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Sample GSM510173 Query DataSets for GSM510173
Status Public on Feb 18, 2010
Title c HUVEC/Hs578T 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/Hs578T
Organism Homo sapiens
Characteristics cell type: HUVEC/Hs578T
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/2006-03/67579.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 1489 603 224 153 1265 450 1455 568 227 155 1231 415 0 0 591 255 38 34 100 97 100 94 1715 1646 2.811 .356 .337 .34 .36 .1 34 466 .41 .98 60 1380 7440 60 66 66 72 0 862 219 643 .508 812 593 1.967 .482 -.976 -1.054
2 8826 456 221 159 8605 297 9018 476 222 161 8797 317 0 0 2980 112 38 37 100 97 100 95 8902 9114 28.973 .035 .036 .03 .04 .01 37 442 .05 .98 70 1530 7440 59 66 80 87 0 652 227 424 .049 680 453 20.275 .051 -4.342 -4.279
3 9523 8475 219 159 9304 8316 8174 7413 220 161 7955 7254 0 0 4293 4831 37 34 100 100 100 100 17620 15209 1.119 .894 .912 .95 .83 .81 26 429 .87 .98 50 1670 7440 60 65 95 100 0 12111 227 11883 1.277 10593 10366 .783 1.303 .353 .382
4 1774 1353 227 160 1547 1193 1765 1188 226 162 1538 1028 0 0 582 654 37 32 100 100 100 100 2740 2566 1.297 .771 .668 .76 .76 .26 37 465 .77 .99 70 1820 7430 58 65 109 116 0 1933 229 1705 1.102 1698 1469 .907 .955 .14 -.066
5 1333 6804 228 163 1105 6641 1418 7191 229 166 1190 7028 0 0 506 2359 36 35 100 100 97 100 7746 8218 .166 6.01 5.906 6.62 5.88 2.8 32 420 4.95 .98 60 1970 7440 60 66 125 131 0 9723 233 9490 8.588 10276 10043 .116 8.439 3.102 3.077
6 796 217 221 161 575 56 810 209 224 164 589 48 0 0 299 76 37 37 100 59 100 41 631 637 10.268 .097 .081 .14 .15 .09 32 430 .29 .89 60 2120 7430 59 65 140 146 0 310 230 80 .139 299 69 7.185 .116 -2.845 -3.102
7 2094 8875 223 164 1871 8711 2100 9090 224 166 1877 8926 0 0 738 2654 38 35 100 100 100 100 10582 10803 .215 4.656 4.755 5.54 4.76 4.25 37 435 4.13 .99 70 2250 7430 58 65 152 159 0 12682 234 12448 6.653 12989 12755 .15 6.795 2.734 2.765
8 972 1349 225 167 747 1182 1054 1280 229 170 829 1113 0 0 255 609 38 36 100 100 100 97 1929 1942 .632 1.582 1.343 1.62 1.56 .77 32 405 1.36 .97 60 2400 7430 59 65 168 174 0 1928 239 1689 2.261 1829 1590 .442 1.919 1.177 .94
9 1477 843 226 167 1251 676 1603 867 227 168 1377 700 0 0 424 197 39 36 100 100 100 100 1927 2077 1.851 .54 .508 .6 .56 .3 52 415 .57 .98 80 2540 7430 58 66 181 189 0 1205 239 966 .772 1239 1000 1.295 .726 -.373 -.461
10 5472 2357 228 161 5244 2196 5616 2398 228 166 5388 2237 0 0 1287 855 38 36 100 100 100 100 7440 7625 2.388 .419 .415 .41 .42 .14 52 385 .44 .98 80 2700 7420 57 65 197 205 0 3368 230 3138 .598 3427 3197 1.671 .593 -.741 -.753
11 2736 13039 229 165 2507 12874 3018 14370 232 168 2789 14205 0 0 766 4419 44 38 100 100 100 100 15381 16994 .195 5.135 5.093 5.29 5.26 1.7 52 383 4.76 .99 80 2840 7420 57 65 211 219 0 18633 236 18397 7.338 20534 20299 .136 7.278 2.875 2.864
12 13266 21529 230 165 13036 21364 16809 26485 235 167 16579 26320 0 0 6911 9757 47 35 100 100 100 100 34400 42899 .61 1.639 1.588 2.27 1.64 1.92 60 389 1.62 .99 80 2980 7430 58 66 225 233 0 30765 236 30529 2.342 37847 37611 .427 2.269 1.228 1.182
13 3717 4804 230 170 3487 4634 3836 5074 233 173 3606 4904 0 0 926 888 42 38 100 100 100 100 8121 8510 .752 1.329 1.36 1.45 1.28 .66 34 411 1.28 .99 60 3130 7420 58 64 241 247 0 6865 243 6622 1.899 7251 7008 .527 1.943 .925 .959
14 2305 658 234 175 2071 483 2352 660 234 177 2118 485 0 0 560 110 38 37 100 100 100 100 2554 2603 4.288 .233 .229 .24 .25 .07 60 411 .28 .97 80 3270 7420 57 65 254 262 0 940 250 690 .333 943 693 3.001 .327 -1.585 -1.612
15 1033 561 227 170 806 391 1086 564 231 174 859 394 0 0 151 94 38 36 100 100 100 100 1197 1253 2.061 .485 .459 .48 .47 .1 37 435 .56 .99 70 3410 7410 56 63 268 275 0 802 243 559 .693 806 563 1.443 .655 -.529 -.609
16 9067 9589 229 170 8838 9419 10050 10141 229 173 9821 9971 0 0 2980 1954 37 37 100 100 100 100 18257 19792 .938 1.066 1.015 1.21 1.02 .58 37 449 1.04 .99 70 3560 7420 57 64 283 290 0 13703 243 13460 1.523 14491 14248 .657 1.451 .607 .537
17 4248 11753 234 174 4014 11579 4436 12359 234 178 4202 12185 0 0 797 2663 38 37 100 100 100 100 15593 16387 .347 2.885 2.9 2.92 2.94 .74 44 406 2.77 .99 70 3700 7420 57 64 297 304 0 16795 249 16546 4.122 17661 17412 .243 4.144 2.043 2.051
18 1871 590 239 183 1632 407 1909 599 240 183 1670 416 0 0 314 113 39 40 100 100 100 100 2039 2086 4.01 .249 .249 .24 .26 .06 52 389 .32 .99 80 3850 7410 56 64 312 320 0 843 262 582 .356 856 594 2.806 .356 -1.489 -1.49
19 7511 9886 238 183 7273 9703 8377 10864 240 185 8139 10681 0 0 2616 2513 39 41 100 100 100 100 16976 18820 .75 1.334 1.312 1.74 1.3 1.8 69 364 1.3 .99 90 3990 7420 56 65 325 334 0 14127 262 13865 1.906 15524 15263 .525 1.875 .931 .907
20 14192 9591 241 177 13951 9414 14380 10184 243 184 14139 10007 0 0 4589 3975 42 44 100 100 100 100 23365 24146 1.482 .675 .708 .69 .67 .33 69 393 .67 .98 90 4140 7410 55 64 340 349 0 13705 253 13452 .964 14553 14300 1.037 1.011 -.053 .016

Total number of rows: 43008

Table truncated, full table size 9549 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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