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Sample GSM259462 Query DataSets for GSM259462
Status Public on Aug 26, 2008
Title BY4741 mock (2)
Sample type RNA
 
Channel 1
Source name BY4741 tot. RNA extract (2)
Organism Saccharomyces cerevisiae
Characteristics BY4741 tot. RNA extract (2)
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name BY4741 RNA-IP (2)
Organism Saccharomyces cerevisiae
Characteristics BY4741 RNA-IP (2)
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/2003-01/36817.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
1 180 37 176 40 4 -3 175 37 181 40 -1 -3 0 0 35 5 41 5 16 6 5 0 1 -4 null null null .179 .179 2.747 80 455 .024 .15 100 2710 16690 36 46 22 32 -50 962 1040 -78 null 962 -78 null null null null
2 190 38 187 40 3 -2 184 39 194 40 -3 -1 0 0 38 5 48 5 16 12 0 0 1 -4 null null null .182 .17 3.249 80 432 .025 .23 100 2890 16690 36 46 40 50 -50 988 1040 -52 null 1014 -26 null null null null
3 197 38 192 41 5 -3 189 38 201 41 -3 -3 0 0 42 5 46 6 13 5 3 0 2 -6 null null null .175 .2 2.749 80 420 .028 .22 100 3060 16690 36 46 57 67 -50 988 1066 -78 null 988 -78 null null null null
4 194 39 194 41 0 -2 191 40 201 41 -3 -1 0 0 44 5 44 6 16 3 6 1 -2 -4 null null null .173 .14 3.672 80 420 .029 .2 100 3230 16690 36 46 74 84 -50 1014 1066 -52 null 1040 -26 null null null null
5 210 41 194 42 16 -1 204 41 202 42 10 -1 0 0 51 5 46 5 21 12 10 1 15 9 null null null .142 .126 3.98 80 420 .027 .23 100 3400 16690 36 46 91 101 -50 1066 1092 -26 null 1066 -26 null null null null
6 216 42 201 43 15 -1 206 42 217 43 5 -1 0 0 47 6 71 6 15 7 0 1 14 4 null null null .155 .112 4.289 80 430 .032 .26 100 3570 16680 35 45 108 118 -50 1092 1118 -26 null 1092 -26 null null null null
7 230 43 208 43 22 0 217 42 221 44 9 -1 0 0 99 7 84 7 20 13 6 2 22 8 null null null .103 .093 2.796 80 430 .037 .5 100 3750 16680 35 45 126 136 -50 1118 1118 0 null 1092 -26 null null null null
8 258 44 208 43 50 1 252 43 215 43 44 0 0 0 76 6 79 6 33 20 6 3 51 44 50 .02 null .091 .081 2.861 80 406 .032 .37 100 3920 16680 35 45 143 153 -50 1144 1118 26 .52 1118 0 1.922 null -.943 null
9 246 43 196 43 50 0 236 42 209 43 40 -1 0 0 83 7 78 7 31 13 10 3 50 39 null null null .092 .094 3.12 80 432 .04 .48 100 4090 16680 35 45 160 170 -50 1118 1118 0 null 1092 -26 null null null null
10 1069 74 197 43 872 31 972 73 207 43 775 30 0 0 389 16 72 6 100 95 100 90 903 805 28.129 .036 .039 .034 .035 1.362 80 440 .035 .92 100 4260 16690 36 46 177 187 0 1925 1118 806 .925 1899 780 1.082 1.007 -.113 .01
11 276 44 210 43 66 1 258 45 207 43 48 2 0 0 102 6 77 6 33 22 8 5 67 50 66 .015 .042 .102 .09 2.891 80 464 .032 .43 100 4430 16680 35 45 194 204 -50 1144 1118 26 .394 1170 52 2.538 1.084 -1.343 .116
12 294 46 237 44 57 2 283 45 240 45 46 1 0 0 109 6 74 6 30 18 7 5 59 47 28.5 .035 .022 .087 .061 3.583 80 401 .031 .44 100 4600 16680 35 45 211 221 -50 1196 1144 52 .913 1170 26 1.096 .565 -.132 -.823
13 3351 163 228 44 3123 119 3552 174 237 45 3324 130 0 0 1120 48 76 6 99 98 98 95 3242 3454 26.244 .038 .039 .039 .039 1.329 120 539 .037 .97 120 4770 16690 35 47 227 239 0 4239 1144 3095 .991 4526 3381 1.009 1.017 -.013 .025
14 25458 768 245 47 25213 721 24689 734 260 47 24444 687 0 0 6692 167 86 7 100 100 100 100 25934 25131 34.969 .029 .028 .029 .029 1.12 80 402 .028 .99 100 4950 16680 35 45 246 256 0 19975 1222 18752 .744 19090 17868 1.345 .731 -.427 -.452
15 63767 5418 221 47 63546 5371 65535 5358 251 48 65314 5311 83 0 6032 948 95 10 100 100 100 100 68917 70625 11.831 .085 .081 .084 .083 1.145 80 501 .083 .98 110 5110 16670 33 44 261 272 0 140916 1222 139693 2.198 139355 138133 .455 2.115 1.136 1.081
16 2574 143 201 45 2373 98 2608 146 220 46 2407 101 0 0 815 36 70 9 100 100 100 98 2471 2508 24.214 .041 .042 .041 .04 1.212 80 511 .04 .97 110 5290 16680 34 45 279 290 0 3719 1170 2549 1.074 3797 2627 .931 1.091 .103 .126
17 1161 81 201 44 960 37 1219 85 207 44 1018 41 0 0 335 16 42 5 100 95 100 93 997 1059 25.946 .039 .04 .037 .039 1.352 80 497 .037 .93 110 5470 16680 34 45 297 308 0 2107 1144 962 1.002 2211 1066 .998 1.048 .003 .067
18 13429 555 199 43 13230 512 13364 554 201 43 13165 511 0 0 3004 112 43 5 100 100 100 100 13742 13676 25.84 .039 .039 .039 .039 1.067 80 497 .038 .99 110 5640 16670 33 44 314 325 0 14435 1118 13317 1.007 14409 13291 .994 1.01 .009 .014
19 1567 98 201 43 1366 55 1581 95 208 43 1380 52 0 0 533 27 56 5 100 100 100 98 1421 1432 24.836 .04 .038 .038 .041 1.397 80 491 .04 .95 110 5810 16670 33 44 331 342 0 2549 1118 1430 1.047 2471 1352 .955 .98 .067 -.029
20 2811 145 218 43 2593 102 2317 129 234 44 2099 86 0 0 1259 48 73 6 100 100 100 100 2695 2185 25.422 .039 .041 .04 .039 1.208 80 496 .038 .98 110 5990 16670 33 44 349 360 0 3771 1118 2653 1.023 3355 2237 .977 1.066 .033 .092

Total number of rows: 9984

Table truncated, full table size 2150 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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