NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM259465 Query DataSets for GSM259465
Status Public on Aug 26, 2008
Title BY4741 mock (4)
Sample type RNA
 
Channel 1
Source name BY4741 tot. RNA extract (4)
Organism Saccharomyces cerevisiae
Characteristics BY4741 tot. RNA extract (4)
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name BY4741 RNA-IP (4)
Organism Saccharomyces cerevisiae
Characteristics BY4741 RNA-IP (4)
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol Gerber et al. (2004) PLoS Biology; The protocol can be found in the Series supplementary file
 
 
Hybridization protocol not provided
Scan protocol Scanner Make = Axon Instruments (V1.00); Scanner Model = GenePix 4000B [81971]; Scanning software = AxImageIO
Description Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/37362.gif
Strain Name: not tagged
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 Jan 25, 2008
Last update date Aug 26, 2008
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 GPL6419
Series (1)
GSE10279 Khd1p associated mRNAs

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 96 36 82 29 14 7 82 31 84 29 0 2 0 0 44 18 18 4 23 28 15 17 21 2 2 .5 null .322 .253 2.902 80 464 .256 .74 100 2250 17610 36 46 20 30 -50 344 277 67 4.771 296 19 .21 null 2.254 null
2 118 37 91 30 27 7 96 30 95 31 5 0 0 0 64 21 24 6 30 21 15 16 34 5 3.857 .259 null .385 .379 3.143 80 428 .273 .79 100 2420 17610 36 46 37 47 -50 353 286 67 2.474 286 0 .404 null 1.307 null
3 98 36 85 30 13 6 85 32 89 31 0 2 0 0 45 14 21 5 15 22 11 12 19 2 2.167 .462 null .356 .333 3.692 80 428 .208 .69 100 2590 17610 36 46 54 64 -50 344 286 57 4.404 305 19 .227 null 2.139 null
4 94 32 87 29 7 3 88 30 89 30 1 1 0 0 27 10 17 4 18 20 7 13 10 2 2.333 .429 1 .351 .333 2.917 80 429 .2 .59 100 2760 17610 36 46 71 81 -50 305 277 29 4.09 286 10 .245 9.543 2.032 3.254
5 104 36 88 31 16 5 93 31 89 31 5 0 0 0 44 13 15 5 30 27 15 17 21 5 3.2 .313 null .434 .449 2.737 80 429 .226 .72 100 2930 17610 36 46 88 98 -50 344 296 48 2.982 296 0 .335 null 1.576 null
6 121 38 94 32 27 6 101 33 107 34 7 1 0 0 68 15 36 7 16 28 12 13 33 8 4.5 .222 .143 .447 .471 2.816 80 432 .171 .74 100 3100 17600 35 45 105 115 -50 363 305 57 2.121 315 10 .472 1.363 1.085 .447
7 166 45 115 35 51 10 153 41 118 37 38 6 0 0 63 14 37 8 50 37 17 15 61 44 5.1 .196 .158 .223 .219 2.99 80 444 .15 .7 100 3270 17600 35 45 122 132 -50 429 334 95 1.871 391 57 .534 1.507 .904 .591
8 154 45 104 35 50 10 136 41 109 35 32 6 0 0 70 16 30 7 51 41 18 17 60 38 5 .2 .188 .242 .222 2.711 80 426 .176 .75 100 3450 17600 35 45 140 150 -50 429 334 95 1.909 391 57 .524 1.789 .933 .839
9 156 41 101 33 55 8 135 37 103 33 34 4 0 0 81 19 25 6 63 33 30 15 63 38 6.875 .145 .118 .218 .22 2.966 80 432 .186 .84 100 3620 17600 35 45 157 167 -50 391 315 76 1.388 353 38 .72 1.123 .473 .167
10 471 77 107 36 364 41 472 71 112 36 365 35 0 0 62 19 30 6 100 100 100 100 405 400 8.878 .113 .096 .104 .097 1.471 52 354 .111 .88 90 3790 17610 36 45 174 183 0 735 344 391 1.075 678 334 .93 .915 .104 -.128
11 177 45 120 36 57 9 151 40 123 36 31 4 0 0 88 19 31 7 50 31 23 16 66 35 6.333 .158 .129 .217 .241 3.071 80 469 .176 .75 100 3960 17600 35 45 191 201 -50 429 344 86 1.507 382 38 .664 1.231 .591 .3
12 289 76 152 43 137 33 247 52 162 45 95 9 0 0 144 42 68 13 66 41 25 33 170 104 4.152 .241 .095 .175 .162 3.891 12 104 .197 .85 50 4130 17640 41 46 210 215 -100 725 410 315 2.299 496 86 .435 .904 1.201 -.145
13 1108 146 115 34 993 112 1102 143 119 35 987 109 0 0 181 28 35 8 100 100 100 100 1105 1096 8.866 .113 .11 .111 .11 1.359 80 498 .106 .93 110 4310 17620 36 47 225 236 0 1393 324 1069 1.076 1365 1040 .929 1.054 .106 .076
14 23378 1483 107 33 23271 1450 27682 1656 116 35 27575 1623 0 0 11735 706 38 8 100 100 100 99 24721 29198 16.049 .062 .059 .065 .061 1.569 120 499 .06 .97 120 4480 17620 36 48 242 254 0 14152 315 13837 .595 15803 15488 1.682 .562 -.75 -.832
15 47209 4790 116 36 47093 4754 60297 5816 126 38 60181 5780 16 0 22614 2162 43 9 100 100 100 100 51847 65961 9.906 .101 .096 .109 .101 1.489 120 526 .098 .98 120 4650 17620 36 48 259 271 0 45711 344 45367 .963 55502 55159 1.038 .917 -.054 -.126
16 1908 194 99 32 1809 162 1871 189 105 33 1772 157 0 0 398 34 28 7 100 100 100 100 1971 1929 11.167 .09 .089 .09 .088 1.191 80 449 .086 .97 110 4820 17620 36 47 276 287 0 1851 305 1546 .855 1804 1498 1.17 .846 -.227 -.242
17 1023 106 96 31 927 75 1023 104 98 31 927 73 0 0 175 19 20 4 100 100 100 100 1002 1000 12.36 .081 .079 .08 .082 1.333 80 485 .076 .94 110 4990 17610 35 46 293 304 0 1012 296 716 .772 992 697 1.295 .751 -.373 -.412
18 9465 1005 95 31 9370 974 10024 1047 99 31 9929 1016 0 0 2308 204 25 5 100 100 100 100 10344 10945 9.62 .104 .102 .106 .103 1.17 80 490 .099 .98 110 5160 17600 34 45 310 321 0 9591 296 9295 .992 9992 9696 1.008 .977 -.012 -.034
19 1397 141 95 31 1302 110 1366 143 98 32 1271 112 0 0 321 25 25 7 100 100 100 100 1412 1383 11.836 .084 .088 .084 .088 1.269 80 479 .081 .95 110 5340 17610 35 46 328 339 0 1346 296 1050 .806 1365 1069 1.24 .841 -.311 -.25
20 1007 122 96 31 911 91 981 119 99 32 885 88 0 0 193 24 20 6 100 100 100 100 1002 973 10.011 .1 .099 .098 .098 1.292 80 406 .096 .95 100 5510 17610 36 46 346 356 0 1164 296 868 .953 1136 840 1.049 .949 -.069 -.076

Total number of rows: 9984

Table truncated, full table size 2093 Kbytes.




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