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Sample GSM510161 Query DataSets for GSM510161
Status Public on Feb 18, 2010
Title c HUVEC/MDA-MB-231 co-culture 1
Sample type RNA
 
Channel 1
Source name stratagene human reference
Organism Homo sapiens
Characteristics reference: Stratagene Universal reference; pooled from 11 cell lines
Extracted molecule total RNA
Extraction 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: Martin,,Buess
Label Cy3
Label protocol amplified RNA dircect inocorporaton; The protocol was modified for amplified RNA: 1. 6ug of amplified RNA and 10ug of random hexamer primer were mixed in a total volume of 15.4 ul. Then the described protocol was followed.; Protocol Type = Labeling; Performer: Martin,,Buess
 
Channel 2
Source name HUVEC/MDA-MB-231
Organism Homo sapiens
Characteristics cell type: HUVEC/MDA-MB-231
cell line: co-culture
Growth protocol Endothelial co-culture conditions; Human mammary epithelial cells (HMEC) (Cambrex Bio Science Walkersville, Inc) were expanded in mammary epithelial basal medium supplemented with bovine pituitary extract, human EGF, insulin and antibiotics (Clonetics, Cambrex Bio Science Walkersville, Inc). MCF-7, T47D, MDA-MB231, SKBR-3, Hs578T, BT549 (ATTC) were propagated in DMEM supplemented with 10% FBS (HyClone, Logan UT), glutamine, 100U/ml penicillin and 100 μg/ml streptomycin (GIBCO, Grand Island, N.Y.). HUVEC (ATTC) AND HDMEC (Cambrex Bio Science Walkersville, Inc) were expanded in endothelial basal media (CAMBREX Bio Science Rockland, Inc Rockland, Maine) supplemented with hEGF, Hydrocortisone, GA-1000 (Gentamicin, Amphotericin-B), 5% FBS, VEGF, hFGF-B (w/ heparin), R3 -IGF-and ascorbic acid. For co-culture experiments the cells were cultivated for 48 hours at 50,000 cells/cm2 in endothelial basal media (CAMBREX Bio Science Rockland, Inc Rockland, Maine) with 0.2% FBS, which was a good universal media for all cells involved.; Protocol Type = Biological Sample; Performer: Martin,,Buess
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: Martin,,Buess
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: Martin,,Buess
Label Cy5
Label protocol amplified RNA direct incorporation method; The protocol was modified for amplified RNA: 6ug of amplified RNA was mixed with 10ug of random hexamer primer pd(N)6( Procuct number 27-2166-01, Amersham Biosciences) in a total volume of 15.4 ul. Then the protocol was followed as described; Protocol Type = Labeling; Performer: Martin,,Buess
 
 
Hybridization protocol not provided
Scan protocol GenePix 4000A
Description Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67575.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 Feb 16, 2010
Last update date Feb 17, 2010
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 GPL10054
Series (1)
GSE20364 Breast cancer endothelial interaction

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 1447 751 184 84 1263 667 1332 297 186 85 1148 213 0 0 654 1839 31 23 100 91 100 88 1930 1361 1.894 .528 .186 .48 .2 1.19 34 464 .53 .73 60 1210 5850 66 72 81 87 -100 1223 137 1086 .86 484 347 1.163 .302 -.218 -1.727
2 1990 114 182 91 1808 23 1868 109 184 92 1686 18 0 0 635 35 30 23 100 49 100 24 1831 1704 78.609 .013 .011 .02 .02 .02 37 442 .06 .73 70 1350 5850 65 72 94 101 0 186 148 37 .021 177 29 48.284 .017 -5.593 -5.846
3 1978 2204 183 92 1795 2112 1687 1895 184 95 1504 1803 0 0 1033 1445 30 26 100 97 100 97 3907 3307 .85 1.177 1.199 1.78 1.35 2.33 34 426 1.14 .93 60 1500 5850 66 72 110 116 -100 3588 150 3438 1.916 3085 2935 .522 1.952 .938 .965
4 719 212 183 90 536 122 731 193 183 91 548 103 0 0 183 117 30 25 100 84 100 66 658 651 4.393 .228 .188 .25 .25 .17 32 448 .3 .88 60 1640 5860 67 73 124 130 0 345 147 199 .371 314 168 2.699 .306 -1.432 -1.708
5 636 756 183 92 453 664 664 724 184 93 481 632 0 0 229 345 30 24 100 97 100 97 1117 1113 .682 1.466 1.314 2.13 1.59 1.82 32 435 1.17 .94 60 1800 5860 67 73 140 146 -100 1231 150 1081 2.386 1179 1029 .419 2.139 1.255 1.097
6 811 121 188 92 623 29 809 75 188 93 621 -17 0 0 143 141 31 24 100 15 100 15 652 604 21.483 .047 null .21 .06 .3 26 442 .15 .33 50 1940 5850 66 71 154 159 0 197 150 47 .076 122 -28 13.195 null -3.722 null
7 937 992 184 92 753 900 957 1001 183 93 773 909 0 0 223 292 30 22 100 100 100 100 1653 1682 .837 1.195 1.176 1.26 1.23 .46 37 442 1.05 .98 70 2080 5850 65 72 167 174 0 1615 150 1465 1.946 1630 1480 .514 1.915 .96 .937
8 584 481 184 97 400 384 635 491 186 99 451 394 0 0 167 133 32 22 94 100 94 97 784 845 1.042 .96 .874 1.45 .85 1.9 34 444 .79 .97 60 2230 5850 66 72 183 189 0 783 158 625 1.563 799 641 .64 1.422 .644 .508
9 463 227 185 98 278 129 466 215 188 99 281 117 0 0 106 62 30 24 100 98 98 90 407 398 2.155 .464 .416 .54 .43 .44 60 413 .5 .95 80 2380 5840 64 72 197 205 0 370 160 210 .755 350 190 1.324 .678 -.405 -.561
10 4450 1474 189 98 4261 1376 4464 1430 189 99 4275 1332 0 0 1621 599 31 25 100 98 100 98 5637 5607 3.097 .323 .312 .32 .33 .14 60 381 .33 .98 80 2520 5840 64 72 211 219 0 2400 160 2240 .526 2328 2169 1.902 .507 -.928 -.979
11 1508 1594 189 104 1319 1490 1554 1599 188 108 1365 1495 0 0 325 261 31 29 100 100 100 100 2809 2860 .885 1.13 1.095 1.34 1.1 1.28 52 379 1.04 .98 80 2670 5850 65 73 226 234 0 2595 169 2426 1.839 2603 2434 .544 1.783 .879 .834
12 4408 10593 189 109 4219 10484 4727 11266 191 113 4538 11157 0 0 1670 3139 34 37 100 100 100 100 14703 15695 .402 2.485 2.459 3.2 2.56 2.48 60 373 2.38 .98 80 2810 5850 65 73 240 248 0 17246 177 17069 4.046 18342 18164 .247 4.003 2.016 2.001
13 965 1389 185 105 780 1284 1011 1362 187 107 826 1257 0 0 338 480 34 31 98 100 96 100 2064 2083 .607 1.646 1.522 2.99 1.52 4.37 52 357 1.38 .97 80 2960 5850 65 73 255 263 0 2261 171 2090 2.68 2217 2046 .373 2.478 1.422 1.309
14 1683 509 180 101 1503 408 1747 441 180 103 1567 340 0 0 527 541 31 25 100 100 100 100 1911 1907 3.684 .271 .217 .28 .24 .41 69 397 .31 .79 90 3100 5840 63 72 268 277 -100 829 164 664 .442 718 554 2.263 .353 -1.178 -1.501
15 403 317 185 102 218 215 417 294 189 105 232 192 0 0 99 185 30 27 95 98 90 95 433 424 1.014 .986 .828 1.39 .81 2.48 60 358 .77 .91 80 3250 5850 65 73 284 292 -100 516 166 350 1.606 479 313 .623 1.347 .683 .43
16 4903 10502 190 107 4713 10395 5668 12282 193 109 5478 12175 0 0 2272 4779 29 27 100 100 100 100 15108 17653 .453 2.206 2.223 3.52 2.27 4.99 60 363 2.15 .97 80 3400 5850 65 73 299 307 0 17098 174 16924 3.591 19996 19822 .278 3.618 1.844 1.855
17 1310 5408 188 110 1122 5298 1390 5486 190 112 1202 5376 0 0 401 985 31 27 100 100 98 100 6420 6578 .212 4.722 4.473 6.93 4.76 7.3 52 331 4 .98 80 3540 5850 65 73 313 321 0 8805 179 8625 7.688 8932 8752 .13 7.282 2.943 2.864
18 1298 1792 191 108 1107 1684 1045 749 192 109 854 641 0 0 1962 4734 32 26 99 100 96 100 2791 1495 .657 1.521 .751 2.13 .75 5.59 70 361 1.36 .77 90 3680 5840 63 72 326 335 -100 2917 176 2742 2.477 1219 1044 .404 1.222 1.308 .289
19 3093 3698 195 113 2898 3585 3226 3790 196 114 3031 3677 0 0 641 700 32 28 100 100 100 100 6483 6708 .808 1.237 1.213 1.32 1.25 .54 70 339 1.19 .98 90 3840 5840 63 72 342 351 -100 6021 184 5837 2.014 6170 5986 .497 1.975 1.01 .982
20 13063 5644 193 118 12870 5526 14394 6317 195 120 14201 6199 0 0 3455 1865 32 29 100 100 100 100 18396 20400 2.329 .429 .437 .43 .43 .16 70 333 .44 .98 90 3980 5840 63 72 356 365 -100 9189 192 8997 .699 10284 10092 1.431 .711 -.517 -.493

Total number of rows: 43008

Table truncated, full table size 9499 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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