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Sample GSM469364 Query DataSets for GSM469364
Status Public on Jan 21, 2010
Title BTU 26 Normal 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 26 Normal 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 5761 3422 621 572 5140 2850 6390 3785 635 594 5769 3213 0 0 2399 1291 179 184 98 98 93 92 7990 8982 1.804 .554 .557 .587 .567 1.548 80 513 .536 .96 110 1740 5010 19 30 44 55 0 2094 350 1744 .339 2316 1966 2.947 .341 -1.559 -1.553
2 5296 3321 641 587 4655 2734 5556 3391 680 646 4915 2804 0 0 2438 1370 308 294 97 93 90 90 7389 7719 1.703 .587 .57 .618 .582 1.586 80 240 .553 .94 100 1910 5020 21 31 62 72 0 2032 359 1673 .359 2075 1716 2.783 .349 -1.476 -1.518
3 33841 57524 645 573 33196 56951 39925 65535 661 626 39280 64962 0 72 13864 16590 218 272 98 98 97 98 90147 104242 .583 1.716 1.654 1.951 1.644 1.656 80 262 1.641 .97 110 2050 5010 19 30 75 86 -100 35198 351 34848 1.05 40100 39749 .953 1.012 .07 .017
4 7032 4377 642 548 6390 3829 7470 4565 636 572 6828 4017 0 0 1978 1171 97 163 100 97 97 96 10219 10845 1.669 .599 .588 .619 .609 1.289 80 294 .584 .98 110 2180 5010 19 30 88 99 0 2678 335 2343 .367 2793 2458 2.727 .36 -1.448 -1.474
5 3126 2404 638 566 2488 1838 3097 2402 642 659 2459 1836 0 0 308 341 105 386 100 100 100 100 4326 4295 1.354 .739 .747 .732 .748 1.241 80 238 .718 .87 100 2330 5020 21 31 104 114 0 1471 346 1125 .452 1470 1123 2.212 .457 -1.146 -1.13
6 38841 65535 648 622 38193 64913 38587 65535 658 709 37939 64913 0 100 4665 0 106 381 100 100 100 100 103106 102852 .588 1.7 1.711 1.712 1.711 1.126 80 245 1.731 .96 100 2480 5020 21 31 119 129 -100 40100 381 39719 1.04 40100 39719 .962 1.047 .057 .066
7 1216 1189 648 619 568 570 1248 1187 653 635 600 568 0 0 184 265 95 196 97 93 95 77 1138 1168 .996 1.004 .947 .996 1.066 1.672 80 215 1.205 .73 100 2620 5020 21 31 133 143 0 728 379 349 .614 726 348 1.629 .579 -.704 -.788
8 43055 64397 662 609 42393 63788 43934 65535 719 923 43272 64926 0 93 4885 5789 561 2524 100 100 100 100 106181 108198 .665 1.505 1.5 1.507 1.492 1.084 80 323 1.537 .98 100 2760 5020 21 31 147 157 -100 39404 373 39031 .921 40100 39727 1.086 .918 -.119 -.123
9 869 910 683 647 186 263 863 947 694 678 180 300 0 0 124 204 114 205 68 65 40 28 449 480 .707 1.414 1.667 1.909 1.617 2.867 32 154 5.157 .25 60 2930 5030 24 30 166 172 0 557 396 161 .865 579 184 1.156 1.02 -.209 .028
10 885 1031 721 716 164 315 830 1073 736 724 109 357 0 0 189 258 110 201 50 58 25 33 479 466 .521 1.921 3.275 2.673 2.156 3.316 12 68 2.45 .67 40 3090 5000 22 26 183 187 0 631 438 193 1.175 657 218 .851 2.004 .233 1.003
11 2807 7025 672 624 2135 6401 2787 6957 693 642 2115 6333 0 0 381 1013 240 175 100 100 100 100 8536 8448 .334 2.998 2.994 2.999 2.996 1.146 80 277 3.011 .96 100 3230 5020 21 31 194 204 0 4299 382 3917 1.835 4257 3875 .545 1.832 .875 .874
12 923 981 667 620 256 361 920 972 668 622 253 352 0 0 107 209 99 155 95 80 70 61 617 605 .709 1.41 1.391 1.173 1.378 2.955 80 266 2.025 .51 110 3380 5030 21 32 208 219 0 600 379 221 .863 595 215 1.159 .851 -.213 -.232
13 1665 2195 664 593 1001 1602 1741 2217 658 598 1077 1624 0 0 309 462 91 145 97 97 97 97 2603 2701 .625 1.6 1.508 1.602 1.589 1.373 80 280 1.631 .93 110 3530 5020 20 31 223 234 0 1343 363 980 .979 1357 994 1.021 .923 -.03 -.116
14 1457 4772 646 594 811 4178 1473 4972 644 596 827 4378 0 0 269 1152 88 151 96 98 96 98 4989 5205 .194 5.152 5.294 5.205 5.15 1.284 80 277 5.44 .94 110 3670 5020 20 31 237 248 0 2920 363 2556 3.152 3042 2679 .317 3.239 1.656 1.696
15 754 901 647 586 107 315 746 917 649 613 99 331 0 0 103 182 97 174 50 75 17 44 422 430 .34 2.944 3.343 2.866 2.252 3.686 52 138 7.133 .23 80 3810 5030 23 31 253 261 0 551 359 193 1.801 561 203 .555 2.046 .849 1.033
16 5526 6741 644 589 4882 6152 5696 6688 648 608 5052 6099 0 0 908 868 97 203 100 100 100 100 11034 11151 .794 1.26 1.207 1.296 1.258 1.376 80 276 1.253 .98 110 3950 5020 20 31 265 276 0 4125 360 3764 .771 4092 3732 1.297 .739 -.375 -.437
17 835 1200 634 568 201 632 842 1166 638 578 208 598 0 0 104 291 108 145 83 96 47 92 833 806 .318 3.144 2.875 3.086 2.641 2.28 80 211 4.804 .53 100 4090 5030 22 32 280 290 0 734 348 387 1.924 713 366 .52 1.759 .944 .815
18 653 746 613 569 40 177 660 720 610 583 47 151 0 0 92 221 87 157 28 47 6 28 217 198 .226 4.425 3.213 2.735 2.75 4.869 80 269 9.309 .18 100 4240 5000 19 29 295 305 -50 456 348 108 2.708 441 92 .369 1.966 1.437 .975
19 673 768 590 584 83 184 663 746 600 583 73 162 0 0 108 199 90 149 43 55 16 33 267 235 .451 2.217 2.219 1.902 1.694 3.49 80 264 6.087 .24 100 4390 5000 19 29 310 320 -50 470 357 113 1.356 456 99 .737 1.358 .44 .441
20 641 756 594 546 47 210 637 751 613 555 43 205 0 0 89 197 216 143 3 56 0 31 257 248 .224 4.468 4.767 1.977 1.987 4.982 80 270 13.073 .13 100 4530 5000 19 29 324 334 -50 463 334 128 2.734 460 125 .366 2.917 1.451 1.545

Total number of rows: 49152

Table truncated, full table size 11156 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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