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Sample GSM510196 Query DataSets for GSM510196
Status Public on Feb 18, 2010
Title c HUVEC monoculture 1
Sample type RNA
 
Channel 1
Source name stratagene universal 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
Organism Homo sapiens
Characteristics cell type: HUVEC
cell line: monoculture
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, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67551.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) [email protected]
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 3516 1116 247 203 3269 913 3372 998 250 206 3125 795 0 0 1605 474 45 45 100 100 100 100 4182 3920 3.581 .279 .254 .27 .28 .05 26 480 .32 1 50 1590 7540 67 72 66 71 0 1361 248 1113 .341 1217 970 2.936 .31 -1.554 -1.688
2 5382 5545 248 195 5134 5350 5594 5691 250 198 5346 5496 0 0 1607 1685 46 44 100 100 100 100 10484 10842 .96 1.042 1.028 1.06 1.04 .29 34 455 1.03 1 60 1730 7540 67 73 80 86 0 6762 238 6525 1.271 6940 6703 .787 1.254 .346 .326
3 11118 5618 245 189 10873 5429 10107 4829 247 190 9862 4640 0 0 4023 2284 43 40 100 100 100 100 16302 14502 2.003 .499 .47 .48 .49 .07 21 473 .5 .99 50 1870 7540 67 72 94 99 0 6851 230 6621 .609 5889 5659 1.642 .574 -.716 -.801
4 1890 616 238 179 1652 437 1929 540 241 180 1691 361 0 0 671 264 42 40 100 97 100 97 2089 2052 3.78 .265 .213 .25 .25 .09 32 462 .33 .98 60 2020 7540 67 73 109 115 0 751 218 533 .323 659 440 3.1 .26 -1.632 -1.941
5 1648 1760 239 184 1409 1576 1877 1989 238 185 1638 1805 0 0 754 870 44 41 100 100 100 100 2985 3443 .894 1.119 1.102 1.15 1.11 .39 32 441 1.06 .99 60 2170 7540 67 73 124 130 0 2146 224 1922 1.364 2426 2201 .733 1.344 .448 .426
6 1208 200 244 198 964 2 1238 195 247 202 994 -3 0 0 223 45 45 45 100 14 100 5 966 991 482 .002 null .04 .04 .03 21 476 -1 -1 50 2310 7540 67 72 138 143 0 244 241 2 .003 238 -4 395.226 null -8.627 null
7 2758 2677 246 209 2512 2468 2982 2852 251 211 2736 2643 0 0 987 944 49 44 100 100 100 100 4980 5379 1.018 .982 .966 1 .98 .34 34 460 .97 .99 60 2460 7530 66 72 153 159 0 3265 255 3010 1.198 3478 3223 .835 1.178 .261 .236
8 2033 1936 250 199 1783 1737 2022 1578 254 200 1772 1379 0 0 595 823 50 43 100 100 100 100 3520 3151 1.026 .974 .778 .96 .99 .26 21 479 .94 .98 50 2600 7530 66 71 167 172 0 2361 243 2118 1.188 1924 1682 .842 .949 .249 -.075
9 1425 382 251 192 1174 190 1426 366 255 195 1175 174 0 0 326 85 45 41 100 100 100 92 1364 1349 6.179 .162 .148 .16 .16 .07 37 470 .28 .98 70 2750 7520 64 71 181 188 0 466 234 232 .197 446 212 5.067 .181 -2.341 -2.469
10 7825 2558 256 197 7569 2361 8127 2610 261 199 7871 2413 0 0 2710 991 50 41 100 100 100 100 9930 10284 3.206 .312 .307 .31 .31 .1 52 386 .32 .99 80 2900 7530 65 73 196 204 0 3120 240 2879 .38 3183 2943 2.629 .374 -1.394 -1.419
11 7734 833 255 192 7479 641 7928 822 258 196 7673 630 0 0 1257 127 49 48 100 100 100 100 8120 8303 11.668 .086 .082 .08 .09 .01 34 439 .11 .99 60 3050 7520 65 71 212 218 0 1016 234 782 .105 1002 768 9.567 .1 -3.258 -3.32
12 13967 24453 249 203 13718 24250 17117 29628 257 215 16868 29425 0 0 6073 10226 56 64 100 100 100 100 37968 46293 .566 1.768 1.744 1.84 1.79 .47 44 445 1.74 .99 70 3190 7520 64 71 225 232 0 29822 248 29574 2.156 36133 35885 .464 2.127 1.108 1.089
13 3350 5762 234 198 3116 5564 3460 6277 244 209 3226 6079 0 0 806 1383 52 55 100 100 100 100 8680 9305 .56 1.786 1.884 1.82 1.79 .39 32 440 1.72 1 60 3340 7530 66 72 241 247 0 7027 241 6786 2.178 7655 7414 .459 2.298 1.123 1.2
14 3182 1122 235 201 2947 921 3048 1106 242 204 2813 905 0 0 503 258 47 42 100 100 100 100 3868 3718 3.2 .313 .322 .3 .31 .05 44 441 .35 .99 70 3490 7520 64 71 255 262 0 1368 245 1123 .381 1349 1104 2.624 .392 -1.392 -1.35
15 806 492 241 210 565 282 824 509 244 213 583 299 0 0 116 72 42 44 100 100 100 100 847 882 2.004 .499 .513 .51 .51 .21 32 403 .62 .99 60 3630 7530 66 72 270 276 0 600 256 344 .609 621 365 1.643 .625 -.716 -.677
16 10171 17963 246 211 9925 17752 10837 19026 251 212 10591 18815 0 0 2649 4474 47 44 100 100 100 100 27677 29406 .559 1.789 1.777 1.87 1.79 .62 37 465 1.77 1 70 3770 7520 64 71 283 290 0 21907 257 21650 2.181 23203 22946 .458 2.167 1.125 1.115
17 4027 10324 245 217 3782 10107 4115 11386 250 217 3870 11169 0 0 976 2710 47 46 100 100 100 100 13889 15039 .374 2.672 2.886 2.75 2.78 .78 37 440 2.57 1 70 3920 7520 64 71 298 305 0 12591 265 12326 3.259 13886 13621 .307 3.52 1.704 1.815
18 1497 1086 244 213 1253 873 1514 1103 247 214 1270 890 0 0 298 189 50 44 100 100 100 100 2126 2160 1.435 .697 .701 .71 .7 .18 44 425 .73 .99 70 4070 7520 64 71 313 320 0 1324 260 1065 .85 1345 1085 1.177 .855 -.235 -.227
19 8554 10258 245 212 8309 10046 8897 10918 250 219 8652 10706 0 0 1474 2121 47 59 100 100 100 100 18355 19358 .827 1.209 1.237 1.21 1.23 .24 52 366 1.2 1 80 4220 7520 64 72 328 336 0 12510 259 12252 1.475 13315 13057 .678 1.509 .56 .594
20 17548 12697 246 204 17302 12493 20782 14993 250 211 20536 14789 0 0 7289 4902 50 59 100 100 100 100 29795 35325 1.385 .722 .72 .77 .72 .28 69 410 .72 1 90 4360 7510 62 71 341 350 0 15485 249 15236 .881 18285 18036 1.136 .878 -.183 -.187

Total number of rows: 43008

Table truncated, full table size 9473 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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