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Sample GSM675167 Query DataSets for GSM675167
Status Public on Feb 08, 2012
Title SLF1 overexpression 6h (1)
Sample type RNA
 
Channel 1
Source name BY4741 (control vector, pBG1805)
Organism Saccharomyces cerevisiae
Characteristics reference: BY4741 (control vector, pBG1805)
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name SLF1Overexpression (6h-1)
Organism Saccharomyces cerevisiae
Characteristics experiment: SLF1Overexpression (6h-1)
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol GenePix 4200A
Description Simple annotation: Absolute transcript levels, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2011-02/92020.gif
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 Feb 14, 2011
Last update date Feb 08, 2012
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)
GSE27311 SLF1 overexpression versus control cells
GSE27312 Slf1p and Sro9p affinity isolations; SLF1 overexpression

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
1 263 435 29 107 234 328 263 438 33 110 234 331 0 0 74 99 16 29 100 100 100 100 562 565 .713 1.402 1.415 1.412 1.414 1.267 32 236 1.468 .93 70 2140 7130 33 40 42 49 0 481 118 363 1.551 484 366 .645 1.565 .633 .646
2 146 214 30 109 116 105 127 211 36 110 97 102 0 0 47 51 25 30 100 93 96 81 221 199 1.105 .905 1.052 .85 .832 1.834 32 236 1.126 .76 70 2370 7130 33 40 65 72 0 237 121 116 1.001 233 113 .999 1.163 .002 .218
3 125 215 29 108 96 107 119 197 34 110 90 89 0 0 36 49 15 27 100 100 96 87 203 179 .897 1.115 .989 1.073 1.17 1.804 32 236 1.355 .68 70 2590 7130 33 40 87 94 0 238 119 118 1.233 218 98 .811 1.094 .302 .129
4 87 169 31 109 56 60 79 170 37 111 48 61 0 0 47 32 21 28 87 81 59 53 116 109 .933 1.071 1.271 1.343 1.291 3.516 32 236 1.293 .38 70 2810 7130 33 40 109 116 0 187 121 66 1.185 188 67 .844 1.406 .245 .491
5 127 197 30 108 97 89 118 194 33 111 88 86 0 0 62 35 12 25 93 100 90 84 186 174 1.09 .918 .977 1.073 .79 2.732 32 176 .847 .55 60 3030 7130 34 40 132 138 0 218 119 98 1.015 215 95 .985 1.081 .021 .112
6 132 206 31 113 101 93 137 197 34 113 106 84 0 0 42 57 13 24 93 90 93 78 194 190 1.086 .921 .792 .91 .878 1.866 32 176 1.181 .67 60 3260 7120 33 39 155 161 0 228 125 103 1.019 218 93 .982 .877 .027 -.19
7 164 255 30 107 134 148 168 260 35 108 138 153 0 0 41 66 15 24 100 100 100 96 282 291 .905 1.104 1.109 1.051 1.015 1.564 32 176 1.261 .84 60 3480 7130 34 40 177 183 0 282 118 164 1.222 288 169 .819 1.226 .289 .294
8 262 369 28 113 234 256 244 371 32 114 216 258 0 0 78 93 11 27 100 100 100 100 490 474 .914 1.094 1.194 1.08 1.129 1.516 32 236 1.178 .91 70 3700 7120 32 39 198 205 0 408 125 283 1.21 410 285 .826 1.321 .275 .402
9 78 161 28 107 50 54 71 167 32 111 43 60 0 0 33 35 12 27 96 75 81 53 104 103 .926 1.08 1.395 .952 1.13 2.568 32 176 1.501 .44 60 3920 7130 34 40 221 227 0 178 118 60 1.195 185 66 .837 1.543 .257 .626
10 122 229 29 111 93 118 75 172 33 111 46 61 0 0 159 253 12 29 90 75 71 53 211 107 .788 1.269 1.326 1.229 1.2 2.654 32 176 1.611 .92 60 4140 7130 34 40 243 249 0 253 123 131 1.404 190 67 .712 1.467 .489 .553
11 315 454 33 114 282 340 314 453 1124 406 281 339 0 0 93 106 6998 1984 0 0 0 0 622 620 .829 1.206 1.206 1.213 1.195 1.426 32 236 1.315 .89 70 4350 7120 32 39 263 270 0 502 126 376 1.334 501 375 .75 1.334 .415 .416
12 124 205 30 109 94 96 116 201 38 112 86 92 0 0 38 38 28 30 100 96 84 84 190 178 .979 1.021 1.07 1.013 1.087 1.514 32 176 1.173 .73 60 4570 7120 33 39 286 292 0 227 121 106 1.13 222 102 .885 1.183 .176 .243
13 285 353 32 109 253 244 290 358 36 112 258 249 0 0 96 80 17 27 100 100 98 100 497 507 1.037 .964 .965 .999 1.009 1.587 52 340 .952 .88 80 4790 7130 33 41 307 315 0 390 121 270 1.067 396 275 .937 1.068 .093 .094
14 114 211 33 111 81 100 110 211 36 112 77 100 0 0 42 56 15 26 92 88 90 78 181 177 .81 1.235 1.299 1.117 1.253 2.36 52 340 1.57 .7 80 5020 7130 33 41 330 338 0 233 123 111 1.366 233 111 .732 1.437 .45 .523
15 93 176 34 107 59 69 96 178 38 111 62 71 0 0 37 44 17 26 82 78 73 59 128 133 .855 1.169 1.145 1.351 1.337 3.258 52 420 1.713 .53 90 5230 7120 31 40 350 359 0 195 118 76 1.294 197 79 .773 1.267 .371 .341
16 643 664 31 109 612 555 675 686 34 110 644 577 0 0 223 205 13 27 100 100 100 100 1167 1221 1.103 .907 .896 .917 .912 1.311 52 340 .913 .96 80 5450 7130 33 41 373 381 0 734 121 614 1.003 759 638 .997 .991 .005 -.013
17 145 215 33 113 112 102 131 209 36 114 98 96 0 0 56 50 14 27 100 96 90 81 214 194 1.098 .911 .98 .92 1.046 2.095 32 236 .98 .72 70 5670 7120 32 39 395 402 0 238 125 113 1.007 231 106 .993 1.084 .011 .116
18 112 212 32 111 80 101 112 210 34 112 80 99 0 0 41 48 12 26 94 94 90 88 181 179 .792 1.263 1.238 1.31 1.373 2.733 52 340 1.426 .71 80 5890 7130 33 41 417 425 0 235 123 112 1.397 232 110 .716 1.369 .482 .453
19 158 225 33 110 125 115 156 217 37 112 123 107 0 0 53 54 14 28 100 96 100 84 240 230 1.087 .92 .87 .856 1.044 2.433 32 236 1.046 .7 70 6110 7130 33 40 439 446 0 249 122 127 1.018 240 118 .983 .962 .025 -.055
20 61 143 31 116 30 27 62 133 35 117 31 17 0 0 24 34 17 33 58 33 41 16 57 48 1.111 .9 .548 1.121 .594 4.463 12 68 1.274 .39 40 2130 7340 56 60 43 47 0 158 128 30 .996 147 19 1.004 .607 -.006 -.721

Total number of rows: 10944

Table truncated, full table size 2311 Kbytes.




Supplementary data files not provided
Processed data provided as supplementary file
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