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Sample GSM90541 Query DataSets for GSM90541
Status Public on Jan 04, 2006
Title Puf3_delta vs. WT, SC_glycerol (1)
Sample type RNA
 
Channel 1
Source name BY4741 tot. RNA (1)
Organism Saccharomyces cerevisiae
Characteristics BY4741 tot. RNA (1)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Puf3_delta tot. RNA (1)
Organism Saccharomyces cerevisiae
Characteristics Puf3_delta tot. RNA (1)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Mutant vs Wild-type, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46742.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)
GSE3969 Puf3delta vs. wild type comparison
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 96 69 93 59 3 10 93 65 103 69 0 6 0 0 20 22 41 36 5 11 0 2 13 6 .3 3.333 null .665 .6 3.537 80 484 4.333 .09 100 2270 16280 63 73 50 60 -50 93 80 13 4.492 88 8 .223 null 2.167 null
2 105 68 100 67 5 1 105 65 133 94 5 -2 0 0 29 28 131 108 1 0 0 0 6 3 5 .2 null .876 .889 3.541 80 436 .211 .54 100 2440 16280 63 73 67 77 -50 92 90 1 .27 88 -3 3.711 null -1.892 null
3 115 82 102 71 13 11 108 80 119 83 6 9 0 0 31 23 64 51 5 3 2 0 24 15 1.182 .846 1.5 .828 1.116 3.305 80 440 .329 .37 100 2610 16280 63 73 84 94 -50 110 96 15 1.14 108 12 .877 2.021 .189 1.015
4 106 68 102 70 4 -2 97 65 108 74 -5 -5 0 0 38 20 29 26 13 8 3 2 2 -10 null null null 1.039 1.055 3.234 80 440 .387 .25 100 2780 16280 63 73 101 111 -50 92 94 -3 null 88 -7 null null null null
5 126 85 116 77 10 8 119 80 119 82 3 3 0 0 44 32 31 33 15 16 5 1 18 6 1.25 .8 1 .598 .604 2.827 80 462 1.19 .34 100 2950 16280 63 73 118 128 -50 115 104 11 1.078 108 4 .928 1.348 .108 .43
6 113 77 108 72 5 5 107 72 116 80 -1 0 0 0 35 26 38 35 7 7 5 3 10 -1 1 1 null .75 .813 4.18 80 462 1.652 .36 100 3130 16280 63 73 136 146 -50 104 97 7 1.348 97 0 .742 null .43 null
7 115 66 103 64 12 2 108 62 107 69 5 -2 0 0 33 26 27 28 23 12 13 2 14 3 6 .167 null .872 .83 2.983 80 450 .815 .28 100 3300 16280 63 73 153 163 -50 89 86 3 .225 84 -3 4.453 null -2.155 null
8 131 90 109 74 22 16 116 81 112 80 7 7 0 0 54 38 27 33 28 23 13 11 38 14 1.375 .727 1 1.043 1.185 5.069 80 450 .841 .34 100 3470 16280 63 73 170 180 -50 121 100 22 .98 109 9 1.02 1.348 -.029 .43
9 126 79 116 78 10 1 112 74 121 85 -4 -4 0 0 46 33 31 35 20 11 12 5 11 -8 10 .1 null .783 .909 4.078 80 450 .956 .34 100 3640 16280 63 73 187 197 -50 106 105 1 .135 100 -5 7.421 null -2.892 null
10 130 86 116 76 14 10 111 73 120 80 -5 -3 0 0 53 51 31 30 23 15 11 8 24 -8 1.4 .714 null .643 .639 3.578 80 440 1.123 .51 100 3810 16290 64 74 204 214 -50 116 102 13 .963 98 -4 1.039 null -.055 null
11 156 119 115 80 41 39 136 100 119 85 21 20 0 0 85 70 29 36 40 41 27 18 80 41 1.051 .951 .952 .883 1.086 3.515 80 440 .841 .59 100 3980 16290 64 74 221 231 -50 160 108 53 1.282 135 27 .78 1.283 .358 .36
12 154 108 133 95 21 13 132 89 146 103 -1 -6 0 0 77 69 65 54 13 12 10 8 34 -7 1.615 .619 null .968 .824 3.824 80 428 .877 .67 100 4150 16290 64 74 238 248 -50 146 128 18 .834 120 -8 1.199 null -.262 null
13 1756 1266 166 124 1590 1142 1774 1263 185 139 1608 1139 0 0 395 303 89 79 100 100 100 100 2732 2747 1.392 .718 .708 .712 .751 1.341 80 451 .713 .92 110 4310 16310 65 76 253 264 0 1706 167 1539 .968 1702 1535 1.033 .954 -.047 -.067
14 11902 13264 156 113 11746 13151 13749 15307 201 127 13593 15194 0 0 5202 5982 258 64 99 100 99 100 24897 28787 .893 1.12 1.118 1.142 1.117 1.82 120 571 1.136 .96 130 4480 16300 63 76 269 282 0 17873 152 17721 1.509 20626 20474 .663 1.506 .593 .591
15 20723 22719 145 102 20578 22617 27725 26747 181 115 27580 26645 0 0 14361 16231 253 62 100 100 99 100 43195 54225 .91 1.099 .966 1.088 1.12 1.841 156 583 1.119 .95 140 4650 16320 65 79 286 300 0 30614 137 30477 1.481 36042 35905 .675 1.302 .567 .381
16 3939 3183 150 108 3789 3075 4276 3503 156 117 4126 3395 0 0 2045 1632 44 47 100 100 100 100 6864 7521 1.232 .812 .823 .857 .862 1.792 120 485 .796 .94 120 4820 16310 65 77 304 316 0 4289 146 4144 1.094 4720 4575 .914 1.109 .129 .149
17 871 679 154 110 717 569 894 691 160 116 740 581 0 0 256 246 43 38 99 96 99 93 1286 1321 1.26 .794 .785 .707 .805 1.962 120 587 .817 .94 130 5000 16300 63 76 321 334 0 915 148 767 1.069 931 783 .935 1.058 .097 .081
18 6042 5359 160 119 5882 5240 6721 5740 167 125 6561 5621 0 0 2518 2096 42 40 100 100 100 100 11122 12182 1.123 .891 .857 .953 .913 1.641 120 542 .875 .95 130 5170 16310 64 77 338 351 0 7221 160 7061 1.2 7735 7574 .833 1.154 .264 .207
19 1422 1156 153 114 1269 1042 1479 1208 160 121 1326 1094 0 0 561 471 45 45 100 100 100 100 2311 2420 1.218 .821 .825 .826 .847 1.65 120 529 .815 .92 120 5350 16300 64 76 357 369 0 1558 154 1404 1.106 1628 1474 .904 1.112 .146 .153
20 1494 1139 149 115 1345 1024 1527 1105 154 119 1378 990 0 0 486 352 39 38 100 100 100 100 2369 2368 1.313 .761 .718 .786 .708 1.616 80 456 .739 .9 110 5530 16310 65 76 375 386 0 1535 155 1380 1.026 1489 1334 .975 .968 .037 -.047

Total number of rows: 9984

Table truncated, full table size 2169 Kbytes.




Supplementary data files not provided

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