NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM93704 Query DataSets for GSM93704
Status Public on Jan 28, 2006
Title Tendon Shear 12 Hour
Sample type RNA
 
Channel 1
Source name Control Tenocytes at 12 Hours
Organism Mus musculus
Characteristics Control Tenocytes at 12 Hours
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Sheared at 50 RPM at 12 Hours
Organism Mus musculus
Characteristics Sheared at 50 RPM at 12 Hours
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Stimulation, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32666.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 24, 2006
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 GPL2727
Series (1)
GSE4096 Mechanical shear effects on flexor tendon cells

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
1 333 175 143 100 190 75 352 173 145 104 209 73 0 0 90 47 20 30 91 87 90 61 265 282 2.533 .395 .349 1 1 1 80 380 1 .65 100 1860 8520 160 170 117 127 0 265 152 114 .598 262 111 1.672 .529 -.742 -.918
2 866 1219 139 104 727 1115 1000 1345 144 110 861 1241 0 0 337 451 27 45 91 96 90 96 1842 2102 .652 1.534 1.441 1 1 1 80 286 1 .89 100 2000 8540 162 172 131 141 0 1847 158 1689 2.324 2038 1880 .43 2.184 1.216 1.127
3 1039 605 140 102 899 503 1120 646 144 109 980 544 0 0 346 204 28 46 95 96 95 95 1402 1524 1.787 .56 .555 1 1 1 80 327 1 .86 100 2150 8540 162 172 146 156 0 917 155 762 .848 979 824 1.18 .841 -.238 -.25
4 412 185 141 99 271 86 432 188 145 105 291 89 0 0 94 50 26 34 96 86 96 59 357 380 3.151 .317 .306 1 1 1 52 290 1 .66 90 2290 8520 160 169 160 169 0 280 150 130 .481 285 135 2.08 .463 -1.056 -1.11
5 503 313 142 103 361 210 458 278 145 107 316 175 0 0 189 120 22 31 100 95 96 92 571 491 1.719 .582 .554 1 1 1 80 325 1 .83 100 2440 8530 161 171 175 185 0 474 156 318 .881 421 265 1.135 .839 -.182 -.253
6 2776 1908 140 106 2636 1802 3282 2195 142 109 3142 2089 0 0 1345 929 19 32 97 98 96 95 4438 5231 1.463 .684 .665 1 1 1 120 373 1 .91 120 2590 8540 161 173 189 201 0 2891 161 2730 1.036 3326 3165 .965 1.007 .051 .011
7 450 408 138 104 312 304 471 416 140 106 333 312 0 0 165 190 19 29 91 86 91 85 616 645 1.026 .974 .937 1 1 1 80 308 1 .85 100 2730 8530 161 171 204 214 0 618 158 461 1.476 630 473 .677 1.42 .562 .505
8 484 279 135 97 349 182 530 273 137 99 395 176 0 0 155 95 20 30 92 93 91 90 531 571 1.918 .521 .446 1 1 1 80 285 1 .78 100 2880 8540 162 172 219 229 0 423 147 276 .79 414 267 1.266 .675 -.34 -.567
9 2807 5319 134 98 2673 5221 3393 6345 392 172 3259 6247 0 0 1695 3562 3389 609 47 79 0 73 7894 9506 .512 1.953 1.917 1 1 1 120 450 1 .43 120 3020 8530 160 172 232 244 0 8059 148 7911 2.959 9614 9465 .338 2.904 1.565 1.538
10 297 256 139 108 158 148 253 225 147 142 114 117 0 0 154 123 75 258 69 19 38 0 306 231 1.068 .937 1.026 1 1 1 52 190 1 .69 80 3190 8550 164 172 251 259 0 388 164 224 1.419 341 177 .705 1.555 .505 .637
11 697 858 141 108 556 750 753 940 149 117 612 832 0 0 273 362 51 57 93 95 91 92 1306 1444 .741 1.349 1.359 1 1 1 80 370 1 .88 110 3310 8530 160 171 261 272 0 1300 164 1136 2.044 1424 1261 .489 2.06 1.031 1.043
12 532 295 147 111 385 184 594 308 155 119 447 197 0 0 219 121 52 57 91 82 86 68 569 644 2.092 .478 .441 1 1 1 80 362 1 .85 100 3460 8530 161 171 277 287 0 447 168 279 .724 467 298 1.381 .668 -.466 -.583
13 400 212 147 106 253 106 429 211 149 109 282 105 0 0 110 58 20 32 94 88 92 78 359 387 2.387 .419 .372 1 1 1 52 277 1 .74 90 3600 8530 161 170 291 300 0 321 161 161 .635 320 159 1.575 .564 -.656 -.826
14 474 322 142 109 332 213 443 282 145 116 301 173 0 0 187 163 21 51 96 88 96 73 545 474 1.559 .642 .575 1 1 1 52 285 1 .77 90 3750 8520 160 169 306 315 0 488 165 323 .972 427 262 1.029 .871 -.041 -.2
15 11204 13812 142 110 11062 13702 12957 15690 155 121 12815 15580 0 0 5286 6049 171 70 95 100 95 100 24764 28395 .807 1.239 1.216 1 1 1 120 464 1 .93 130 3900 8540 160 173 319 332 0 20927 167 20761 1.877 23773 23606 .533 1.842 .908 .881
16 969 620 139 106 830 514 1052 674 141 111 913 568 0 0 325 232 33 39 95 93 93 92 1344 1481 1.615 .619 .622 1 1 1 80 361 1 .88 110 4050 8530 160 171 335 346 0 939 161 779 .938 1021 861 1.066 .943 -.092 -.085
17 389 162 135 104 254 58 411 164 136 111 276 60 0 0 151 64 19 32 84 59 84 46 312 336 4.379 .228 .217 1 1 1 32 152 1 .54 60 4190 8530 163 169 352 358 0 245 158 88 .346 248 91 2.89 .329 -1.531 -1.602
18 4023 11256 137 113 3886 11143 4241 10393 157 153 4104 10280 0 0 2219 6017 97 137 94 100 94 96 15029 14384 .349 2.867 2.505 1 1 1 52 295 1 .88 90 4340 8530 161 170 365 374 0 17055 171 16883 4.345 15747 15576 .23 3.795 2.119 1.924
19 238 159 137 115 101 44 242 146 151 142 105 31 0 0 86 50 72 116 69 9 32 0 145 136 2.295 .436 .295 1 1 1 52 304 1 .58 90 4480 8520 160 169 379 388 -50 241 174 67 .66 221 47 1.515 .447 -.599 -1.161
20 2323 3227 135 108 2188 3119 2349 3423 137 111 2214 3315 0 0 1092 1575 25 34 96 100 96 98 5307 5529 .702 1.426 1.497 1 1 1 80 357 1 .92 100 4630 8530 161 171 394 404 0 4889 164 4726 2.16 5186 5023 .463 2.269 1.111 1.182

Total number of rows: 42624

Table truncated, full table size 8904 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap