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Sample GSM675166 Query DataSets for GSM675166
Status Public on Feb 08, 2012
Title SLF1 overexpression 24h (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 (24h-1)
Organism Saccharomyces cerevisiae
Characteristics experiment: SLF1Overexpression (24h-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/2011-02/92021.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
1 245 292 41 59 204 233 250 281 42 61 209 222 0 0 57 76 10 11 100 100 100 100 437 431 .876 1.142 1.062 1.126 1.151 1.309 32 176 1.171 .95 60 2120 6800 37 43 65 71 0 293 59 234 1.145 282 223 .873 1.065 .195 .091
2 68 74 41 58 27 16 67 69 42 59 26 11 0 0 16 14 10 10 83 50 66 33 43 37 1.688 .593 .423 .503 .596 3.724 12 104 .692 .46 50 2340 6800 37 42 87 92 0 74 58 16 .594 69 11 1.683 .424 -.751 -1.238
3 153 186 43 59 110 127 156 190 43 59 113 131 0 0 33 36 11 11 100 100 100 100 237 244 .866 1.155 1.159 1.153 1.091 1.422 32 236 1.162 .89 70 2560 6790 35 42 108 115 0 186 59 127 1.157 190 131 .864 1.162 .211 .217
4 45 58 43 58 2 0 46 57 43 58 3 -1 0 0 10 12 11 11 17 18 2 3 2 2 null null null 1.105 1.258 2.966 80 560 1.39 .11 100 2780 6790 34 44 129 139 -50 58 58 0 null 57 -1 null null null null
5 45 59 42 61 3 -2 46 59 44 61 4 -2 0 0 10 12 14 12 13 11 2 1 1 2 null null null 1.257 1.142 3.456 80 560 1.208 .09 100 3000 6790 34 44 151 161 -50 59 61 -2 null 59 -2 null null null null
6 46 57 43 62 3 -5 45 55 44 63 2 -7 0 0 11 10 14 11 20 8 0 0 -2 -5 null null null 1.559 1.538 3.597 80 560 .068 .03 100 3220 6790 34 44 173 183 -50 57 62 -5 null 55 -7 null null null null
7 92 112 43 62 49 50 93 112 44 63 50 50 0 0 23 22 9 12 93 93 90 87 99 100 .98 1.02 1 .907 .98 2.198 32 176 1.018 .79 60 3450 6790 36 42 198 204 0 112 62 50 1.023 112 50 .978 1.002 .033 .003
8 214 161 45 64 169 97 219 160 46 66 174 96 0 0 57 39 14 16 100 100 100 96 266 270 1.742 .574 .552 .561 .521 1.519 32 236 .16 .65 70 3670 6790 35 42 219 226 0 161 64 97 .575 160 96 1.738 .553 -.798 -.855
9 66 70 44 62 22 8 61 68 47 63 17 6 0 0 17 13 24 14 43 28 9 6 30 23 2.75 .364 .353 .586 .667 2.893 32 176 .431 .28 60 3900 6790 36 42 243 249 0 70 62 8 .365 68 6 2.743 .354 -1.456 -1.499
10 78 74 40 60 38 14 73 77 42 61 33 17 0 0 22 12 11 10 91 66 83 41 52 50 2.714 .368 .515 .508 .419 2.444 12 104 .052 .16 50 4110 6780 35 40 264 269 0 74 60 14 .369 77 17 2.708 .516 -1.437 -.953
11 199 244 40 58 159 186 212 246 41 59 172 188 0 0 48 58 10 10 100 100 100 100 345 360 .855 1.17 1.093 1.165 1.13 1.331 32 236 1.164 .95 70 4330 6800 36 43 285 292 0 245 58 186 1.173 247 188 .853 1.096 .23 .132
12 80 79 41 58 39 21 77 82 43 59 36 24 0 0 20 14 11 11 96 75 81 50 60 60 1.857 .538 .667 .583 .491 1.824 32 176 .466 .45 60 4560 6790 36 42 309 315 0 79 58 21 .54 82 24 1.853 .668 -.89 -.582
13 80 77 39 57 41 20 76 78 39 58 37 21 0 0 24 17 8 11 96 68 90 37 61 58 2.05 .488 .568 .607 .576 2.163 32 176 .414 .46 60 4770 6790 36 42 330 336 0 77 57 20 .489 78 21 2.045 .569 -1.032 -.814
14 73 83 39 55 34 28 69 85 40 56 30 30 0 0 19 12 11 10 87 87 75 75 62 60 1.214 .824 1 .815 .8 2.829 32 236 .739 .54 70 4990 6790 35 42 351 358 0 83 55 28 .826 85 30 1.211 1.002 -.277 .003
15 72 72 40 54 32 18 72 72 41 54 32 18 0 0 18 13 9 11 90 59 75 34 50 50 1.778 .563 .563 .564 .65 2.347 32 176 .501 .49 60 5210 6780 35 41 374 380 0 72 54 18 .564 72 18 1.774 .564 -.827 -.827
16 391 359 37 54 354 305 408 367 38 55 371 313 0 0 174 161 9 10 100 100 100 96 659 684 1.161 .862 .844 .83 .845 1.285 52 340 .885 .99 80 5440 6800 36 44 396 404 0 360 54 306 .864 368 314 1.158 .846 -.211 -.242
17 96 107 39 54 57 53 94 109 39 54 55 55 0 0 20 18 9 10 100 100 100 96 110 110 1.075 .93 1 .922 .975 1.488 32 236 .933 .79 70 5660 6790 35 42 418 425 0 107 54 53 .932 109 55 1.073 1.002 -.102 .003
18 75 85 38 55 37 30 76 83 40 55 38 28 0 0 16 17 9 11 96 87 90 59 67 66 1.233 .811 .737 .771 .829 2.169 32 236 .935 .6 70 5880 6800 36 43 440 447 0 85 55 30 .813 83 28 1.23 .739 -.299 -.437
19 79 105 38 54 41 51 78 103 39 54 40 49 0 0 16 24 11 11 100 96 84 87 92 89 .804 1.244 1.225 1.091 1.16 2.251 32 236 1.376 .79 70 6110 6790 35 42 463 470 0 105 54 51 1.247 103 49 .802 1.228 .318 .296
20 48 61 43 58 5 3 46 61 44 59 3 3 0 0 12 11 13 11 18 17 5 5 8 6 1.667 .6 1 1.356 1.444 3.426 80 560 3.448 .06 100 2110 7010 56 66 62 72 -50 61 58 3 .601 61 3 1.663 1.002 -.734 .003

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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