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Sample GSM510164 Query DataSets for GSM510164
Status Public on Feb 18, 2010
Title c HDMEC/BT549 co-culture 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 HDMEC/BT549
Organism Homo sapiens
Characteristics cell type: HDMEC/BT549
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/2006-03/67591.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 3160 836 252 167 2908 669 2849 838 253 169 2597 671 0 0 1051 285 49 40 100 100 100 100 3577 3268 4.347 .23 .258 .22 .23 .05 32 480 .27 .99 60 2040 6060 52 58 64 70 0 1522 304 1218 .419 1525 1221 2.388 .47 -1.256 -1.088
2 11748 710 238 144 11510 566 12792 766 246 146 12554 622 0 0 3673 220 63 38 100 100 100 100 12076 13176 20.336 .049 .05 .04 .05 .01 34 457 .06 .99 60 2200 6060 52 58 80 86 0 1292 262 1030 .09 1394 1132 11.172 .09 -3.482 -3.471
3 15581 6878 228 120 15353 6758 14979 7209 231 125 14751 7089 0 0 6051 3043 39 37 100 100 100 100 22111 21840 2.272 .44 .481 .42 .44 .08 26 453 .45 .99 50 2340 6060 52 57 94 99 0 12520 218 12302 .801 13123 12904 1.248 .875 -.32 -.193
4 2281 1577 224 120 2057 1457 2282 1534 228 123 2058 1414 0 0 694 635 42 37 100 100 100 100 3514 3472 1.412 .708 .687 .7 .67 .26 32 445 .68 .99 60 2490 6070 53 59 109 115 0 2871 218 2652 1.289 2792 2574 .776 1.251 .367 .323
5 2839 5207 227 131 2612 5076 2905 5689 234 133 2678 5558 0 0 700 1372 43 39 100 100 100 100 7688 8236 .515 1.943 2.075 1.97 2 .42 26 466 1.82 .99 50 2640 6060 52 57 124 129 0 9478 238 9240 3.537 10356 10117 .283 3.778 1.823 1.918
6 1308 293 241 139 1067 154 1327 300 247 141 1086 161 0 0 304 80 55 39 100 85 100 77 1221 1247 6.929 .144 .148 .13 .15 .06 26 449 .23 .98 50 2780 6060 52 57 138 143 0 533 253 280 .263 546 293 3.806 .27 -1.928 -1.89
7 3266 5175 241 144 3025 5031 3427 5460 247 148 3186 5316 0 0 1019 1682 55 42 100 100 100 100 8056 8502 .601 1.663 1.669 1.71 1.69 .46 32 438 1.57 1 60 2920 6060 52 58 152 158 0 9420 262 9158 3.027 9939 9677 .33 3.037 1.598 1.603
8 1490 1325 240 144 1250 1181 1441 1268 245 146 1201 1124 0 0 430 487 44 43 100 100 100 100 2431 2325 1.058 .945 .936 .93 .93 .19 32 422 .88 .99 60 3080 6060 52 58 168 174 0 2412 262 2150 1.72 2308 2046 .581 1.704 .782 .769
9 2063 454 248 147 1815 307 2168 445 255 149 1920 298 0 0 434 104 54 41 100 100 100 98 2122 2218 5.912 .169 .155 .16 .17 .06 44 394 .22 .99 70 3210 6060 51 58 180 187 0 826 268 559 .308 810 542 3.248 .283 -1.699 -1.824
10 11986 3063 246 126 11740 2937 11805 3196 250 127 11559 3070 0 0 2237 663 58 40 100 100 100 100 14677 14629 3.997 .25 .266 .24 .25 .03 52 384 .26 1 80 3360 6050 50 58 195 203 0 5576 229 5346 .455 5818 5588 2.196 .483 -1.135 -1.049
11 8549 5149 221 93 8328 5056 8911 5343 239 114 8690 5250 0 0 1373 902 94 107 100 100 100 100 13384 13940 1.647 .607 .604 .6 .6 .06 52 381 .6 1 80 3510 6050 50 58 210 218 0 9373 169 9203 1.105 9726 9557 .905 1.1 .144 .137
12 30326 27845 242 135 30084 27710 39380 34615 258 152 39138 34480 0 0 14866 13229 92 104 100 100 100 100 57794 73618 1.086 .921 .881 1.03 .92 .49 60 394 .92 1 80 3660 6050 50 58 225 233 0 50686 246 50441 1.677 63010 62764 .596 1.604 .746 .681
13 7006 6284 258 164 6748 6120 7430 6398 262 168 7172 6234 0 0 1611 1312 50 42 100 100 100 100 12868 13406 1.103 .907 .869 .92 .92 .18 34 405 .89 1 60 3800 6050 51 57 240 246 0 11439 299 11140 1.651 11646 11348 .606 1.582 .723 .662
14 2655 664 259 173 2396 491 2783 677 261 177 2524 504 0 0 655 185 50 44 100 99 100 99 2887 3028 4.88 .205 .2 .2 .2 .07 69 420 .25 .99 90 3940 6040 48 57 252 261 0 1209 315 894 .373 1232 917 2.681 .363 -1.423 -1.46
15 1444 23315 264 192 1180 23123 1584 25941 266 194 1320 25749 0 0 355 6611 53 47 100 100 100 100 24303 27069 .051 19.596 19.507 20.24 20 4.44 44 402 15.78 1 70 4090 6050 50 57 268 275 0 42440 349 42091 35.67 47221 46871 .028 35.508 5.157 5.15
16 17629 18505 269 206 17360 18299 18726 19740 272 208 18457 19534 0 0 4822 5586 51 46 100 100 100 100 35659 37991 .949 1.054 1.058 1.03 1.06 .15 37 430 1.06 1 70 4240 6050 50 57 283 290 0 33685 375 33310 1.919 35933 35558 .521 1.927 .94 .946
17 5850 14760 262 200 5588 14560 6337 15839 266 207 6075 15639 0 0 1635 3939 49 49 100 100 100 100 20148 21714 .384 2.606 2.574 2.68 2.63 .57 44 378 2.5 1 70 4380 6050 50 57 297 304 0 26868 364 26504 4.743 28832 28468 .211 4.686 2.246 2.228
18 2128 642 259 195 1869 447 2274 651 262 202 2015 456 0 0 407 134 47 48 100 100 100 100 2316 2471 4.181 .239 .226 .23 .23 .05 60 396 .31 .99 80 4530 6040 49 57 312 320 0 1169 355 814 .435 1185 830 2.297 .412 -1.2 -1.279
19 10779 12782 266 204 10513 12578 10868 13030 270 209 10602 12826 0 0 1703 2350 49 53 100 100 100 100 23091 23428 .836 1.196 1.21 1.19 1.2 .13 60 342 1.19 1 80 4670 6050 50 58 326 334 0 23267 371 22896 2.178 23719 23347 .459 2.202 1.123 1.139
20 26318 16760 259 198 26059 16562 28758 18215 267 202 28499 18017 0 0 6636 4180 53 53 100 100 100 100 42621 46516 1.573 .636 .632 .63 .63 .08 70 374 .64 1 90 4820 6040 48 57 340 349 -100 30508 360 30148 1.157 33157 32796 .864 1.151 .21 .203

Total number of rows: 43008

Table truncated, full table size 9512 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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