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Sample GSM469367 Query DataSets for GSM469367
Status Public on Jan 21, 2010
Title BTU 15 Normal Fibroblasts with IGF I
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 Normal Fibroblasts with IGF I
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 4325 2689 469 468 3856 2221 4230 2636 472 486 3761 2168 0 0 584 480 77 141 100 100 100 100 6077 5929 1.736 .576 .576 .569 .579 1.206 52 329 .565 .96 90 1560 5090 20 29 15 24 0 2097 365 1732 .449 2056 1691 2.226 .45 -1.155 -1.154
2 3785 2360 477 491 3308 1869 4145 2354 479 513 3668 1863 0 0 1180 677 84 150 96 97 95 95 5177 5531 1.77 .565 .508 .578 .559 1.319 80 250 .548 .96 100 1710 5100 21 31 30 40 0 1840 383 1457 .441 1836 1453 2.27 .396 -1.183 -1.336
3 25128 54977 462 492 24666 54485 29740 65535 466 508 29278 65043 0 71 11371 20266 80 148 98 100 96 98 79151 94321 .453 2.209 2.222 2.707 2.165 1.834 80 275 2.143 .98 110 1850 5090 19 30 43 54 -100 42871 384 42487 1.722 51104 50720 .581 1.732 .784 .793
4 4060 2423 460 476 3600 1947 4402 2620 464 484 3942 2144 0 0 1425 760 77 136 96 96 95 95 5547 6086 1.849 .541 .544 .585 .54 1.795 80 262 .528 .97 100 2000 5100 21 31 59 69 0 1889 371 1518 .422 2043 1672 2.371 .424 -1.246 -1.237
5 2313 2497 470 505 1843 1992 2337 2471 484 620 1867 1966 0 0 291 384 103 428 100 100 100 100 3835 3833 .925 1.081 1.053 1.076 1.055 1.256 52 230 1.09 .9 90 2140 5090 20 29 73 82 0 1947 394 1553 .843 1927 1533 1.186 .821 -.247 -.284
6 38018 64754 502 560 37516 64194 39607 65535 511 646 39105 64975 0 96 9070 4052 97 384 100 100 100 100 101710 104080 .584 1.711 1.662 1.808 1.662 1.49 80 287 1.664 .96 100 2290 5100 21 31 88 98 -100 50495 437 50058 1.334 51104 50667 .749 1.296 .416 .374
7 767 798 503 552 264 246 795 805 512 581 292 253 0 0 87 115 103 165 93 75 75 28 510 545 1.073 .932 .866 .837 1.031 2.47 32 153 1.898 .39 60 2430 5090 22 28 104 110 0 622 430 192 .727 628 197 1.376 .676 -.461 -.566
8 31049 65001 494 526 30555 64475 31114 65535 506 581 30620 65009 0 90 3576 2546 104 296 100 100 100 100 95030 95629 .474 2.11 2.123 2.123 2.123 1.112 52 253 2.1 .99 90 2580 5090 20 29 117 126 -100 50687 410 50277 1.645 51104 50694 .608 1.656 .718 .727
9 575 597 458 491 117 106 563 574 473 497 105 83 0 0 131 148 94 168 52 30 30 10 223 188 1.104 .906 .79 .761 .795 3.686 80 320 2.201 .22 100 2730 5080 19 29 132 142 -50 466 383 83 .706 448 65 1.415 .616 -.501 -.698
10 525 551 444 447 81 104 521 548 450 461 77 101 0 0 97 156 77 130 50 42 21 12 185 178 .779 1.284 1.312 1.488 1.598 3.361 80 303 4.376 .25 100 2880 5080 19 29 147 157 -50 430 349 81 1.001 427 79 .999 1.023 .002 .033
11 3888 10504 443 468 3445 10036 3950 10334 447 485 3507 9866 0 0 390 1322 81 143 100 100 100 100 13481 13373 .343 2.913 2.813 2.905 2.891 1.099 52 246 2.924 .99 90 3020 5100 21 30 161 170 0 8191 365 7826 2.272 8058 7693 .44 2.194 1.184 1.133
12 684 795 444 496 240 299 688 777 445 506 244 281 0 0 115 171 91 134 90 86 69 55 539 525 .803 1.246 1.152 1.262 1.374 2.237 52 236 1.569 .6 90 3170 5110 22 31 176 185 0 620 387 233 .971 606 219 1.029 .898 -.042 -.155
13 1783 2332 447 494 1336 1838 1912 2445 450 504 1465 1951 0 0 549 729 78 135 93 98 92 96 3174 3416 .727 1.376 1.332 1.444 1.402 1.489 80 247 1.391 .96 100 3330 5100 21 31 192 202 0 1818 385 1433 1.073 1907 1521 .932 1.038 .101 .054
14 1516 4112 449 504 1067 3608 1600 4445 451 513 1151 3941 0 0 389 1152 77 137 96 100 96 100 4675 5092 .296 3.381 3.424 3.459 3.371 1.336 80 221 3.431 .96 100 3470 5100 21 31 206 216 0 3207 393 2813 2.637 3466 3073 .379 2.67 1.399 1.417
15 433 564 426 479 7 85 424 550 431 488 -2 71 0 0 86 154 75 136 20 33 7 13 92 69 .082 12.143 null 1.617 1.642 4.014 80 287 -1 -1 100 3610 5080 19 29 220 230 -50 440 374 66 9.469 429 55 .106 null 3.243 null
16 7573 11561 419 461 7154 11100 8472 12694 424 463 8053 12233 0 0 3004 4091 80 135 98 98 97 98 18254 20286 .645 1.552 1.519 1.712 1.544 1.613 80 251 1.528 .98 100 3760 5100 21 31 235 245 0 9015 359 8656 1.21 9899 9539 .827 1.185 .275 .244
17 502 718 412 439 90 279 493 742 417 469 81 303 0 0 71 184 81 150 50 68 15 50 369 384 .323 3.1 3.741 4.152 3.055 3.478 32 137 10.818 .16 60 3900 5090 22 28 251 257 0 560 342 218 2.417 579 236 .414 2.917 1.273 1.544
18 407 508 402 439 5 69 403 498 410 456 1 59 0 0 74 133 76 127 15 31 5 8 74 60 .072 13.8 59 2.368 2.108 4.809 80 352 -10.913 -.1 100 4050 5080 19 29 264 274 -50 396 342 54 10.761 388 46 .093 46.008 3.428 5.524
19 444 574 410 439 34 135 431 576 426 470 21 137 0 0 48 186 93 148 16 50 0 16 169 158 .252 3.971 6.524 4.868 6.421 3.018 12 68 76.131 .03 40 4180 5050 19 23 280 284 0 448 342 105 3.096 449 107 .323 5.087 1.631 2.347
20 416 558 398 444 18 114 400 555 400 459 2 111 0 0 75 143 72 143 23 43 5 11 132 113 .158 6.333 55.5 1.56 1.872 4.726 80 339 41.538 .03 100 4340 5080 19 29 293 303 -50 435 346 89 4.939 433 87 .202 43.279 2.304 5.436

Total number of rows: 49152

Table truncated, full table size 10978 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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