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Sample GSM510165 Query DataSets for GSM510165
Status Public on Feb 18, 2010
Title c HDMEC/SKBR-3 co-culture 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 HDMEC/SKBR-3
Organism Homo sapiens
Characteristics cell type: HDMEC/SKBR3
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/2006-03/67599.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 1161 372 174 142 987 230 1149 391 180 146 975 249 0 0 280 100 40 41 100 94 100 91 1217 1224 4.291 .233 .255 .22 .24 .09 32 467 .32 .98 60 1840 6280 57 63 45 51 0 574 219 355 .36 603 384 2.78 .394 -1.475 -1.343
2 9642 502 181 148 9461 354 10052 553 187 151 9871 405 0 0 2626 178 43 42 100 91 100 88 9815 10276 26.726 .037 .041 .03 .04 .01 34 452 .05 .99 60 1990 6270 56 62 60 66 0 775 228 546 .058 853 625 17.317 .063 -4.114 -3.981
3 9556 6866 186 160 9370 6706 10535 7440 189 164 10349 7280 0 0 3233 3283 43 49 100 100 100 100 16076 17629 1.397 .716 .703 .67 .74 .23 26 450 .73 .99 50 2140 6270 56 61 75 80 0 10597 247 10350 1.105 11483 11236 .905 1.086 .143 .119
4 1998 2298 176 152 1822 2146 2109 2660 180 157 1933 2508 0 0 731 1059 38 49 100 100 100 94 3968 4441 .849 1.178 1.297 1.18 1.23 .49 34 451 1.16 .98 60 2280 6270 56 62 89 95 0 3547 235 3312 1.818 4105 3871 .55 2.002 .862 1.002
5 1881 1230 174 146 1707 1084 2019 1182 180 150 1845 1036 0 0 611 489 38 45 100 100 100 100 2791 2881 1.575 .635 .562 .65 .66 .24 32 438 .66 .98 60 2430 6270 56 62 104 110 0 1898 225 1673 .98 1824 1599 1.02 .867 -.029 -.207
6 762 141 169 144 593 -3 791 145 176 150 622 1 0 0 196 54 36 41 100 15 100 8 590 623 null null .002 .07 .05 .07 26 444 .2 .1 50 2570 6280 57 62 118 123 0 218 222 -5 null 224 2 null .002 null -8.655
7 3046 1219 169 153 2877 1066 3203 1319 174 155 3034 1166 0 0 796 442 37 42 100 100 100 97 3943 4200 2.699 .371 .384 .35 .38 .13 32 451 .41 .99 60 2720 6270 56 62 133 139 0 1881 236 1645 .572 2036 1800 1.749 .593 -.806 -.754
8 899 1218 180 158 719 1060 895 1100 184 160 715 942 0 0 297 587 41 44 100 100 100 97 1779 1657 .678 1.474 1.317 1.45 1.41 .48 32 426 1.34 .99 60 2870 6270 56 62 148 154 0 1880 244 1636 2.275 1698 1454 .439 2.033 1.186 1.024
9 2740 474 180 154 2560 320 2780 486 185 158 2600 332 0 0 442 117 42 44 100 98 100 91 2880 2932 8 .125 .128 .11 .12 .04 44 415 .18 .99 70 3010 6260 54 61 161 168 0 732 238 494 .193 750 512 5.183 .197 -2.374 -2.343
10 9290 2633 181 146 9109 2487 9606 2840 187 151 9425 2694 0 0 2715 946 41 41 100 100 100 100 11596 12119 3.663 .273 .286 .26 .27 .08 60 385 .29 .99 80 3160 6260 54 62 176 184 0 4064 225 3838 .421 4383 4158 2.373 .441 -1.247 -1.181
11 15006 773 187 148 14819 625 15094 764 192 160 14907 616 0 0 1692 113 46 60 100 100 100 100 15444 15523 23.71 .042 .041 .03 .04 .01 44 393 .05 1 70 3300 6260 54 61 190 197 0 1193 228 965 .065 1179 951 15.363 .064 -3.941 -3.971
12 19577 30223 184 158 19393 30065 21333 35672 190 171 21149 35514 0 0 12923 18563 47 73 100 100 100 100 49458 56663 .645 1.55 1.679 2.06 1.54 1.4 60 392 1.55 .99 80 3440 6260 54 62 204 212 0 46645 244 46401 2.393 55055 54811 .418 2.592 1.259 1.374
13 8979 7749 179 151 8800 7598 9535 8263 185 159 9356 8112 0 0 1748 1558 43 52 100 100 100 100 16398 17468 1.158 .863 .867 .88 .84 .23 37 424 .86 .99 70 3590 6260 54 61 219 226 0 11960 233 11727 1.333 12753 12520 .75 1.338 .414 .42
14 2003 504 183 151 1820 353 2065 521 185 156 1882 370 0 0 379 135 40 41 100 100 100 100 2173 2252 5.156 .194 .197 .18 .19 .07 60 404 .25 .98 80 3740 6260 54 62 234 242 0 778 233 545 .299 804 571 3.341 .303 -1.74 -1.721
15 1072 31807 184 159 888 31648 1157 35490 186 162 973 35331 0 0 284 9092 38 41 100 100 100 100 32536 36304 .028 35.64 36.311 35.31 50 5.93 44 402 28.9 .99 70 3890 6260 54 61 249 256 0 49090 245 48845 55.005 54774 54529 .018 56.042 5.781 5.808
16 17881 18828 178 156 17703 18672 20377 20921 182 159 20199 20765 0 0 5402 4684 40 42 100 100 100 100 36375 40964 .948 1.055 1.028 1.13 1.04 .45 37 431 1.04 .99 70 4030 6260 54 61 263 270 0 29059 241 28818 1.628 32289 32048 .614 1.587 .703 .666
17 11109 13845 178 152 10931 13693 11419 14175 183 157 11241 14023 0 0 1642 1308 41 46 100 100 100 100 24624 25264 .798 1.253 1.247 1.26 1.23 .17 37 416 1.23 .99 70 4170 6260 54 61 277 284 0 21368 235 21133 1.933 21877 21643 .517 1.925 .951 .945
18 2120 7190 183 154 1937 7036 2245 7668 188 161 2062 7514 0 0 429 1627 40 46 100 100 100 100 8973 9576 .275 3.632 3.644 3.73 3.7 1.03 60 374 3.38 .99 80 4320 6260 54 62 292 300 0 11097 238 10859 5.606 11835 11597 .178 5.624 2.487 2.492
19 11378 14876 183 153 11195 14723 12280 16235 188 159 12097 16082 0 0 2899 3591 40 48 100 100 100 100 25918 28179 .76 1.315 1.329 1.34 1.33 .26 70 340 1.3 1 90 4470 6260 53 62 306 315 -100 22959 236 22723 2.03 25057 24820 .493 2.052 1.021 1.037
20 29631 14779 185 161 29446 14618 32836 16147 190 167 32651 15986 0 0 7730 3799 45 52 100 100 100 100 44064 48637 2.014 .496 .49 .5 .5 .12 70 354 .5 .99 90 4620 6260 53 62 321 330 -100 22809 248 22561 .766 24921 24672 1.305 .756 -.384 -.404

Total number of rows: 43008

Table truncated, full table size 9516 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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