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Sample GSM78469 Query DataSets for GSM78469
Status Public on Oct 18, 2005
Title SW872 x SR21
Sample type RNA
 
Channel 1
Source name SR21
Organism Homo sapiens
Characteristics SR21
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name SW872
Organism Homo sapiens
Characteristics SW872
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA coimmunoprecipitation, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-08/9244.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Oct 17, 2005
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
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 GPL2948
Series (2)
GSE3461 Gene expression in miscellaneous human tissues and cell lines
GSE4345 In Vivo Regulation of Human Skeletal Muscle Gene Expression by Thyroid Hormone

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
VALUE 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
LOG_RAT2N_MEDIAN 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 VALUE LOG_RAT2N_MEDIAN
1 63 167 60 153 3 14 null null 67 167 null null null null null null null null 7 17 null null null null .214 4.667 null null 3.054 null 80 469 .357 .18 null null null 19 29 17 27 0 162 148 14 4.667 null null .214 null 2.222 null
2 87 178 74 157 13 21 null null 83 171 null null null null null null null null 7 18 null null null null .619 1.615 null null 2.05 null 80 333 .164 .18 null null null 19 29 32 42 0 172 152 20 1.538 null null .65 null .621 null
3 106 199 80 150 26 49 null null 94 163 null null null null null null null null 8 31 null null null null .531 1.885 null null 3.88 null 80 333 .114 .11 null null null 19 29 47 57 0 193 145 48 1.846 null null .542 null .885 null
4 135 290 84 175 51 115 null null 109 189 null null null null null null null null 18 31 null null null null .443 2.255 null null 2.322 null 80 391 1.638 .79 null null null 19 29 62 72 0 281 169 112 2.196 null null .455 null 1.135 null
5 2691 1521 114 207 2577 1314 null null 132 218 null null null null null null null null 94 96 null null null null 1.961 .51 null null .518 null 52 236 .512 .95 null null null 20 28 78 86 0 1476 200 1276 .495 null null 2.02 null -1.014 null
6 81 168 96 176 -15 -8 null null 173 190 null null null null null null null null 0 7 null null null null null null null null 1.74 null 80 346 .09 .05 null null null 19 29 92 102 0 163 170 -7 null null null null null null null
7 893 348 220 201 673 147 null null 471 224 null null null null null null null null 31 25 null null null null 4.578 .218 null null .255 null 80 317 .191 .66 null null null 19 29 107 117 -100 337 195 142 .211 null null 4.739 null -2.245 null
8 1060 346 178 186 882 160 null null 332 204 null null null null null null null null 60 49 null null null null 5.513 .181 null null .187 null 120 437 .128 .47 null null null 18 31 121 134 -100 335 180 155 .176 null null 5.69 null -2.509 null
9 428 223 218 208 210 15 null null 338 231 null null null null null null null null 17 11 null null null null 14 .071 null null .515 null 80 314 .274 .89 null null null 18 28 137 147 -100 216 201 15 .071 null null 14 null -3.807 null
10 492 257 173 190 319 67 null null 275 204 null null null null null null null null 43 41 null null null null 4.761 .21 null null .326 null 80 467 .165 .51 null null null 17 28 153 164 -100 249 184 65 .204 null null 4.908 null -2.295 null
11 258 209 126 215 132 -6 null null 185 228 null null null null null null null null 35 5 null null null null null null null null .358 null 80 382 .047 .1 null null null 18 28 167 177 -100 202 208 -6 null null null null null null null
12 3063 1785 112 223 2951 1562 null null 118 231 null null null null null null null null 100 100 null null null null 1.889 .529 null null .54 null 52 322 .525 .95 null null null 19 28 184 193 0 1733 216 1517 .514 null null 1.945 null -.96 null
13 1918 1289 120 249 1798 1040 null null 247 293 null null null null null null null null 98 98 null null null null 1.729 .578 null null .552 null 80 320 .561 .93 null null null 19 29 199 209 0 1251 241 1010 .562 null null 1.78 null -.832 null
14 9104 6012 137 295 8967 5717 null null 614 468 null null null null null null null null 100 100 null null null null 1.568 .638 null null .608 null 80 320 .646 .95 null null null 18 28 213 223 0 5836 286 5550 .619 null null 1.616 null -.692 null
15 525 1193 120 271 405 922 null null 435 389 null null null null null null null null 3 88 null null null null .439 2.277 null null 2.647 null 80 363 .413 .65 null null null 18 28 228 238 0 1158 263 895 2.21 null null .453 null 1.144 null
16 1154 4970 113 250 1041 4720 null null 122 254 null null null null null null null null 100 100 null null null null .221 4.534 null null 4.577 null 80 366 4.272 .97 null null null 18 28 244 254 0 4825 242 4583 4.402 null null .227 null 2.138 null
17 11024 5977 115 254 10909 5723 null null 121 264 null null null null null null null null 100 100 null null null null 1.906 .525 null null .517 null 80 325 .515 .98 null null null 18 28 259 269 0 5802 246 5556 .509 null null 1.963 null -.973 null
18 125 284 114 253 11 31 null null 117 265 null null null null null null null null 21 23 null null null null .355 2.818 null null 2.545 null 80 334 .216 .08 null null null 17 27 273 283 0 275 245 30 2.727 null null .367 null 1.447 null
19 5023 3935 113 255 4910 3680 null null 118 271 null null null null null null null null 100 100 null null null null 1.334 .749 null null .747 null 52 315 .717 .96 null null null 17 26 289 298 0 3820 247 3573 .728 null null 1.374 null -.459 null
20 830 554 112 270 718 284 null null 119 275 null null null null null null null null 100 84 null null null null 2.528 .396 null null .426 null 52 345 .354 .63 null null null 18 27 305 314 0 537 262 275 .383 null null 2.611 null -1.385 null

Total number of rows: 24192

Table truncated, full table size 5798 Kbytes.




Supplementary data files not provided
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