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Sample GSM195069 Query DataSets for GSM195069
Status Public on Feb 08, 2008
Title HOP-62
Sample type RNA
 
Channel 1
Source name HOP-62
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/2002-03/26857.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
1 901 1267 145 138 756 1129 910 1284 145 137 765 1146 0 0 253 367 24 30 98 100 98 100 1885 1911 .67 1.493 1.498 1.49 1.497 1.264 80 446 1.508 .97 110 1840 8040 54 65 70 81 0 1306 142 1164 1.54 1324 1181 .65 1.544 .623 .627
2 637 646 151 141 486 505 669 668 154 141 518 527 0 0 202 201 25 33 100 100 100 100 991 1045 .962 1.039 1.017 1.044 1.038 1.391 120 390 1.034 .95 120 1990 8040 54 66 85 97 0 666 145 521 1.071 689 543 .934 1.049 .099 .069
3 3787 2525 151 138 3636 2387 4113 2491 155 142 3962 2353 0 0 1521 1402 30 37 100 100 100 100 6023 6315 1.523 .656 .594 .598 .692 1.735 120 439 .7 .91 120 2130 8040 54 66 99 111 0 2603 142 2461 .677 2568 2426 1.478 .612 -.563 -.708
4 8791 13208 153 147 8638 13061 8895 13459 157 166 8742 13312 0 0 3036 4688 43 166 100 100 100 100 21699 22054 .661 1.512 1.523 1.505 1.516 1.217 80 371 1.526 .98 110 2270 8040 54 65 113 124 0 13616 152 13465 1.559 13875 13724 .642 1.57 .64 .651
5 1493 2100 160 145 1333 1955 1439 2146 163 166 1279 2001 0 0 366 519 42 163 100 100 100 100 3288 3280 .682 1.467 1.565 1.469 1.438 1.208 80 389 1.528 .95 110 2420 8040 54 65 128 139 0 2165 149 2015 1.512 2212 2063 .661 1.613 .596 .69
6 517 844 156 147 361 697 523 829 158 150 367 682 0 0 140 280 30 46 100 100 100 100 1058 1049 .518 1.931 1.858 1.928 1.985 1.306 80 358 1.971 .95 100 2570 8040 55 65 144 154 0 870 152 719 1.99 855 703 .502 1.916 .993 .938
7 2198 492 149 144 2049 348 2312 482 150 147 2163 338 0 0 470 157 26 33 100 98 100 98 2397 2501 5.888 .17 .156 .155 .162 1.592 80 388 .166 .89 110 2710 8040 54 65 157 168 0 507 148 359 .175 497 348 5.711 .161 -2.514 -2.634
8 7870 15673 146 143 7724 15530 8527 17530 148 146 8381 17387 0 0 3473 6956 23 33 100 100 100 100 23254 25768 .497 2.011 2.075 1.994 1.969 1.557 120 478 2.026 .98 120 2860 8040 54 66 172 184 0 16158 147 16010 2.073 18072 17925 .482 2.139 1.052 1.097
9 1633 2326 150 146 1483 2180 1618 2456 151 147 1468 2310 0 0 474 598 23 32 100 100 100 100 3663 3778 .68 1.47 1.574 1.487 1.428 1.24 80 353 1.476 .97 110 3010 8040 54 65 187 198 0 2398 151 2247 1.515 2532 2381 .66 1.622 .6 .698
10 548 686 154 149 394 537 570 669 156 150 416 520 0 0 163 235 24 33 100 100 98 100 931 936 .734 1.363 1.25 1.381 1.382 1.548 80 273 1.426 .89 100 3150 8050 56 66 202 212 0 707 154 554 1.405 690 536 .712 1.289 .491 .366
11 4432 3925 159 151 4273 3774 4865 4101 164 167 4706 3950 0 0 1523 1417 42 124 100 100 100 100 8047 8656 1.132 .883 .839 .87 .883 1.243 80 372 .904 .98 110 3290 8040 54 65 215 226 0 4046 156 3891 .911 4228 4072 1.098 .865 -.135 -.209
12 2583 2831 165 155 2418 2676 2488 2679 174 190 2323 2524 0 0 968 1073 60 197 100 100 100 100 5094 4847 .904 1.107 1.087 1.11 1.062 1.292 52 305 1.138 .97 90 3440 8030 54 63 231 240 0 2919 160 2759 1.141 2762 2602 .876 1.12 .19 .164
13 1160 2092 156 152 1004 1940 1079 1988 159 160 923 1836 0 0 539 939 31 80 100 100 100 100 2944 2759 .518 1.932 1.989 1.96 1.909 1.267 80 360 1.898 .98 100 3600 8040 55 65 247 257 0 2157 157 2000 1.992 2049 1893 .502 2.051 .994 1.036
14 451 511 151 152 300 359 458 500 150 152 307 348 0 0 190 237 25 36 90 92 88 86 659 655 .836 1.197 1.134 1.221 1.202 2.029 52 223 1.249 .92 80 3750 8040 56 64 263 271 0 527 157 370 1.234 515 359 .811 1.169 .303 .225
15 10891 10465 147 152 10744 10313 11799 11038 148 151 11652 10886 0 0 3841 3666 28 34 100 100 100 100 21057 22538 1.042 .96 .934 .954 .945 1.172 80 415 .969 .99 110 3880 8040 54 65 274 285 0 10789 157 10632 .99 11379 11223 1.011 .963 -.015 -.054
16 2351 4080 148 156 2203 3924 2369 4057 149 156 2221 3901 0 0 555 994 27 33 100 100 100 100 6127 6122 .561 1.781 1.756 1.799 1.761 1.24 80 361 1.81 .97 100 4030 8040 55 65 290 300 0 4206 161 4045 1.836 4182 4022 .545 1.811 .877 .857
17 430 380 148 153 282 227 414 371 149 154 266 218 0 0 119 97 24 34 100 100 100 98 509 484 1.242 .805 .82 .812 .81 1.542 52 234 .793 .86 80 4170 8040 56 64 305 313 0 392 158 234 .83 382 225 1.205 .845 -.269 -.243
18 402 469 148 152 254 317 385 454 149 153 237 302 0 0 125 151 23 32 100 100 98 100 571 539 .801 1.248 1.274 1.253 1.242 1.482 52 231 1.273 .91 80 4320 8050 57 65 320 328 0 484 157 327 1.287 468 311 .777 1.314 .364 .394
19 2649 1767 150 150 2499 1617 2694 1845 152 153 2544 1695 0 0 631 402 22 35 100 100 100 100 4116 4239 1.545 .647 .666 .649 .631 1.216 80 423 .647 .97 110 4460 8040 54 65 332 343 0 1822 155 1667 .667 1902 1747 1.499 .687 -.584 -.542
20 548 439 152 149 396 290 581 423 153 155 429 274 0 0 163 161 23 37 100 98 100 88 686 703 1.366 .732 .639 .655 .702 1.864 52 301 .759 .88 90 4610 8040 55 64 348 357 0 453 154 299 .755 436 282 1.325 .658 -.406 -.603

Total number of rows: 43008

Table truncated, full table size 9356 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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