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Sample GSM90532 Query DataSets for GSM90532
Status Public on Jan 04, 2006
Title Puf3 IP (3)
Sample type RNA
 
Channel 1
Source name Puf3 tot. RNA extract (3)
Organism Saccharomyces cerevisiae
Characteristics Puf3 tot. RNA extract (3)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Puf3 RNA-IP (3)
Organism Saccharomyces cerevisiae
Characteristics Puf3 RNA-IP (3)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36813.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 Jan 03, 2006
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) [email protected]
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL3300
Series (2)
GSE3968 Puf proteins, RNA co-immunopurification
GSE4393 Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast

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
1 174 73 181 77 -7 -4 171 71 189 79 -10 -6 0 0 35 17 45 20 11 6 0 1 -11 -16 null null null .373 .407 3.078 80 464 .25 .34 100 2650 16580 57 67 32 42 -50 286 302 -16 null 278 -24 null null null null
2 415 134 184 75 231 59 297 108 190 78 113 33 0 0 233 68 42 19 76 65 60 45 290 146 3.915 .255 .292 .29 .299 2.03 80 381 .248 .88 100 2820 16590 58 68 49 59 0 525 294 231 1.001 423 129 .999 1.145 .002 .195
3 1104 234 187 75 917 159 1067 217 194 78 880 142 0 0 463 90 45 20 100 100 100 96 1076 1022 5.767 .173 .161 .167 .168 1.332 80 408 .166 .91 100 2980 16580 57 67 65 75 0 917 294 623 .68 851 557 1.471 .633 -.557 -.661
4 232 85 187 75 45 10 214 81 197 78 27 6 0 0 80 22 53 20 30 27 16 8 55 33 4.5 .222 .222 .341 .31 3.264 80 445 .121 .33 100 3160 16570 56 66 83 93 -50 333 294 39 .871 318 24 1.148 .871 -.199 -.199
5 222 86 192 76 30 10 216 84 200 78 24 8 0 0 54 22 48 20 28 35 8 8 40 32 3 .333 .333 .511 .461 3.851 80 426 .178 .41 100 3340 16570 56 66 101 111 -50 337 298 39 1.307 329 31 .765 1.307 .386 .386
6 201 84 186 72 15 12 188 81 196 78 2 9 0 0 55 27 65 28 17 18 5 3 27 11 1.25 .8 4.5 .355 .318 3.043 80 432 .219 .36 100 3510 16570 56 66 118 128 -50 329 282 47 3.136 318 35 .319 17.64 1.649 4.141
7 1048 315 198 77 850 238 1068 317 207 80 870 240 0 0 255 71 77 24 100 100 100 100 1088 1110 3.571 .28 .276 .281 .292 1.301 52 341 .268 .94 90 3680 16580 57 66 135 144 0 1235 302 933 1.098 1243 941 .911 1.081 .134 .113
8 802 229 212 77 590 152 760 205 223 80 548 128 0 0 340 87 58 18 100 100 98 96 742 676 3.882 .258 .234 .261 .262 1.493 80 425 .235 .9 100 3850 16570 56 66 152 162 0 898 302 596 1.01 804 502 .99 .916 .014 -.127
9 876 223 205 75 671 148 554 169 214 78 349 94 0 0 809 155 51 19 100 96 92 82 819 443 4.534 .221 .269 .247 .25 1.852 52 280 .184 .9 80 4020 16570 57 65 170 178 0 874 294 580 .865 662 368 1.157 1.056 -.21 .078
10 1140 321 221 79 919 242 1092 324 235 81 871 245 0 0 369 79 68 19 100 100 100 100 1161 1116 3.798 .263 .281 .271 .261 1.243 52 375 .238 .95 90 4180 16570 56 65 185 194 0 1258 310 949 1.032 1270 960 .969 1.103 .046 .141
11 759 204 231 82 528 122 524 158 245 84 293 76 0 0 602 131 69 19 88 88 73 76 650 369 4.328 .231 .259 .235 .246 2.186 52 340 .197 .87 90 4370 16580 57 66 204 213 0 800 321 478 .906 619 298 1.104 1.017 -.143 .024
12 1822 476 214 81 1608 395 1723 473 228 84 1509 392 0 0 767 165 62 21 100 100 100 100 2003 1901 4.071 .246 .26 .248 .243 1.262 80 379 .231 .96 100 4530 16570 56 66 220 230 0 1866 318 1548 .963 1854 1537 1.039 1.018 -.055 .026
13 3236 776 201 77 3035 699 3155 774 211 79 2954 697 0 0 1305 334 53 19 100 97 100 95 3734 3651 4.342 .23 .236 .211 .229 1.673 120 473 .229 .97 120 4700 16570 55 67 236 248 0 3042 302 2740 .903 3034 2732 1.108 .925 -.147 -.113
14 25735 4277 199 77 25536 4200 26489 4639 207 78 26290 4562 0 0 8572 1551 50 17 100 100 100 100 29736 30852 6.08 .164 .174 .155 .167 1.512 120 447 .163 .98 120 4870 16570 55 67 253 265 0 16766 302 16464 .645 18185 17883 1.551 .68 -.633 -.556
15 50912 11580 201 77 50711 11503 60171 13071 207 78 59970 12994 31 0 18459 4814 47 17 100 100 100 100 62214 72964 4.409 .227 .217 .203 .23 1.751 120 492 .228 .98 120 5040 16570 55 67 270 282 0 45393 302 45091 .889 51238 50936 1.125 .849 -.169 -.236
16 4131 812 186 73 3945 739 4176 833 193 75 3990 760 0 0 1576 329 41 17 99 97 99 96 4684 4750 5.338 .187 .19 .177 .191 1.586 120 495 .187 .96 120 5220 16570 55 67 288 300 0 3183 286 2897 .734 3265 2979 1.362 .747 -.446 -.421
17 2206 518 184 72 2022 446 2099 517 192 75 1915 445 0 0 609 127 55 22 100 100 100 100 2468 2360 4.534 .221 .232 .221 .225 1.254 80 420 .212 .96 110 5380 16560 54 65 304 315 0 2031 282 1748 .865 2027 1744 1.157 .911 -.21 -.135
18 13304 3205 173 68 13131 3137 14618 3600 180 70 14445 3532 0 0 4875 1212 51 16 99 100 99 100 16268 17977 4.186 .239 .245 .236 .237 1.89 120 484 .235 .98 120 5560 16560 54 66 322 334 0 12563 267 12297 .936 14112 13845 1.068 .958 -.095 -.061
19 2001 521 160 68 1841 453 1977 524 162 72 1817 456 0 0 960 250 45 22 97 95 96 94 2294 2273 4.064 .246 .251 .238 .244 1.446 120 500 .243 .96 120 5730 16570 55 67 339 351 0 2042 267 1776 .965 2054 1787 1.037 .984 -.052 -.024
20 2498 622 162 67 2336 555 2463 610 164 70 2301 543 0 0 1428 349 45 16 93 95 92 90 2891 2844 4.209 .238 .236 .222 .229 1.604 80 357 .234 .97 100 5930 16550 54 64 360 370 0 2438 263 2176 .931 2391 2129 1.074 .925 -.103 -.112

Total number of rows: 9984

Table truncated, full table size 2226 Kbytes.




Supplementary data files not provided
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