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Sample GSM543587 Query DataSets for GSM543587
Status Public on Dec 06, 2010
Title Map1 Overexpression (2)
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/2008-10/81691.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
1 178 414 32 38 146 376 175 433 33 38 143 395 0 0 52 90 7 5 100 100 100 100 522 538 .388 2.575 2.762 2.658 2.674 1.273 32 236 2.567 .95 70 2220 7120 60 67 78 85 0 196 18 178 1.222 205 187 .818 1.31 .289 .39
2 51 65 33 39 18 26 51 66 33 39 18 27 0 0 9 11 6 6 96 93 75 90 44 45 .692 1.444 1.5 1.41 1.4 1.837 32 176 1.562 .71 60 2440 7110 60 66 101 107 0 31 19 12 .685 31 13 1.459 .712 -.545 -.491
3 86 146 35 40 51 106 85 145 37 39 50 105 0 0 19 32 13 6 100 100 93 100 157 155 .481 2.078 2.1 2.096 2.223 1.346 32 236 2.113 .91 70 2670 7110 59 66 123 130 0 69 19 50 .986 69 50 1.014 .996 -.02 -.005
4 42 53 32 38 10 15 43 51 33 38 11 13 0 0 9 11 6 5 62 81 46 56 25 24 .667 1.5 1.182 1.295 1.208 2.886 32 176 1.428 .35 60 2900 7110 60 66 147 153 0 25 18 7 .712 24 6 1.405 .561 -.491 -.835
5 59 95 32 38 27 57 59 99 32 38 27 61 0 0 12 18 5 5 93 100 90 100 84 88 .474 2.111 2.259 2.41 2.225 1.98 32 176 2.082 .84 60 3110 7110 60 66 168 174 0 45 18 27 1.002 47 29 .998 1.072 .002 .1
6 48 65 32 38 16 27 47 64 33 38 15 26 0 0 12 16 6 5 75 84 59 81 43 41 .593 1.688 1.733 1.669 1.667 2.293 32 176 1.684 .67 60 3340 7110 60 66 191 197 0 31 18 13 .801 30 12 1.249 .822 -.321 -.282
7 107 250 32 38 75 212 110 264 32 38 78 226 0 0 23 74 5 6 100 100 100 100 287 304 .354 2.827 2.897 2.741 2.736 1.301 32 176 2.987 .95 60 3560 7110 60 66 213 219 0 119 18 101 1.341 125 107 .746 1.375 .423 .459
8 262 726 32 39 230 687 270 738 32 38 238 699 0 0 51 206 5 5 100 100 100 100 917 937 .335 2.987 2.937 2.913 2.928 1.176 32 176 3.127 .98 60 3780 7110 60 66 235 241 0 344 19 326 1.417 350 332 .706 1.393 .503 .479
9 55 93 33 37 22 56 56 94 34 37 23 57 0 0 12 24 7 5 87 96 65 96 78 80 .393 2.545 2.478 2.69 2.649 1.627 32 176 2.5 .81 60 4000 7110 60 66 257 263 0 44 18 27 1.208 45 27 .828 1.176 .272 .234
10 47 67 32 37 15 30 47 64 32 37 15 27 0 0 9 9 6 6 83 100 66 100 45 42 .5 2 1.8 1.989 1.783 1.907 12 104 1.724 .76 50 4210 7110 60 65 278 283 0 32 18 14 .949 30 13 1.054 .854 -.076 -.228
11 210 585 32 38 178 547 209 569 32 38 177 531 0 0 50 147 6 5 100 100 100 100 725 708 .325 3.073 3 3.079 3.091 1.186 32 176 3.146 .97 60 4430 7110 60 66 300 306 0 278 18 260 1.458 270 252 .686 1.423 .544 .509
12 129 295 31 37 98 258 126 296 32 38 95 259 0 0 26 43 5 5 100 100 100 100 356 354 .38 2.633 2.726 2.709 2.638 1.24 32 176 2.671 .96 60 4650 7110 60 66 322 328 0 140 18 122 1.249 140 123 .801 1.293 .321 .371
13 47 71 33 38 14 33 47 69 33 38 14 31 0 0 9 21 5 6 76 92 65 76 47 45 .424 2.357 2.214 2.21 2.23 2.225 52 340 2.987 .65 80 4860 7110 59 67 342 350 0 34 18 16 1.118 33 15 .894 1.05 .161 .071
14 48 72 32 38 16 34 44 65 33 38 12 27 0 0 18 26 15 7 40 85 13 73 50 39 .471 2.125 2.25 2.051 2.2 2.333 120 792 2.155 .63 120 5070 7090 55 67 361 373 0 34 18 16 1.008 31 13 .992 1.067 .012 .094
15 52 84 33 40 19 44 51 86 35 40 18 46 0 0 11 16 22 8 32 100 0 100 63 64 .432 2.316 2.556 2.67 2.684 2.087 52 340 .557 .51 80 5300 7110 59 67 386 394 0 40 19 21 1.099 41 22 .91 1.212 .136 .278
16 136 379 32 37 104 342 136 385 32 37 104 348 0 0 41 154 5 4 100 100 98 100 446 452 .304 3.288 3.346 3.167 3.298 1.319 52 340 3.498 .96 80 5520 7110 59 67 408 416 0 180 18 162 1.56 183 165 .641 1.587 .642 .667
17 59 117 33 38 26 79 56 118 33 38 23 80 0 0 13 33 5 5 100 100 90 96 105 103 .329 3.038 3.478 3.089 2.862 1.704 32 236 3.231 .83 70 5740 7110 59 66 430 437 0 56 18 37 1.441 56 38 .694 1.65 .528 .723
18 44 62 32 38 12 24 44 60 32 38 12 22 0 0 9 12 5 5 73 96 53 88 36 34 .5 2 1.833 2.252 1.624 2.608 52 340 2.329 .57 80 5960 7110 59 67 452 460 0 29 18 11 .949 28 10 1.054 .87 -.076 -.201
19 59 112 32 38 27 74 60 114 33 38 28 76 0 0 10 19 6 5 96 100 90 100 101 104 .365 2.741 2.714 2.941 2.847 1.5 32 236 3.073 .83 70 6180 7110 59 66 474 481 0 53 18 35 1.3 54 36 .769 1.288 .379 .365
20 43 42 33 38 10 4 35 40 34 39 2 2 0 0 34 9 10 8 23 23 9 5 14 4 2.5 .4 1 .605 .823 3.806 52 340 .3 .49 80 2230 7310 79 87 79 87 0 20 18 2 .19 19 1 5.27 .474 -2.398 -1.076

Total number of rows: 10944

Table truncated, full table size 2226 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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