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Sample GSM543589 Query DataSets for GSM543589
Status Public on Dec 06, 2010
Title Map1 Overexpression (3)
Sample type RNA
 
Channel 1
Source name BY4741 pBG1805 empty vector
Organism Saccharomyces cerevisiae
Characteristics cell line: BY4741
plasmid: pBG1805 empty vector
Growth protocol 100 ml of BY4741 cells bearing plasmid pBG1805-Map1 (MAP1 with a galactose inducible promotor) or the empty plasmid pBG1805 (=control) were grown in synthetic medium lacking uracil (SC-Ura) at 30C to an OD600 of 0.45- 0.5. Expression was induced with 2% galactose for 1.5 h
Extracted molecule total RNA
Extraction protocol cells were harvested by centrifugation, washed twice with 800 ul of ice-cold sterile water and frozen in liquid nitrogen. RNA was isolated by hot-phenol extraction for further microarray analysis. Therefore, total RNA isolated from the control (empty plasmid) and from MAP1 overexpressing cells was reverse transcribed using a mixture of oligo-dT and random nonamer oligos in the presence of amino-allyl dUTP/dNTP mixture, and cDNAs were fluorescently labeled with Cy3 and Cy5 dyes, respectively
Label Cy3
Label protocol not provided
 
Channel 2
Source name BY4741 pBG1805-Map1p
Organism Saccharomyces cerevisiae
Characteristics cell line: BY4741
plasmid: pBG1805-Map1p
Growth protocol 100 ml of BY4741 cells bearing plasmid pBG1805-Map1 (MAP1 with a galactose inducible promotor) or the empty plasmid pBG1805 (=control) were grown in synthetic medium lacking uracil (SC-Ura) at 30C to an OD600 of 0.45- 0.5. Expression was induced with 2% galactose for 1.5 h
Extracted molecule total RNA
Extraction protocol cells were harvested by centrifugation, washed twice with 800 ul of ice-cold sterile water and frozen in liquid nitrogen. RNA was isolated by hot-phenol extraction for further microarray analysis. Therefore, total RNA isolated from the control (empty plasmid) and from MAP1 overexpressing cells was reverse transcribed using a mixture of oligo-dT and random nonamer oligos in the presence of amino-allyl dUTP/dNTP mixture, and cDNAs were fluorescently labeled with Cy3 and Cy5 dyes, respectively
Label Cy5
Label protocol not provided
 
 
Hybridization protocol competitively hybridized on yeast oligo microarrays over night at 42 degrees in formamide-based hybridization buffer
Scan protocol GenePix 4200A 01
Description Simple annotation: Mutant vs Wild-type, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2008-10/81692.gif
allele name: MAP1
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, 2010
Last update date Dec 06, 2010
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 (1)
GSE21850 Map1p overexpression versus control cells microarrays

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
1 370 902 32 44 338 858 332 873 32 45 300 829 0 0 260 721 6 6 100 98 96 98 1196 1129 .394 2.538 2.763 1.931 2.457 1.764 52 340 2.662 .99 80 2220 6770 97 105 78 86 0 502 24 478 1.413 486 461 .708 1.538 .499 .621
2 56 96 31 45 25 51 53 100 33 46 22 55 0 0 12 20 9 17 93 96 65 78 76 77 .49 2.04 2.5 2.216 2.176 1.56 32 176 2.186 .86 60 2440 6750 96 102 101 107 0 53 25 28 1.136 56 31 .881 1.392 .183 .477
3 212 388 33 44 179 344 208 372 34 47 175 328 0 0 97 207 12 22 98 98 94 94 523 503 .52 1.922 1.874 1.823 1.913 1.418 52 340 2.002 .98 80 2660 6760 96 104 122 130 0 216 24 191 1.07 207 183 .935 1.043 .097 .061
4 48 73 34 48 14 25 45 66 37 51 11 18 0 0 13 36 14 16 34 56 9 12 39 29 .56 1.786 1.636 1.688 1.59 2.105 32 176 3.405 .61 60 2890 6770 98 104 146 152 0 41 27 14 .994 37 10 1.006 .911 -.009 -.135
5 61 114 32 44 29 70 56 102 32 44 24 58 0 0 23 43 4 5 96 100 93 100 99 82 .414 2.414 2.417 2.707 2.455 1.971 32 176 2.579 .76 60 3110 6760 97 103 168 174 0 63 24 39 1.344 57 32 .744 1.345 .426 .428
6 49 67 33 43 16 24 48 63 33 44 15 20 0 0 11 16 5 5 81 84 65 78 40 35 .667 1.5 1.333 1.46 1.55 2.316 32 176 1.601 .71 60 3330 6760 97 103 190 196 0 37 24 13 .835 35 11 1.198 .742 -.26 -.43
7 196 302 32 44 164 258 191 340 32 44 159 296 0 0 52 101 5 6 100 100 100 100 422 455 .636 1.573 1.862 1.456 1.575 1.44 32 236 1.644 .98 70 3550 6760 96 103 211 218 0 168 24 144 .876 189 165 1.142 1.036 -.192 .051
8 283 523 33 46 250 477 278 536 34 47 245 490 0 0 55 129 5 7 100 100 100 100 727 735 .524 1.908 2 1.875 1.818 1.207 32 236 1.863 .96 70 3770 6760 96 103 233 240 0 291 26 266 1.062 298 273 .942 1.113 .087 .155
9 81 108 32 46 49 62 77 109 34 49 45 63 0 0 22 24 9 15 100 96 100 90 111 108 .79 1.265 1.4 1.257 1.244 1.516 32 176 1.281 .83 60 3990 6760 97 103 256 262 0 60 26 35 .704 61 35 1.42 .779 -.506 -.36
10 49 72 32 45 17 27 50 73 34 47 18 28 0 0 8 14 16 29 53 43 3 3 44 46 .63 1.588 1.556 1.405 1.5 1.811 32 176 1.893 .75 60 4210 6760 97 103 278 284 0 40 25 15 .884 41 16 1.131 .866 -.178 -.208
11 1177 2343 32 43 1145 2300 1250 2596 32 44 1218 2553 0 0 904 1892 4 5 100 100 100 100 3445 3771 .498 2.009 2.096 1.698 1.934 1.583 52 340 2.056 .99 80 4430 6760 96 104 299 307 0 1304 24 1280 1.118 1445 1421 .894 1.167 .161 .222
12 176 288 32 45 144 243 182 292 33 47 150 247 0 0 48 72 10 13 100 100 100 100 387 397 .593 1.688 1.647 1.684 1.629 1.272 32 236 1.554 .86 70 4650 6770 97 104 321 328 0 160 25 135 .939 163 137 1.065 .917 -.09 -.126
13 58 90 33 45 25 45 60 89 39 54 27 44 0 0 11 19 80 92 0 1 0 0 70 71 .556 1.8 1.63 1.833 1.8 1.682 52 340 2.15 .84 80 4870 6770 97 105 343 351 0 50 25 25 1.002 50 24 .998 .907 .003 -.141
14 65 103 32 46 33 57 63 103 40 55 31 57 0 0 15 20 80 92 1 3 0 0 90 88 .579 1.727 1.839 1.799 1.836 1.655 52 340 1.822 .85 80 5090 6770 97 105 365 373 0 57 26 32 .961 57 32 1.04 1.023 -.057 .033
15 64 98 33 49 31 49 65 101 34 51 32 52 0 0 13 20 7 14 94 92 86 80 80 84 .633 1.581 1.625 1.629 1.57 1.709 52 420 1.876 .81 90 5320 6760 95 104 387 396 0 55 27 27 .88 56 29 1.137 .905 -.185 -.145
16 181 365 34 50 147 315 184 386 51 65 150 336 0 0 54 134 101 109 75 92 15 69 462 486 .467 2.143 2.24 2.087 2.163 1.265 52 340 2.092 .89 80 5530 6760 96 104 409 417 0 203 28 175 1.193 215 187 .838 1.247 .254 .318
17 59 111 32 47 27 64 57 109 34 50 25 62 0 0 17 36 23 31 57 76 17 48 91 87 .422 2.37 2.48 2.217 2.1 1.763 52 340 1.683 .92 80 5750 6760 96 104 431 439 0 62 26 36 1.319 61 35 .758 1.38 .4 .465
18 54 78 32 46 22 32 55 78 34 50 23 32 0 0 10 19 15 20 76 78 15 32 54 55 .688 1.455 1.391 1.405 1.4 2.093 52 340 2.098 .71 80 5980 6770 97 105 454 462 0 43 26 18 .81 43 18 1.235 .774 -.305 -.369
19 54 93 33 49 21 44 48 89 34 52 15 40 0 0 21 42 6 17 63 60 55 52 65 55 .477 2.095 2.667 1.968 2.148 2.111 80 560 2.293 .84 100 6200 6750 94 104 475 485 0 52 27 24 1.166 50 22 .857 1.484 .222 .57
20 48 70 32 44 16 26 49 68 33 44 17 24 0 0 9 14 11 8 65 87 25 78 42 41 .615 1.625 1.412 1.646 1.909 2.453 32 236 1.862 .62 70 2220 6980 118 125 78 85 0 39 24 14 .905 38 13 1.106 .786 -.145 -.348

Total number of rows: 10944

Table truncated, full table size 2246 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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