516 .561
12 47 89 34 69 13 20 49 87 35 71 15 18 0 0 7 19 6 15 83 50 58 41 33 33 .65 1.538 1.2 1.41 2 2.435 12 68 6.322 .29 40 4570 6970 55 59 315 319 0 174 135 39 3.004 170 35 .333 2.343 1.587 1.228
13 127 123 32 67 95 56 116 120 33 67 84 53 0 0 42 33 6 13 100 92 98 86 151 137 1.696 .589 .631 .55 .616 1.837 52 340 .548 .96 80 4800 6990 55 63 336 344 0 240 131 109 1.151 234 103 .869 1.232 .203 .301
14 184 149 33 69 151 80 184 146 35 70 151 77 0 0 57 40 11 14 100 96 100 92 231 228 1.888 .53 .51 .508 .493 1.42 52 340 .557 .91 80 5010 6990 55 63 357 365 0 291 135 156 1.034 285 150 .967 .996 .049 -.006
15 100 105 33 67 67 38 98 104 34 67 65 37 0 0 24 19 5 14 100 92 100 61 105 102 1.763 .567 .569 .546 .518 1.674 52 340 .603 .72 80 5230 6990 55 63 379 387 0 205 131 74 1.107 203 72 .903 1.111 .147 .152
16 482 264 35 67 447 197 513 268 39 69 478 201 0 0 189 91 28 18 98 98 98 94 644 679 2.269 .441 .421 .421 .443 1.366 52 340 .44 .96 80 5450 7000 56 64 401 409 0 515 131 385 .861 523 392 1.162 .821 -.217 -.284
17 146 121 35 68 111 53 143 120 40 70 108 52 0 0 57 37 35 19 92 80 80 59 164 160 2.094 .477 .481 .432 .47 1.993 52 340 .492 .81 80 5670 6990 55 63 423 431 0 236 133 103 .932 234 102 1.073 .94 -.101 -.089
18 98 105 35 68 63 37 95 105 43 72 60 37 0 0 35 24 58 24 51 71 7 23 100 97 1.703 .587 .617 .544 .62 2.378 52 340 .457 .74 80 5900 6990 55 63 446 454 0 205 133 72 1.147 205 72 .872 1.204 .198 .268
19 109 110 32 67 77 43 114 116 34 68 82 49 0 0 46 29 16 14 86 78 80 69 120 131 1.791 .558 .598 .584 .545 2.175 52 340 .555 .78 80 6120 7000 56 64 468 476 0 215 131 84 1.09 226 96 .917 1.167 .125 .223
20 39 75 31 69 8 6 40 73 32 69 9 4 0 0 9 17 8 12 59 34 18 9 14 13 1.333 .75 .444 1.3 1.495 2.473 32 176 4.291 .27 60 2140 7210 78 84 71 77 0 146 135 12 1.464 143 8 .683 .868 .55 -.205

Total number of rows: 10944

Table truncated, full table size 2277 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap