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Sample GSM510175 Query DataSets for GSM510175
Status Public on Feb 18, 2010
Title c BT549 monoculture 2
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 BT549
Organism Homo sapiens
Characteristics cell type: BT549
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/2006-03/67597.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 1292 898 197 128 1095 770 1319 937 200 131 1122 809 0 0 428 307 38 37 100 100 100 94 1865 1931 1.422 .703 .721 .79 .7 .58 34 463 .69 .99 60 2200 6770 62 68 45 51 0 961 137 824 .753 1003 866 1.328 .772 -.41 -.373
2 7047 337 205 121 6842 216 7527 333 206 124 7322 212 0 0 2281 118 39 33 100 94 100 91 7058 7534 31.676 .032 .029 .02 .03 .01 34 426 .05 .99 60 2340 6770 62 68 59 65 0 361 130 231 .034 357 227 29.587 .031 -4.887 -5.012
3 7217 3902 198 129 7019 3773 7889 4041 200 131 7691 3912 0 0 3485 1891 37 35 100 100 100 100 10792 11603 1.86 .538 .509 .57 .54 .27 32 421 .54 .99 60 2490 6770 62 68 74 80 0 4178 138 4039 .575 4326 4188 1.738 .545 -.797 -.877
4 1382 2754 196 138 1186 2616 1310 2337 197 143 1114 2199 0 0 446 1395 36 39 100 100 100 100 3802 3313 .453 2.206 1.974 2.18 2.27 .77 32 446 2.02 .98 60 2640 6770 62 68 89 95 0 2948 148 2801 2.361 2502 2354 .423 2.113 1.24 1.08
5 1386 4105 206 146 1180 3959 1433 4231 209 146 1227 4085 0 0 226 671 41 37 100 100 100 100 5139 5312 .298 3.355 3.329 3.4 3.45 .55 26 456 2.91 .99 50 2780 6770 62 67 103 108 0 4395 156 4239 3.592 4530 4373 .278 3.564 1.845 1.834
6 815 293 208 142 607 151 855 271 211 143 647 129 0 0 178 96 42 35 100 92 100 77 758 776 4.02 .249 .199 .23 .22 .13 26 449 .37 .96 50 2930 6770 62 67 118 123 0 314 152 162 .266 290 138 3.755 .213 -1.909 -2.228
7 1629 3851 202 135 1427 3716 1761 3972 205 137 1559 3837 0 0 435 987 39 34 100 100 100 100 5143 5396 .384 2.604 2.461 2.71 2.63 .72 32 439 2.33 .99 60 3080 6770 62 68 133 139 0 4123 145 3978 2.788 4252 4108 .359 2.635 1.479 1.398
8 1119 380 210 140 909 240 1067 369 239 156 857 229 0 0 216 119 250 136 100 81 100 29 1149 1086 3.788 .264 .267 .25 .26 .08 21 471 .34 .98 50 3220 6760 61 66 147 152 0 407 150 257 .283 395 245 3.538 .286 -1.823 -1.806
9 1288 660 214 142 1074 518 1376 688 246 160 1162 546 0 0 273 188 264 144 100 98 95 86 1592 1708 2.073 .482 .47 .46 .49 .13 44 419 .51 .99 70 3370 6750 59 66 161 168 0 707 152 555 .516 737 585 1.937 .503 -.954 -.991
10 9653 6613 214 153 9439 6460 9956 6864 217 158 9742 6711 0 0 2043 1386 40 43 100 100 100 100 15899 16453 1.461 .684 .689 .68 .68 .08 52 377 .69 1 80 3510 6750 59 67 175 183 0 7080 164 6916 .733 7349 7185 1.365 .738 -.449 -.439
11 4264 8435 223 157 4041 8278 4435 8607 234 184 4212 8450 0 0 796 1166 89 120 100 100 100 100 12319 12662 .488 2.049 2.006 2.12 2 .58 52 368 1.95 .99 80 3660 6760 60 68 190 198 0 9031 168 8862 2.193 9215 9047 .456 2.148 1.133 1.103
12 18762 28214 225 149 18537 28065 22692 35078 239 176 22467 34929 0 0 8590 12295 89 121 100 100 100 100 46602 57396 .661 1.514 1.555 1.72 1.54 .83 60 390 1.5 .99 80 3800 6750 59 67 204 212 0 30206 160 30047 1.621 37555 37395 .617 1.664 .697 .735
13 4325 9103 218 146 4107 8957 4354 9700 225 152 4136 9554 0 0 1314 2260 57 48 100 100 100 100 13064 13690 .459 2.181 2.31 2.29 2.17 .53 37 402 2.08 .99 70 3940 6750 59 66 218 225 0 9746 156 9589 2.335 10385 10229 .428 2.473 1.223 1.306
14 2450 1833 214 142 2236 1691 2592 1773 215 142 2378 1631 0 0 851 960 42 37 100 99 99 97 3927 4009 1.322 .756 .686 .75 .71 .27 79 397 .74 .98 100 4080 6740 57 67 231 241 -100 1962 152 1810 .81 1898 1746 1.235 .734 -.305 -.446
15 823 32911 219 134 604 32777 810 41434 221 138 591 41300 0 0 413 16302 40 39 93 100 88 100 33381 41891 .018 54.267 69.882 33.9 50 10.5 60 384 39.36 .99 80 4240 6750 59 67 248 256 0 35235 143 35091 58.098 44360 44216 .017 74.816 5.86 6.225
16 15171 21542 216 142 14955 21400 16282 22786 221 157 16066 22644 0 0 3894 4615 43 79 100 100 100 100 36355 38710 .699 1.431 1.409 1.47 1.45 .31 37 438 1.42 .99 70 4380 6750 59 66 262 269 0 23063 152 22911 1.532 24395 24243 .653 1.509 .615 .594
17 3384 18983 218 142 3166 18841 3553 20140 222 161 3335 19998 0 0 754 3257 46 83 100 100 100 100 22007 23333 .168 5.951 5.996 6.19 5.88 1.54 44 401 5.55 .99 70 4530 6750 59 66 277 284 0 20323 152 20171 6.371 21562 21410 .157 6.42 2.672 2.683
18 1799 2265 225 144 1574 2121 1918 2424 227 148 1693 2280 0 0 542 680 49 42 100 100 100 100 3695 3973 .742 1.348 1.347 1.48 1.37 .72 52 369 1.25 .99 80 4680 6750 59 67 292 300 0 2425 154 2271 1.443 2595 2441 .693 1.442 .529 .528
19 4901 11307 223 153 4678 11154 4974 11869 225 158 4751 11716 0 0 1341 2662 44 44 100 100 100 100 15832 16467 .419 2.384 2.466 2.47 2.5 .64 70 336 2.31 .99 90 4820 6740 57 66 305 314 -100 12105 164 11942 2.553 12707 12543 .392 2.64 1.352 1.401
20 17189 13808 235 151 16954 13657 18902 13934 236 158 18667 13783 0 0 6593 6698 43 46 100 100 100 100 30611 32450 1.241 .806 .738 .91 .76 .54 80 312 .8 .98 100 4970 6750 58 68 320 330 -100 14783 162 14621 .862 14918 14756 1.16 .79 -.214 -.339

Total number of rows: 43008

Table truncated, full table size 9652 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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