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Sample GSM675157 Query DataSets for GSM675157
Status Public on Feb 08, 2012
Title Slf1 3
Sample type RNA
 
Channel 1
Source name SLF1-TAP total RNA
Organism Saccharomyces cerevisiae
Characteristics reference: SLF1-TAP total RNA
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name SLF1-TAP IP RNA
Organism Saccharomyces cerevisiae
Characteristics experiment: SLF1-TAP IP RNA
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: RNA coimmunoprecipitation, Copper
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74825.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 GPL8306
Series (2)
GSE27310 Slf1p and Sro9p affinity isolations
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
1 295 125 30 54 265 71 308 125 30 54 278 71 0 0 83 29 4 10 100 96 100 93 336 349 3.732 .268 .255 .253 .246 1.351 32 176 .268 .94 60 1960 6920 29 35 37 43 0 793 343 451 1.701 793 451 .588 1.621 .766 .697
2 72 59 30 52 42 7 74 59 29 54 44 7 0 0 13 10 5 9 100 43 100 12 49 51 6 .167 .159 .172 .279 3.006 32 176 .142 .21 60 2180 6920 29 35 59 65 0 375 330 44 1.058 375 44 .945 1.01 .081 .014
3 299 104 29 52 270 52 349 109 29 53 320 57 0 0 108 16 5 9 100 96 100 93 322 377 5.192 .193 .178 .203 .183 1.49 32 176 .177 .9 60 2400 6930 30 36 81 87 0 660 330 330 1.222 692 362 .818 1.131 .29 .177
4 36 54 30 52 6 2 34 54 30 53 4 2 0 0 10 9 5 9 37 22 32 3 8 6 3 .333 .5 1.098 1 3.808 80 560 8.703 .08 100 2620 6930 28 38 101 111 -50 343 330 13 2.116 343 13 .473 3.174 1.081 1.666
5 74 57 30 53 44 4 75 54 30 53 45 1 0 0 11 10 4 8 100 41 100 8 48 46 11 .091 .022 .258 .291 2.234 12 104 .072 .11 50 2840 6920 29 34 125 130 0 362 336 25 .577 343 6 1.733 .141 -.793 -2.826
6 37 53 30 53 7 0 35 52 30 53 5 -1 0 0 10 8 5 9 45 13 30 0 7 4 null null null .702 .6 3.131 80 560 -1 -1 100 3060 6930 28 38 145 155 -50 336 336 0 null 330 -6 null null null null
7 129 61 29 53 100 8 143 61 30 54 114 8 0 0 38 11 4 9 96 37 96 12 108 122 12.5 .08 .07 .102 .104 2.39 32 176 .081 .35 60 3280 6930 30 36 169 175 0 387 336 51 .508 387 51 1.969 .445 -.978 -1.167
8 104 59 30 52 74 7 113 60 30 53 83 8 0 0 29 7 4 9 100 43 100 3 81 91 10.571 .095 .096 .128 .106 2.338 32 176 .069 .24 60 3500 6940 31 37 191 197 0 375 330 44 .6 381 51 1.665 .612 -.736 -.709
9 60 54 30 53 30 1 64 53 32 57 34 0 0 0 13 10 19 41 75 0 18 0 31 34 30 .033 null .435 .432 4.204 32 236 2.967 .69 70 3720 6930 29 36 212 219 0 343 336 6 .212 336 0 4.726 null -2.241 null
10 72 55 29 52 43 3 76 54 30 53 47 2 0 0 17 10 10 10 96 18 84 6 46 49 14.333 .07 .043 .166 .215 2.949 32 176 .108 .18 60 3950 6940 31 37 236 242 0 349 330 19 .443 343 13 2.258 .27 -1.175 -1.888
11 246 88 30 54 216 34 267 81 30 54 237 27 0 0 56 21 5 9 100 100 100 75 250 264 6.353 .157 .114 .14 .141 1.688 12 104 .166 .78 50 4150 6940 31 36 256 261 0 559 343 216 .999 514 171 1.001 .723 -.001 -.468
12 62 52 29 51 33 1 61 53 29 51 32 2 0 0 11 10 5 9 100 21 100 6 34 34 33 .03 .063 .176 .194 2.804 32 176 .218 .24 60 4380 6940 31 37 279 285 0 330 324 6 .192 336 13 5.199 .397 -2.378 -1.334
13 72 51 29 53 43 -2 72 53 29 52 43 0 0 0 11 10 4 9 100 6 100 6 41 43 null null null .13 .114 1.954 32 236 .027 .04 70 4600 6930 29 36 300 307 0 324 336 -13 null 336 0 null null null null
14 74 53 29 53 45 0 73 52 29 54 44 -1 0 0 11 11 7 14 100 12 100 3 45 43 null null null .129 .2 3.147 32 236 .351 .19 70 4820 6930 29 36 322 329 0 336 336 0 null 330 -6 null null null null
15 67 57 30 52 37 5 67 57 29 54 37 5 0 0 9 10 4 10 100 21 100 9 42 42 7.4 .135 .135 .167 .146 2.393 32 236 .209 .25 70 5050 6940 30 37 345 352 0 362 330 32 .858 362 32 1.166 .858 -.221 -.221
16 172 70 29 53 143 17 168 70 29 53 139 17 0 0 38 14 4 11 100 59 100 28 160 156 8.412 .119 .122 .115 .149 2.199 32 236 .122 .57 70 5260 6940 30 37 366 373 0 444 336 108 .755 444 108 1.325 .776 -.406 -.365
17 88 74 30 53 58 21 87 74 30 53 57 21 0 0 16 12 4 8 100 90 100 65 79 78 2.762 .362 .368 .329 .362 2.14 32 236 .359 .63 70 5480 6950 31 38 388 395 0 470 336 133 2.298 470 133 .435 2.339 1.201 1.226
18 52 51 29 51 23 0 51 53 30 55 22 2 0 0 7 11 7 31 100 0 87 0 23 24 null null .091 .29 .316 2.55 32 176 -1 -1 60 5700 6950 32 38 411 417 0 324 324 0 null 336 13 null .577 null -.793
19 69 54 30 52 39 2 69 53 34 54 39 1 0 0 9 10 34 29 75 0 0 0 41 40 19.5 .051 .026 .161 .182 3.008 32 176 .125 .19 60 5920 6940 31 37 433 439 0 343 330 13 .326 336 6 3.072 .163 -1.619 -2.619
20 49 60 30 52 19 8 50 61 30 52 20 9 0 0 9 9 5 8 100 50 81 21 27 29 2.375 .421 .45 .48 .56 2.484 32 176 .622 .35 60 1970 7150 52 58 38 44 0 381 330 51 2.673 387 57 .374 2.856 1.418 1.514

Total number of rows: 10944

Table truncated, full table size 2253 Kbytes.




Supplementary data files not provided
Processed data provided as supplementary file
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