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Sample GSM90530 Query DataSets for GSM90530
Status Public on Jan 04, 2006
Title Puf1 IP (4)
Sample type RNA
 
Channel 1
Source name Puf1 tot. RNA extract (4)
Organism Saccharomyces cerevisiae
Characteristics Puf1 tot. RNA extract (4)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Puf1 RNA-IP (4)
Organism Saccharomyces cerevisiae
Characteristics Puf1 RNA-IP (4)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36820.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
1 149 42 142 43 7 -1 146 43 144 43 4 0 0 0 22 5 22 6 22 7 5 2 6 4 null null null .331 .303 3.273 80 468 .077 .29 100 2720 17100 41 51 27 37 -50 454 465 -11 null 465 0 null null null null
2 148 42 142 44 6 -2 143 42 146 44 1 -2 0 0 27 5 25 6 18 3 8 0 4 -1 null null null .223 .258 2.663 80 415 .079 .35 100 2890 17100 41 51 44 54 -50 454 476 -22 null 454 -22 null null null null
3 151 43 137 43 14 0 147 43 140 43 10 0 0 0 31 5 23 6 30 11 12 0 14 10 null null null .185 .181 3.258 80 420 .062 .27 100 3060 17100 41 51 61 71 -50 465 465 0 null 465 0 null null null null
4 140 41 138 42 2 -1 139 41 140 43 1 -1 0 0 24 6 23 6 12 8 3 1 1 0 null null null .27 .286 3.98 80 433 .065 .24 100 3230 17100 41 51 78 88 -50 443 454 -11 null 443 -11 null null null null
5 145 42 142 43 3 -1 138 42 144 43 -4 -1 0 0 26 6 23 6 17 10 6 0 2 -5 null null null .415 .354 4.087 80 432 .08 .3 100 3410 17100 41 51 96 106 -50 454 465 -11 null 454 -11 null null null null
6 153 44 151 45 2 -1 149 44 178 47 -2 -1 0 0 29 5 75 9 3 2 0 0 1 -3 null null null .252 .293 3.264 80 394 .1 .63 100 3580 17100 41 51 113 123 -50 476 486 -11 null 476 -11 null null null null
7 277 58 152 46 125 12 281 57 176 47 129 11 0 0 103 12 70 9 70 56 43 23 137 140 10.417 .096 .085 .119 .11 2.511 120 594 .102 .83 130 3760 17100 39 52 129 142 -100 627 497 130 1.037 616 119 .964 .922 .053 -.118
8 348 63 154 46 194 17 339 63 167 47 185 17 0 0 104 12 49 7 93 72 83 55 211 202 11.412 .088 .092 .078 .079 1.857 80 425 .093 .82 110 3930 17110 41 52 147 158 -100 681 497 184 .947 681 184 1.056 .993 -.079 -.01
9 327 61 162 47 165 14 243 55 176 48 81 8 0 0 228 23 56 7 55 50 42 30 179 89 11.786 .085 .099 .11 .094 2.041 52 288 .091 .9 80 4090 17100 42 50 165 173 -100 659 508 151 .917 594 86 1.091 1.067 -.125 .094
10 954 120 167 48 787 72 940 118 185 49 773 70 0 0 276 27 57 8 100 100 100 97 859 843 10.931 .091 .091 .091 .092 1.187 80 499 .093 .97 110 4270 17100 40 51 181 192 0 1297 519 778 .989 1275 757 1.011 .979 -.016 -.031
11 284 59 169 47 115 12 284 57 185 49 115 10 0 0 96 11 52 8 71 56 56 27 127 125 9.583 .104 .087 .109 .105 2.192 120 482 .102 .8 120 4460 17100 40 52 200 212 -100 638 508 130 1.128 616 108 .887 .94 .173 -.09
12 291 58 171 48 120 10 290 57 195 50 119 9 0 0 105 13 65 9 67 48 42 23 130 128 12 .083 .076 .11 .093 2.335 80 363 .097 .8 100 4610 17090 40 50 216 226 -50 627 519 108 .901 616 97 1.11 .817 -.151 -.291
13 4459 455 206 51 4253 404 4234 445 228 52 4028 394 0 0 1442 137 84 9 100 100 100 100 4657 4422 10.527 .095 .098 .095 .095 1.083 80 498 .094 .99 110 4790 17090 39 50 233 244 0 4917 551 4366 1.027 4809 4258 .974 1.057 .038 .08
14 37074 2014 285 57 36789 1957 37789 2009 310 59 37504 1952 0 0 10984 636 124 13 100 100 100 100 38746 39456 18.799 .053 .052 .053 .053 1.062 80 490 .053 1 110 4960 17080 38 49 250 261 0 21766 616 21150 .575 21712 21096 1.739 .562 -.799 -.83
15 61402 6705 274 57 61128 6648 64499 6891 295 60 64225 6834 31 0 7030 1081 123 14 100 100 100 100 67776 71059 9.195 .109 .106 .108 .106 1.081 80 511 .109 1 110 5130 17090 39 50 267 278 0 72462 616 71846 1.175 74472 73856 .851 1.15 .233 .202
16 3748 331 188 49 3560 282 3377 313 208 51 3189 264 0 0 1441 101 75 10 100 100 100 100 3842 3453 12.624 .079 .083 .08 .081 1.104 80 470 .076 .99 110 5310 17090 39 50 285 296 0 3577 530 3048 .856 3383 2853 1.168 .895 -.224 -.161
17 1520 165 165 46 1355 119 1407 158 169 47 1242 112 0 0 541 41 34 6 100 100 100 100 1474 1354 11.387 .088 .09 .089 .089 1.182 80 497 .084 .98 110 5470 17080 38 49 301 312 0 1783 497 1286 .949 1708 1210 1.054 .975 -.075 -.037
18 15089 1321 162 46 14927 1275 14314 1213 166 46 14152 1167 0 0 4836 425 32 6 100 100 100 100 16202 15319 11.707 .085 .082 .085 .086 1.072 80 432 .084 1 100 5650 17080 39 49 320 330 0 14276 497 13779 .923 13109 12612 1.083 .891 -.115 -.166
19 1964 194 163 46 1801 148 1775 187 167 46 1612 141 0 0 761 62 30 6 100 100 100 100 1949 1753 12.169 .082 .087 .082 .083 1.195 80 484 .08 .99 110 5820 17070 37 48 336 347 0 2097 497 1599 .888 2021 1524 1.126 .945 -.171 -.081
20 2836 306 165 46 2671 260 2577 278 170 46 2412 232 0 0 993 101 34 6 100 100 100 100 2931 2644 10.273 .097 .096 .097 .098 1.127 80 407 .097 .99 100 6000 17080 39 49 355 365 0 3307 497 2810 1.052 3004 2507 .951 1.039 .073 .056

Total number of rows: 9984

Table truncated, full table size 2129 Kbytes.




Supplementary data files not provided
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