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Sample GSM195076 Query DataSets for GSM195076
Status Public on Feb 08, 2008
Title A549/ATCC
Sample type RNA
 
Channel 1
Source name A549/ATCC
Organism Homo sapiens
Characteristics tumor cell line
Growth protocol Cell lines were grown from the publicly available NCI DTP frozen stocks in RPMI-1640 supplemented with phenol red, glutamine (2 mM) and 5% fetal calf serum. To minimize the contribution of variations in culture conditions or cell density to differential gene expression, we grew each cell line to 80% confluence and isolated mRNA 24 hours after transfer to fresh medium.
Extracted molecule polyA RNA
Extraction protocol To minimize the contribution of variations in culture conditions or cell density to differential gene expression, we grew each cell line to 80% confluence and isolated mRNA 24 hours after transfer to fresh medium. Cells were lysed in buffer containing Protein/Rnase Degrader (Invitrogen) and messenger RNA was purified with the FastTrack 2.0 purification kit (Invitrogen).
Label Cy3
Label protocol For each comparative array hybridization, labeled cDNA was synthesized by reverse transcription from test cell mRNA in the presence of Cy5-dUTP, and from the reference mRNA with Cy3-dUTP, using the Superscript II reverse-transcription kit (Gibco-BRL).
 
Channel 2
Source name Reference Batch CRH
Organism Homo sapiens
Characteristics Tumor cell line pool
Extracted molecule polyA RNA
Extraction protocol To minimize the contribution of variations in culture conditions or cell density to differential gene expression, we grew each cell line to 80% confluence and isolated mRNA 24 hours after transfer to fresh medium. Cells were lysed in buffer containing Protein/Rnase Degrader (Invitrogen) and messenger RNA was purified with the FastTrack 2.0 purification kit (Invitrogen).
Label Cy5
Label protocol For each comparative array hybridization, labeled cDNA was synthesized by reverse transcription from test cell mRNA in the presence of Cy5-dUTP, and from the reference mRNA with Cy3-dUTP, using the Superscript II reverse-transcription kit (Gibco-BRL).
 
 
Hybridization protocol 65°C overnight in a water bath.
Scan protocol All arrays were scanned using GenePix 4000A microarray scanner (Axon Instruments, Union City, CA) and initial data analysis was carried out using GenePix Pro 3.0
Description Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26804.gif
Data processing Array elements were manually flaged to exclude apparent problematic spots. All non-flagged array elements for which the fluorescent intensity in each channel was at least 300 units and the regression correlation between the red and green channels was greater than 0.6 were considered well measured and included in the study. Inclusion of a gene in correlative studies required that greater than 80% of measurements across all the cell lines in the study were present.
 
Submission date May 29, 2007
Last update date Feb 08, 2008
Contact name Douglas Ross
E-mail(s) dross@applied-genomics.com
Phone 650-697-8900
Fax 697-8900
Organization name Applied-Genomics
Street address 863 Mitten Rd #103
City Burlingame
State/province CA
ZIP/Postal code 94010
Country USA
 
Platform ID GPL3043
Series (1)
GSE7947 Gene expression patterns within cell lines are predictive of chemosensitivity

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 1054 1063 173 224 881 839 1004 1056 175 232 831 832 0 0 164 197 30 52 100 100 100 100 1720 1663 1.05 .952 1.001 .942 .945 1.231 52 326 .974 .95 90 1810 8190 46 55 48 57 0 1194 252 943 1.07 1187 935 .935 1.125 .098 .17
2 838 938 174 217 664 721 822 955 176 220 648 738 0 0 158 179 33 50 100 100 100 100 1385 1386 .921 1.086 1.139 1.085 1.083 1.256 80 330 1.097 .96 100 1960 8200 47 57 63 73 0 1054 244 810 1.22 1073 829 .82 1.28 .287 .356
3 5501 974 175 199 5326 775 5984 1001 177 204 5809 802 0 0 1804 384 32 45 100 96 100 95 6101 6611 6.872 .146 .138 .128 .143 1.581 80 390 .15 .95 110 2100 8190 45 56 76 87 0 1094 224 871 .163 1125 901 6.116 .155 -2.613 -2.688
4 10255 9867 177 192 10078 9675 9967 9873 179 195 9790 9681 0 0 4027 3853 34 45 100 100 100 100 19753 19471 1.042 .96 .989 .945 .935 1.222 80 346 .961 .98 100 2250 8190 46 56 92 102 0 11087 216 10871 1.079 11093 10878 .927 1.111 .109 .152
5 1432 781 179 189 1253 592 1474 799 180 192 1295 610 0 0 450 218 34 50 100 98 100 98 1845 1905 2.117 .472 .471 .468 .46 1.345 80 332 .464 .95 100 2400 8200 47 57 107 117 0 878 212 665 .531 898 685 1.884 .529 -.914 -.918
6 509 689 175 185 334 504 504 698 175 190 329 513 0 0 117 156 32 48 100 100 100 100 838 842 .663 1.509 1.559 1.538 1.499 1.376 52 292 1.552 .91 90 2540 8180 45 54 121 130 0 774 208 566 1.695 784 576 .59 1.752 .762 .809
7 2585 523 175 179 2410 344 2714 536 176 183 2539 357 0 0 543 118 32 42 100 100 100 97 2754 2896 7.006 .143 .141 .137 .143 1.354 80 354 .14 .93 100 2690 8190 46 56 136 146 0 588 201 387 .16 602 401 6.235 .158 -2.64 -2.662
8 12184 21298 170 179 12014 21119 12725 22945 173 185 12555 22766 0 0 2980 6599 33 58 100 100 100 100 33133 35321 .569 1.758 1.813 1.711 1.75 1.257 80 416 1.815 .98 110 2830 8190 45 56 149 160 0 23930 201 23729 1.975 25781 25580 .506 2.037 .982 1.027
9 1510 1574 172 181 1338 1393 1624 1576 174 186 1452 1395 0 0 521 538 32 49 100 100 100 100 2731 2847 .961 1.041 .961 1.035 1.044 1.344 80 349 1.044 .97 100 2980 8190 46 56 165 175 0 1769 203 1565 1.17 1771 1567 .855 1.079 .226 .11
10 669 639 176 181 493 458 705 659 176 183 529 478 0 0 166 184 33 39 98 97 98 96 951 1007 1.076 .929 .904 .919 .923 1.777 80 315 .942 .9 100 3130 8190 46 56 180 190 0 718 203 515 1.044 740 537 .958 1.015 .062 .022
11 4193 3219 182 168 4011 3051 4229 3404 180 171 4047 3236 0 0 1174 892 33 50 100 100 100 100 7062 7283 1.315 .761 .8 .757 .762 1.19 80 368 .754 .98 110 3270 8190 45 56 193 204 0 3617 189 3428 .855 3825 3636 1.17 .898 -.227 -.155
12 2120 1817 173 164 1947 1653 1967 1757 175 175 1794 1593 0 0 828 807 33 67 100 100 100 100 3600 3387 1.178 .849 .888 .807 .851 1.347 52 281 .878 .97 90 3410 8180 45 54 208 217 0 2042 184 1857 .954 1974 1790 1.048 .998 -.068 -.003
13 1217 1354 163 162 1054 1192 1249 1384 166 168 1086 1222 0 0 408 432 32 52 100 98 98 98 2246 2308 .884 1.131 1.125 1.125 1.155 1.338 80 355 1.127 .95 100 3560 8190 46 56 223 233 0 1521 182 1339 1.271 1555 1373 .787 1.264 .346 .338
14 437 477 164 157 273 320 449 460 162 158 285 303 0 0 110 146 31 40 100 96 96 93 593 588 .853 1.172 1.063 1.199 1.306 1.443 32 198 1.245 .87 70 3700 8180 46 53 238 245 0 536 176 360 1.317 517 340 .759 1.195 .397 .256
15 13306 11795 166 156 13140 11639 14180 11717 167 158 14014 11561 0 0 3514 3259 30 39 100 100 100 100 24779 25575 1.129 .886 .825 .882 .861 1.242 80 431 .882 .97 110 3850 8190 45 56 251 262 0 13253 175 13078 .995 13165 12990 1.005 .927 -.007 -.109
16 2346 3095 165 150 2181 2945 2355 3057 167 154 2190 2907 0 0 661 806 30 36 100 100 100 100 5126 5097 .741 1.35 1.327 1.361 1.317 1.189 80 333 1.341 .97 100 4000 8190 46 56 267 277 0 3478 169 3309 1.517 3435 3266 .659 1.491 .601 .577
17 488 415 165 150 323 265 495 416 168 154 330 266 0 0 84 82 33 35 100 100 98 100 588 596 1.219 .82 .806 .813 .817 1.503 52 276 .824 .87 90 4140 8190 46 55 281 290 0 466 169 298 .922 467 299 1.085 .906 -.117 -.143
18 425 427 164 146 261 281 422 448 167 148 258 302 0 0 75 88 33 33 100 100 100 94 542 560 .929 1.077 1.171 1.052 1.126 1.535 52 235 1.107 .86 80 4290 8190 47 55 297 305 0 480 164 316 1.21 503 339 .827 1.315 .275 .395
19 3033 3828 164 149 2869 3679 3261 3828 166 151 3097 3679 0 0 674 960 31 36 100 100 100 100 6548 6776 .78 1.282 1.188 1.276 1.285 1.216 80 373 1.285 .97 110 4440 8190 45 56 310 321 0 4301 167 4134 1.441 4301 4134 .694 1.335 .527 .417
20 696 646 166 153 530 493 711 654 169 155 545 501 0 0 180 159 34 35 100 100 98 100 1023 1046 1.075 .93 .919 .947 .957 1.475 52 281 .94 .92 90 4580 8180 45 54 325 334 0 726 172 554 1.045 735 563 .957 1.033 .064 .047

Total number of rows: 43008

Table truncated, full table size 9466 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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