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Sample GSM469356 Query DataSets for GSM469356
Status Public on Jan 21, 2010
Title BTU 15 Tumor Fibroblasts
Sample type RNA
 
Channel 1
Source name stratagene human reference plus doping controls.
Organism Homo sapiens
Characteristics reference: stratagene human reference plus doping controls.
Extracted molecule total RNA
Extraction protocol StratageneRef; RNA for the reference was pooled from 11 cell lines - obtained from Stratagene.; Protocol Type = Biological Sample; Performer: Michal,,Rajski
Label Cy3
Label protocol MessageAmpII; Total RNA was amplified using the Message AmpTM II aRNA Kit (Ambion, Austin, TX), according to the manufacturer's instructions.; Protocol Type = Amplification; Performer: Michal,,Rajski
Ambion MessageAmpII Amino Allyl and Cy Dye Coupling for Oligo Arrays CH1; RNA was processed using the Message AmpTM II aRNA Kit (Ambion, Austin, TX) according to the protocol of Kate Rubins/Brown Lab ? 04/14/2006 (update 05/25/2006).; Protocol Type = Labeling; Performer: Michal,,Rajski
 
Channel 2
Source name BTU 15 Tumor Fibroblasts
Organism Homo sapiens
Characteristics cell type: Human Primary breast Fibroblasts
Extracted molecule total RNA
Extraction protocol RNeasy; Total RNA was isolated using the RNeasy mini kit (QIAGEN), according to the manufacturer's instructions.; Protocol Type = Extract preparation; Performer: Michal,,Rajski
Label Cy5
Label protocol MessageAmp II; RNA was amplified using the Message AmpTM II aRNA Kit (Ambion, Austin, TX) according to the manufacturer's instructions.; Protocol Type = Amplification; Performer: Michal,,Rajski
Ambion MessageAmpII Amino Allyl and Cy Dye Coupling for Oligo Arrays CH2; RNA was processed using the Message AmpTM II aRNA Kit (Ambion, Austin, TX) according to the protocol of Kate Rubins/Brown Lab ? 04/14/2006 (update 05/25/2006).; Protocol Type = Labeling; Performer: Michal,,Rajski
 
 
Hybridization protocol not provided
Scan protocol GenePix 4100A 01
Description Cell Type: Human Primary breast Fibroblasts
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 Nov 09, 2009
Last update date Jan 21, 2010
Contact name Michal Rajski
E-mail(s) rajski.michal@gmail.com
Organization name University of Zurich
Department Institute of Physiology
Lab 23K86
Street address Winterthurerstrasse 190
City Zurich
ZIP/Postal code CH - 8057
Country Switzerland
 
Platform ID GPL9551
Series (2)
GSE18952 Effects of IGF 1 on primary breast fibroblasts (normal and carcinoma associated)
GSE18955 Effects of IGF 1 on primary breast fibroblasts, MCF-7 breast cancer cells and CCL-171 fibroblasts

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 2338 1502 646 446 1692 1056 2263 1546 651 452 1617 1100 0 0 360 281 92 139 100 100 100 100 2748 2717 1.602 .624 .68 .611 .633 1.304 52 347 .613 .91 90 1780 4980 25 34 29 38 0 1181 351 830 .491 1216 865 2.038 .535 -1.027 -.903
2 14893 46078 641 469 14252 45609 16006 57341 646 487 15365 56872 0 38 6794 22235 92 174 100 100 100 100 59861 72237 .312 3.2 3.701 3.09 3.206 1.362 52 226 3.3 .98 90 1950 4980 25 34 46 55 -100 36232 369 35864 2.516 45089 44720 .397 2.911 1.331 1.541
3 27439 65166 650 469 26789 64697 28498 65535 654 508 27848 65066 0 94 5302 2470 91 212 100 100 100 100 91486 92914 .414 2.415 2.336 2.503 2.336 1.347 52 153 2.445 .97 90 2070 4990 26 35 58 67 -100 51242 369 50873 1.899 51532 51163 .527 1.837 .925 .878
4 2588 1670 635 448 1953 1222 2727 1786 644 459 2092 1338 0 0 751 527 90 135 96 92 93 92 3175 3430 1.598 .626 .64 .63 .623 1.457 80 261 .614 .92 100 2210 4980 25 35 72 82 0 1313 352 961 .492 1404 1052 2.032 .503 -1.023 -.992
5 1405 1202 633 464 772 738 1469 1231 643 490 836 767 0 0 304 337 83 175 95 90 92 85 1510 1603 1.046 .956 .917 .941 .905 1.674 80 266 1.076 .77 110 2360 4990 25 36 86 97 0 945 365 580 .752 968 603 1.33 .721 -.412 -.471
6 31801 65127 636 480 31165 64647 33133 65535 642 517 32497 65055 0 96 9048 2355 85 210 100 100 100 100 95812 97552 .482 2.074 2.002 2.401 2.002 2.195 80 331 2.033 .94 110 2500 4980 24 35 100 111 -100 51211 377 50834 1.631 51532 51155 .613 1.574 .706 .655
7 788 768 658 511 130 257 799 803 656 557 141 292 0 0 113 184 90 234 71 62 28 15 387 433 .506 1.977 2.071 1.458 1.869 2.822 32 157 2.695 .5 60 2650 4970 26 32 118 124 0 604 402 202 1.555 631 230 .643 1.628 .636 .703
8 28868 61675 649 499 28219 61176 31246 65535 667 535 30597 65036 0 85 7135 11079 224 231 100 100 98 100 89395 95633 .461 2.168 2.126 2.317 2.118 1.471 80 374 2.184 .97 110 2800 4990 25 36 130 141 -100 48497 392 48104 1.705 51532 51140 .587 1.671 .77 .741
9 798 690 635 472 163 218 763 678 632 489 128 206 0 0 119 142 87 142 78 69 38 28 381 334 .748 1.337 1.609 1.485 1.462 2.402 52 189 2.359 .3 80 2980 4990 27 35 150 158 0 543 371 171 1.052 533 162 .951 1.265 .073 .34
10 735 701 618 469 117 232 740 720 619 494 122 251 0 0 91 166 81 198 61 59 30 13 349 373 .504 1.983 2.057 1.974 1.765 4.669 52 176 4.995 .24 80 3110 4990 27 35 163 171 0 551 369 182 1.559 566 197 .641 1.618 .641 .694
11 3348 9093 622 459 2726 8634 3424 9249 621 479 2802 8790 0 0 535 1373 87 165 100 100 100 100 11360 11592 .316 3.167 3.137 3.254 3.207 1.366 80 338 3.183 .97 110 3260 4980 24 35 176 187 0 7150 361 6789 2.491 7273 6912 .402 2.467 1.316 1.303
12 864 770 619 475 245 295 860 747 616 485 241 272 0 0 118 178 79 131 91 83 76 55 540 513 .831 1.204 1.129 1.285 1.317 2.523 80 243 1.621 .51 100 3410 4980 25 35 192 202 0 605 374 232 .947 587 214 1.056 .887 -.079 -.172
13 1880 2337 619 489 1261 1848 1974 2493 623 482 1355 2004 0 0 477 818 85 136 96 92 92 92 3109 3359 .682 1.466 1.479 1.459 1.488 1.613 80 224 1.575 .93 100 3550 4990 26 36 206 216 0 1838 385 1453 1.152 1960 1576 .868 1.163 .205 .218
14 1597 5057 623 478 974 4579 1661 5220 623 476 1038 4742 0 0 324 1241 83 135 96 100 95 100 5553 5780 .213 4.701 4.568 4.952 4.7 1.606 80 266 4.698 .94 110 3700 4980 24 35 220 231 0 3976 376 3601 3.697 4105 3729 .271 3.592 1.886 1.845
15 623 640 612 471 11 169 619 652 621 487 7 181 0 0 90 181 85 133 18 58 8 31 180 188 .065 15.364 25.857 3.947 2.862 4.015 80 261 13.789 .09 100 3830 4970 24 34 234 244 -50 503 370 133 12.081 513 142 .083 20.332 3.595 4.346
16 6647 12314 621 479 6026 11835 6987 12320 631 499 6366 11841 0 0 1599 2343 104 146 96 100 96 100 17861 18207 .509 1.964 1.86 2.199 1.93 1.972 80 277 1.944 .94 110 3990 4980 24 35 249 260 0 9683 377 9306 1.544 9688 9311 .648 1.463 .627 .549
17 808 1165 617 491 191 674 799 1154 621 497 182 663 0 0 115 225 105 140 78 98 38 97 865 845 .283 3.529 3.643 3.919 3.465 1.914 80 282 4.153 .47 110 4120 4990 25 36 262 273 0 916 386 530 2.775 907 521 .36 2.864 1.472 1.518
18 672 742 622 474 50 268 646 722 621 492 24 248 0 0 89 138 86 146 31 84 6 34 318 272 .187 5.36 10.333 3.926 2.555 5.72 32 130 17.881 .09 60 4270 4990 28 34 280 286 0 583 373 211 4.215 568 195 .237 8.125 2.075 3.022
19 666 782 630 499 36 283 666 757 635 519 36 258 0 0 95 225 116 158 17 69 3 40 319 294 .127 7.861 7.167 3.016 3.81 5.28 52 200 15.935 .13 80 4440 4970 25 33 296 304 0 615 392 223 6.181 595 203 .162 5.635 2.628 2.495
20 630 715 607 512 23 203 641 683 625 519 34 171 0 0 98 260 132 141 13 57 1 32 226 205 .113 8.826 5.029 3.427 3.639 5.661 80 263 -1 -1 100 4560 4960 23 33 307 317 -50 562 403 160 6.94 537 134 .144 3.955 2.795 1.984

Total number of rows: 49152

Table truncated, full table size 11008 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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