NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM174998 Query DataSets for GSM174998
Status Public on Nov 14, 2007
Title HTB-125/ Hs578T co-culture 1
Sample type RNA
 
Channel 1
Source name stratagene human reference
Organism Homo sapiens
Characteristics StratageneRef; RNA for the reference was pooled from 11 cell lines - obtained from Stratagene.; Protocol Type = Biological Sample; Performer: Martin,,Buess
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label 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
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 HTB-125/ Hs578T
Organism Homo sapiens
Characteristics HTB-125/ Hs578T
LabeledExtract: 59635.Channel_2
Growth protocol 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, MDA-MB436, SKBR-3, Hs578T, BT549, CCL-171, HTB-125 (ATTC) and HDF (Cambrex Bio Science Walkersville, Inc) 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.). 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. Separated co-cultures were kept in Transwell? chambers 0.4μm pore size (Costar, Corning Inc. Corning, NY). Cells negatively tested for mycoplasma infection using MycoAlert Tm (CAMBREX Bio Science Rocland, Inc Rockland, Maine) and VenorGem? (SIGMA, Saint Louis, Missouri) mycoplasma detection kits according to the manufacturer?s instructions.; 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
Label Cy5
Label protocol 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
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 Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1410, 5310; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess
Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.45; Parameter Scan Time = 11:13:00; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 220110; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.53; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess
Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.45; Parameter Scan Time = 11:13:00; Parameter PMT Volts = 620; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 439116; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.49; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess
Description Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59635.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 Mar 13, 2007
Last update date Nov 14, 2007
Contact name Martin Buess
E-mail(s) [email protected]
Phone 41 61 265 25 25
Fax 41 61 265 53 16
Organization name University Hospital Basel
Department Medizinische Onkologie
Street address Petersgraben 4
City Basel
State/province CH
ZIP/Postal code CH-4031 Basel
Country Switzerland
 
Platform ID GPL4990
Series (2)
GSE7260 epithelial-mesenchymal interaction of the breast
GSE7264 An interferon-response induced by tumor-stroma interaction in a subset of human breast cancers

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
1 386 437 163 363 223 74 405 445 166 361 242 82 0 0 76 66 27 47 97 64 97 40 297 324 3.014 .332 .339 .388 .438 3.866 45 208 .366 .43 80 2200 6430 108 116 75 83 0 749 622 127 .568 762 140 1.759 .58 -.815 -.785
2 2106 444 167 352 1939 92 1080 440 167 355 913 88 0 0 1955 84 29 47 100 65 100 43 2031 1001 21.076 .047 .096 .065 .059 2.665 100 278 .034 .67 110 2340 6430 106 117 87 98 0 760 603 158 .081 754 151 12.305 .165 -3.621 -2.599
3 3652 1044 164 345 3488 699 1625 682 167 345 1461 337 0 0 3462 663 31 45 100 95 100 87 4187 1798 4.99 .2 .231 .228 .213 1.8 63 208 .191 .98 90 2480 6430 107 116 102 111 0 1788 591 1197 .343 1168 577 2.913 .395 -1.543 -1.34
4 1113 712 164 352 949 360 1128 704 168 351 964 352 0 0 650 211 30 49 100 98 100 88 1309 1316 2.636 .379 .365 .423 .389 1.563 54 209 .347 .94 80 2630 6430 108 116 118 126 0 1220 603 617 .65 1206 603 1.539 .625 -.622 -.677
5 784 922 164 339 620 583 953 842 167 341 789 503 0 0 486 432 29 52 96 98 93 86 1203 1292 1.063 .94 .638 1.122 .99 1.803 60 228 .907 .96 90 2770 6430 107 116 131 140 0 1579 581 999 1.611 1442 862 .621 1.092 .688 .127
6 434 520 160 326 274 194 461 521 163 331 301 195 0 0 97 69 30 47 100 100 100 93 468 496 1.412 .708 .648 .712 .708 1.564 31 142 .654 .81 60 2920 6420 108 114 148 154 0 891 558 332 1.213 892 334 .825 1.11 .278 .15
7 1709 1339 165 324 1544 1015 1929 1288 165 329 1764 964 0 0 949 617 30 46 100 100 100 100 2559 2728 1.521 .657 .546 .718 .672 1.762 44 238 .638 .96 80 3070 6430 108 116 162 170 0 2293 555 1739 1.126 2206 1651 .888 .936 .171 -.095
8 650 1050 156 316 494 734 555 1055 158 317 399 739 0 0 661 319 30 45 97 100 95 100 1228 1138 .673 1.486 1.852 1.964 2.047 2.365 42 148 .781 .5 70 3210 6430 108 115 176 183 0 1798 541 1257 2.545 1807 1266 .393 3.172 1.348 1.666
9 1170 583 163 308 1007 275 1252 595 164 305 1089 287 0 0 403 122 30 44 100 100 100 95 1282 1376 3.662 .273 .264 .266 .268 1.433 80 298 .27 .92 100 3360 6420 106 116 190 200 0 999 528 471 .468 1019 492 2.138 .451 -1.096 -1.148
10 1238 662 165 299 1073 363 1321 616 166 300 1156 317 0 0 613 185 31 45 100 98 100 97 1436 1473 2.956 .338 .274 .362 .341 1.485 91 231 .312 .95 100 3510 6420 106 116 205 215 0 1134 512 622 .579 1055 543 1.726 .47 -.787 -1.09
11 753 2817 162 297 591 2520 694 2640 164 297 532 2343 0 0 256 970 30 45 100 100 100 100 3111 2875 .235 4.264 4.404 4.325 4.384 1.41 122 379 4.494 .93 120 3650 6410 104 116 218 230 0 4825 509 4316 7.303 4522 4013 .137 7.544 2.869 2.915
12 7286 4244 161 287 7125 3957 2908 2037 162 287 2747 1750 0 0 7559 4028 29 41 100 100 100 100 11082 4497 1.801 .555 .637 .599 .604 1.453 123 376 .535 .98 120 3790 6410 104 116 232 244 0 7269 492 6778 .951 3489 2997 1.051 1.091 -.072 .126
13 1462 2573 160 280 1302 2293 1125 1977 161 281 965 1697 0 0 962 1628 28 41 100 100 100 100 3595 2662 .568 1.761 1.759 1.825 1.816 1.357 112 419 1.744 .98 120 3940 6410 104 116 247 259 0 4407 480 3928 3.017 3386 2907 .332 3.012 1.593 1.591
14 555 404 158 280 397 124 566 402 159 282 408 122 0 0 81 55 30 41 100 92 100 78 521 530 3.202 .312 .299 .283 .328 1.799 52 261 .301 .72 90 4090 6410 105 114 263 272 0 692 480 212 .535 689 209 1.869 .512 -.902 -.965
15 563 426 156 274 407 152 551 430 156 272 395 156 0 0 108 59 28 41 100 97 100 88 559 551 2.678 .373 .395 .352 .351 1.685 45 128 .389 .8 70 4240 6400 105 112 279 286 0 730 469 260 .64 737 267 1.563 .676 -.645 -.564
16 3747 1725 155 266 3592 1459 1525 933 157 268 1370 667 0 0 3953 1511 27 44 100 100 100 99 5051 2037 2.462 .406 .487 .459 .45 1.485 103 405 .385 .98 120 4380 6410 104 116 291 303 0 2955 456 2499 .696 1598 1142 1.437 .834 -.523 -.262
17 1907 1964 159 263 1748 1701 1519 1701 161 264 1360 1438 0 0 1153 1080 29 43 100 100 100 100 3449 2798 1.028 .973 1.057 .995 1.004 1.367 98 329 .958 .98 110 4530 6400 103 114 306 317 0 3364 450 2914 1.667 2914 2463 .6 1.811 .737 .857
18 1115 451 154 254 961 197 1147 448 158 252 993 194 0 0 270 61 31 39 100 98 100 97 1158 1187 4.878 .205 .195 .203 .202 1.396 67 287 .204 .88 100 4680 6400 104 114 322 332 0 772 435 337 .351 767 332 2.848 .335 -1.51 -1.579
19 4779 2963 158 254 4621 2709 5427 2775 162 255 5269 2521 0 0 3289 1966 35 42 100 100 100 100 7330 7790 1.706 .586 .478 .597 .594 1.479 116 442 .585 .98 130 4820 6400 102 115 334 347 0 5075 435 4640 1.004 4753 4318 .996 .82 .006 -.287
20 8286 3224 160 251 8126 2973 9649 3807 166 255 9489 3556 0 0 4831 1758 38 47 100 100 100 100 11099 13045 2.733 .366 .375 .364 .363 1.383 109 366 .359 .98 120 4960 6410 104 116 349 361 0 5522 430 5092 .627 6521 6091 1.596 .642 -.674 -.64

Total number of rows: 43008

Table truncated, full table size 9578 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap