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Sample GSM543842 Query DataSets for GSM543842
Status Public on Dec 06, 2010
Title Meu1 IP (3)B
Sample type RNA
 
Channel 1
Source name Extract tot. RNA Meu1-TAP (3)
Organism Saccharomyces cerevisiae
Characteristics experiment: Extract tot. RNA Meu1-TAP (3)
Growth protocol yeast cells expressing TAP-tagged RBP or the wild-type strain BY4741 (mock control) were grown to mid-log phase in rich medium and harvested by centrifugation.
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name Affinity isolated RNA, Meu1-TAP (3)
Organism Saccharomyces cerevisiae
Characteristics experiment: Affinity isolated RNA, Meu1-TAP (3)
Growth protocol yeast cells expressing TAP-tagged RBP or the wild-type strain BY4741 (mock control) were grown to mid-log phase in rich medium and harvested by centrifugation.
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, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-04/73885.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 May 17, 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 GPL8306
Series (1)
GSE21864 RNA-affinity isolations 13 RBPs

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
1 358 76 34 52 324 24 381 74 34 53 347 22 0 0 116 20 5 8 100 78 100 62 348 369 13.5 .074 .063 .072 .075 1.895 32 176 .075 .71 60 1980 7190 68 74 55 61 0 2409 1648 761 2.348 2346 697 .426 2.01 1.232 1.007
2 88 55 33 52 55 3 90 54 33 52 57 2 0 0 24 10 4 9 100 28 93 6 58 59 18.333 .055 .035 .132 .158 2.697 32 176 .067 .18 60 2190 7190 68 74 76 82 0 1744 1648 95 1.729 1712 63 .578 1.112 .79 .154
3 279 62 33 52 246 10 305 60 33 51 272 8 0 0 112 12 5 9 100 37 100 15 256 280 24.6 .041 .029 .052 .058 2.432 32 176 .044 .51 60 2410 7200 69 75 98 104 0 1965 1648 317 1.289 1902 254 .776 .932 .366 -.101
4 43 56 33 51 10 5 41 56 34 52 8 5 0 0 10 9 4 9 66 30 47 6 15 13 2 .5 .625 .745 .655 3.512 80 560 1.448 .24 100 2630 7180 65 75 118 128 -50 1775 1617 159 15.85 1775 159 .063 19.813 3.986 4.308
5 67 59 35 52 32 7 66 60 36 52 31 8 0 0 12 7 5 10 100 25 100 0 39 39 4.571 .219 .258 .279 .272 1.501 12 104 .14 .19 50 2850 7180 67 72 142 147 0 1870 1648 222 6.934 1902 254 .144 8.181 2.794 3.032
6 40 52 33 51 7 1 38 51 33 52 5 0 0 0 10 9 5 9 48 15 35 6 8 5 7 .143 null .841 .875 3.147 80 560 7.037 .08 100 3070 7180 65 75 162 172 -50 1648 1617 32 4.529 1617 0 .221 null 2.179 null
7 132 53 34 51 98 2 139 52 33 50 105 1 0 0 34 11 5 9 100 28 100 6 100 106 49 .02 .01 .095 .094 2.162 32 176 .019 .1 60 3290 7190 68 74 186 192 0 1680 1617 63 .647 1648 32 1.546 .302 -.628 -1.728
8 66 58 33 50 33 8 68 60 33 51 35 10 0 0 14 11 5 8 93 56 87 21 41 45 4.125 .242 .286 .309 .349 2.141 32 176 .245 .32 60 3510 7180 67 73 208 214 0 1839 1585 254 7.685 1902 317 .13 9.057 2.942 3.179
9 69 56 35 53 34 3 72 57 35 53 37 4 0 0 8 8 5 8 100 25 100 0 37 41 11.333 .088 .108 .22 .292 2.719 12 104 .079 .09 50 3730 7170 66 71 230 235 0 1775 1680 95 2.797 1807 127 .358 3.427 1.484 1.777
10 71 55 34 51 37 4 73 57 35 51 39 6 0 0 14 12 5 8 100 34 96 12 41 45 9.25 .108 .154 .303 .298 1.98 32 176 .198 .29 60 3960 7180 67 73 253 259 0 1744 1617 127 3.427 1807 190 .292 4.877 1.777 2.286
11 492 62 34 51 458 11 546 61 34 51 512 10 0 0 166 9 4 9 100 53 100 18 469 522 41.636 .024 .02 .019 .021 2.291 32 176 .024 .52 60 4180 7190 68 74 275 281 0 1965 1617 349 .761 1934 317 1.313 .619 -.393 -.692
12 57 52 35 52 22 0 55 50 35 52 20 -2 0 0 8 8 5 7 100 16 100 8 22 18 null null null .358 .345 2.212 12 104 -.212 -.05 50 4400 7170 66 71 297 302 0 1648 1648 0 null 1585 -63 null null null null
13 80 55 35 50 45 5 82 56 35 50 47 6 0 0 12 8 4 8 100 31 100 6 50 53 9 .111 .128 .155 .137 2.089 32 236 .115 .21 70 4620 7180 66 73 318 325 0 1744 1585 159 3.522 1775 190 .284 4.047 1.816 2.017
14 75 50 35 51 40 -1 74 48 35 51 39 -3 0 0 11 7 4 8 100 9 100 3 39 36 null null null .121 .127 2.274 32 236 -1 -1 70 4840 7180 66 73 340 347 0 1585 1617 -32 null 1522 -95 null null null null
15 82 53 35 51 47 2 84 54 35 51 49 3 0 0 14 10 4 9 100 18 100 6 49 52 23.5 .043 .061 .13 .14 2.518 32 236 .049 .08 70 5060 7180 66 73 362 369 0 1680 1617 63 1.349 1712 95 .741 1.941 .432 .957
16 296 54 35 51 261 3 298 54 35 51 263 3 0 0 53 10 5 8 100 28 100 15 264 266 87 .011 .011 .031 .032 2.388 32 176 .009 .12 60 5280 7170 66 72 385 391 0 1712 1617 95 .364 1712 95 2.744 .362 -1.457 -1.468
17 110 58 35 50 75 8 110 58 35 50 75 8 0 0 21 9 5 9 100 40 100 18 83 83 9.375 .107 .107 .109 .133 2.506 32 176 .052 .19 60 5500 7170 66 72 407 413 0 1839 1585 254 3.381 1839 254 .296 3.381 1.758 1.758
18 63 53 35 49 28 4 61 52 35 49 26 3 0 0 10 9 4 8 100 31 93 12 32 29 7 .143 .115 .32 .346 2.957 32 236 .225 .23 70 5730 7180 66 73 429 436 0 1680 1553 127 4.529 1648 95 .221 3.658 2.179 1.871
19 91 59 35 51 56 8 92 58 35 51 57 7 0 0 16 11 5 9 100 40 100 18 64 64 7 .143 .123 .179 .177 2.311 32 176 .122 .23 60 5950 7170 66 72 452 458 0 1870 1617 254 4.529 1839 222 .221 3.893 2.179 1.961
20 57 57 34 52 23 5 54 59 34 51 20 7 0 0 13 7 6 8 100 33 83 0 28 27 4.6 .217 .35 .372 .45 2.184 12 104 .452 .33 50 1970 7400 89 94 54 59 0 1807 1648 159 6.891 1870 222 .145 11.095 2.785 3.472

Total number of rows: 10944

Table truncated, full table size 2237 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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