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Sample GSM26018 Query DataSets for GSM26018
Status Public on Jun 30, 2004
Title A404 SMC Differentiation RA96 Replicate 4
Sample type RNA
 
Channel 1
Source name Total RNA from P19 cells, clone A404, labeled with Cyanine-5 (red).
Organism Mus musculus
Extracted molecule total RNA
 
Channel 2
Source name Total RNA from pooled whole mouse embryos e17.5, labeled with Cyanine-3 (green).
Organism Mus musculus
Extracted molecule total RNA
 
 
Description Time point 3.

Undifferentiated P19 mouse embryonal carcinoma cells, clone A404 obtained from Gary K. Owens at University of Virginia were grown in a-minimum essential medium, 7.5% fetal bovine serum, 200 mg/ml L-glutamine, and penicillin/streptomycin.
Cells were plated in 10-cm dishes and grown to near confluence. Medium in a set of plates at ~30% confluence was changed at time 0 to basal medium supplemented with 1 umol/L all trans-retinoic acid, and harvested after 96 hours of incubation (RA96 group). RNA was extracted with Trizol, 5-6 plates per replicate. A common reference consisting of RNA derived from whole 17.5-day mouse embryos was utilized.

RNA was purified and isolated using the Qiagen RNeasy Midi Kit Protocol. Ten ug of total RNA were primed with 2 ul of 100uM T16N2 DNA primer at 70 °C for 10 min, and reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase, and 100 uM each dATP, dTTP, dGTP, with 25 uM dCTP, 25 uM Cy3- or Cy5-dCTP and RNase inhibitor. RNA was then degraded with RNase A, and labeled cDNAs were purified using QIAquick PCR columns. Oligoarray Control Targets and Hybridization Buffer (Agilent In Situ Hybrization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent EZ-Hybe chambers. After hybridization, slides were washed sequentially with 6× SSC/0.005% Triton X-102 and 0.1× SSC/0.005% Triton X-102 before scanning. Slides were hybridized for 17 h at 60°C in a rotating oven, washed, and then scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.6.1.1).
 
Submission date Jun 24, 2004
Last update date Oct 28, 2005
Contact name Joshua M. Spin
E-mail(s) [email protected]
Phone 650-498-6353
Organization name Stanford University
Department Internal Medicine/Cardiovascular Division
Lab Philip S. Tsao Lab
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL1307
Series (1)
GSE1506 A404 Smooth Muscle Cell Differentiation

Data table header descriptions
ID_REF
PositionX Found X coordinate of feature centroid in pixels.
PositionY Found Y coordinate of feature centroid in pixels.
VALUE log(REDsignal/GREENsignal) per feature (processed signals used).
LogRatioError error of the log ratio calculated according to the error model chosen.
PValueLogRatio Significance level of the Log Ratio computed for a feature.
gSurrogateUsed The green surrogate value used.
rSurrogateUsed The red surrogate value used.
gIsFound A boolean used to flag found (strong) features.The flag is applied independently in each channel. A feature is considered found if the found spot centroid is within the bounds of the spot deviation limit with respect to corresponding nominal centroid.
rIsFound A boolean used to flag found (strong) features.The flag is applied independently in each channel. A feature is considered found if the found spot centroid is within the bounds of the spot deviation limit with respect to corresponding nominal centroid.
gProcessedSignal Dye-normalized signal after surrogate "algorithm," green "channel," used for computation of log ratio.
rProcessedSignal Dye-normalized signal after surrogate "algorithm," red "channel," used for computation of log ratio.
gProcessedSigError Standard error of propagated feature "signal," green channel.
rProcessedSigError Standard error of propagated feature "signal," red channel.
gNumPixOLHi Number of outlier pixels per feature with intensity > upper threshold set via the pixel outlier rejection method. The number is computed independently in each channel. These pixels are omitted from all subsequent calculations.
rNumPixOLHi Number of outlier pixels per feature with intensity > upper threshold set via the pixel outlier rejection method. The number is computed independently in each channel. These pixels are omitted from all subsequent calculations.
gNumPixOLLo Number of outlier pixels per feature with intensity < lower threshold set via the pixel outlier rejection method. The number is computed independently in each channel. NOTE: The pixel outlier method is the ONLY step that removes data in Feature Extraction.
rNumPixOLLo Number of outlier pixels per feature with intensity < lower threshold set via the pixel outlier rejection method. The number is computed independently in each channel. NOTE: The pixel outlier method is the ONLY step that removes data in Feature Extraction.
gNumPix Total number of pixels used to compute feature statistics; ie.total number of inlier pixels/per spot; same in both channels.
rNumPix Total number of pixels used to compute feature statistics; ie.total number of inlier pixels/per spot; same in both channels.
gMeanSignal Raw mean signal of feature in green channel (inlier pixels).
rMeanSignal Raw mean signal of feature in red channel (inlier pixels).
gMedianSignal Raw median signal of feature in green channel (inlier pixels).
rMedianSignal Raw median signal of feature in red channel (inlier pixels).
gPixSDev Standard deviation of all inlier pixels per feature; this is computed independently in each channel.
rPixSDev Standard deviation of all inlier pixels per feature; this is computed independently in each channel.
gBGNumPix Total Number of pixels used to compute Local BG statistics per spot; ie.total number of BG inlier pixels; same in both channels.
rBGNumPix Total Number of pixels used to compute Local BG statistics per spot; ie.total number of BG inlier pixels; same in both channels.
gBGMeanSignal Mean local background signal (local to corresponding feature) computed per channel (inlier pixels).
rBGMeanSignal Mean local background signal (local to corresponding feature) computed per channel (inlier pixels).
gBGMedianSignal Median local background signal (local to corresponding feature) computed per channel (inlier pixels).
rBGMedianSignal Median local background signal (local to corresponding feature) computed per channel (inlier pixels).
gBGPixSDev Standard deviation of all inlier pixels per Local BG of each "feature," computed independently in each channel.
rBGPixSDev Standard deviation of all inlier pixels per Local BG of each "feature," computed independently in each channel.
gNumSatPix Total number of saturated pixels per "feature," computed per channel.
rNumSatPix Total number of saturated pixels per "feature," computed per channel.
gIsSaturated Boolean flag indicating if a feature is saturated or not.
rIsSaturated Boolean flag indicating if a feature is saturated or not.
PixCorrelation Ratio of estimated feature covariance in RedGreen space to product of feature Standard Deviation in Red Green space.
BGPixCorrelation Ratio of estimated background covariance in RedGreen space to product of background Standard Deviation in Red Green space.
gIsFeatNonUnifOL Boolean flag indicating if a feature is NonUniformity Outlier or not Green Channel.
rIsFeatNonUnifOL Boolean flag indicating if a feature is NonUniformity Outlier or not Red Channel.
gIsBGNonUnifOL Boolean flag indicating if background is NonUniformity Outlier or not Green Channel.
rIsBGNonUnifOL Boolean flag indicating if background is NonUniformity Outlier or not Red Channel.
gIsFeatPopnOL Boolean flag indicating if a feature is a Population Outlier or not for Green Channel. Probes with replicate features on a microarray are examined using population statistics.
rIsFeatPopnOL Boolean flag indicating if a feature is a Population Outlier or not for Red Channel. Probes with replicate features on a microarray are examined using population statistics.
gIsBGPopnOL Boolean flag indicating if background is a Population Outlier or not for Green Channel.
rIsBGPopnOL Boolean flag indicating if background is a Population Outlier or not for Red Channel.
IsManualFlag Manual Flag.
gBGSubSignal The net g signal following the subtraction of the background from the raw mean g signal.
rBGSubSignal The net r signal following the subtraction of the background from the raw mean r signal.
gBGSubSigError Propagated standard error as computed on net g background subtracted signal.
rBGSubSigError Propagated standard error as computed on net r background subtracted signal.
BGSubSigCorrelation Ratio of estimated background subtracted feature signal covariance in RG space to product of background subtracted feature Standard Deviation in RG space.
gIsPosAndSignif Boolean flag indicating if the mean signal of a feature is greater than the corresponding background (selected by user) and if this difference is significant.
rIsPosAndSignif Boolean flag indicating if the mean signal of a feature is greater than the corresponding background (selected by user) and if this difference is significant.
gPValFeatEqBG P-value from t-test of significance between g Mean signal and g background (selected by user).
rPValFeatEqBG P-value from t-test of significance between r Mean signal and r background (selected by user).
gNumBGUsed Number of local background regions or features used to calculate the background subtraction on this feature g channel.
rNumBGUsed Number of local background regions or features used to calculate the background subtraction on this feature r channel.
gIsWellAboveBG Boolean flag indicating if a feature is WellAbove Background or not.
rIsWellAboveBG Boolean flag indicating if a feature is WellAbove Background or not.
IsUsedBGAdjust A boolean used to flag features used for computation of global BG offset.
gBGUsed Background value (after global background adjust if turned ON) subtracted from the raw mean signal to generate the BG subtracted signal; this value is computed per channel. If global BG subtraction is used the column is identical for every feature in a given channel.
rBGUsed Background value (after global background adjust if turned ON) subtracted from the raw mean signal to generate the BG subtracted signal; this value is computed per channel. If global BG subtraction is used the column is identical for every feature in a given channel.
gBGSDUsed Standard deviation of background used in g channel.
rBGSDUsed Standard deviation of background used in r channel.
IsNormalization A boolean flag which indicates if a feature is used to measure dye bias.
gDyeNormSignal The dye-normalized signal in the indicated channel.
rDyeNormSignal The dye-normalized signal in the indicated channel.
gDyeNormError The standard error associated with the dye normalized signal.
rDyeNormError The standard error associated with the dye normalized signal.
DyeNormCorrelation Dye-normalized red and green pixel correlation.
ErrorModel Indicates the error model that you chose for Feature Extraction or that the software uses if you have chosen the Most Conservative option.

Data table
ID_REF PositionX PositionY VALUE LogRatioError PValueLogRatio gSurrogateUsed rSurrogateUsed gIsFound rIsFound gProcessedSignal rProcessedSignal gProcessedSigError rProcessedSigError gNumPixOLHi rNumPixOLHi gNumPixOLLo rNumPixOLLo gNumPix rNumPix gMeanSignal rMeanSignal gMedianSignal rMedianSignal gPixSDev rPixSDev gBGNumPix rBGNumPix gBGMeanSignal rBGMeanSignal gBGMedianSignal rBGMedianSignal gBGPixSDev rBGPixSDev gNumSatPix rNumSatPix gIsSaturated rIsSaturated PixCorrelation BGPixCorrelation gIsFeatNonUnifOL rIsFeatNonUnifOL gIsBGNonUnifOL rIsBGNonUnifOL gIsFeatPopnOL rIsFeatPopnOL gIsBGPopnOL rIsBGPopnOL IsManualFlag gBGSubSignal rBGSubSignal gBGSubSigError rBGSubSigError BGSubSigCorrelation gIsPosAndSignif rIsPosAndSignif gPValFeatEqBG rPValFeatEqBG gNumBGUsed rNumBGUsed gIsWellAboveBG rIsWellAboveBG IsUsedBGAdjust gBGUsed rBGUsed gBGSDUsed rBGSDUsed IsNormalization gDyeNormSignal rDyeNormSignal gDyeNormError rDyeNormError DyeNormCorrelation ErrorModel
1 37.1416 35.8978 -0.433569 0.060349 6.75E-13 0 0 1 1 1653.18 609.188 21.9649 13.0518 0 0 0 0 62 62 2356.53 542.903 2336.5 544 196.977 76.4767 278 278 91.0576 89.0324 90 89 10.7346 10.6107 0 0 0 0 0.295069 0.000110987 0 0 0 0 0 0 0 0 0 1883.46 454.301 25.0244 9.73337 0.294341 1 1 6.11E-62 9.66E-50 1 1 1 1 0 473.077 88.6025 10.7346 10.6107 0 1653.18 609.188 21.9649 13.0518 0.294341 1
2 57.9049 35.0332 0 0.116169 1 18.9572 0 1 1 18.9572 11.4378 4.99668 1.03804 1 1 0 0 60 60 413.35 106.433 410.5 105.5 18.83 12.7961 276 276 92.3551 87.4167 92 87 9.47325 10.3184 0 0 0 0 0.141241 0.00019425 0 0 0 0 0 0 0 0 0 -61.0248 19.4465 2.49693 1.76487 0.128728 0 1 1.14E-34 1.86E-17 1 1 0 0 0 474.375 86.9868 9.47325 10.3184 0 -122.118 11.4378 4.99668 1.03804 0.128728 0
3 79.3733 35.5234 0.384461926 0.056783 1.28E-11 0 0 1 1 2404.95 5828.65 33.5296 59.3161 0 2 0 0 55 55 3015.18 4776 2933 4719 262.589 353.857 281 281 93.2527 87.4057 94 88 8.56885 10.9782 0 0 0 0 0.705878 0.000279296 0 0 0 0 0 0 0 0 0 2539.91 4689.02 35.4112 47.7185 0.705738 1 1 2.91E-55 1.37E-62 1 1 1 1 0 475.272 86.9758 8.56885 10.9782 0 2404.95 5828.65 33.5296 59.3161 0.705738 1
4 100.826 34.6758 -0.189580188 0.0511967 0.000213078 0 0 1 1 4922.01 3180.99 43.8194 33.9512 1 0 0 0 60 60 5685.4 2641.92 5650.5 2586 359.067 211.15 280 280 96.1214 87.75 96 87.5 9.54969 9.8444 0 0 0 0 0.751286 0.000224056 0 0 0 0 0 0 0 0 0 5207.26 2554.6 46.3589 27.2656 0.751054 1 1 1.59E-70 6.19E-66 1 1 1 1 0 478.141 87.3201 9.54969 9.8444 0 4922.01 3180.99 43.8194 33.9512 0.751054 1
5 121.543 35.6464 0.12315184 0.0502194 0.0141956 0 0 1 1 2565.13 3406.13 18.7092 41.1844 2 0 0 0 57 57 3183.96 2833.88 3138 2815 148.793 250.634 281 281 98.6263 88.3132 97 88 9.95737 9.84386 0 0 0 0 0.597137 -0.000522958 0 0 0 0 0 0 0 0 0 2703.32 2745.99 19.7171 33.2025 0.596772 1 1 1.44E-72 2.93E-60 1 1 1 1 0 480.646 87.8833 9.95737 9.84386 0 2565.13 3406.13 18.7092 41.1844 0.596772 1
6 142.509 35.5937 0.047419222 0.0588019 0.419997 0 0 1 1 452.472 504.674 7.03833 9.38096 2 1 0 0 57 57 1043.53 433.561 1046 436 65.5951 48.4009 277 277 101.664 87.444 102 87 9.8749 10.4764 0 0 0 0 0.459352 -0.000392163 0 0 0 0 0 0 0 0 0 559.842 346.547 8.70852 6.44168 0.456089 1 1 1.51E-54 1.32E-50 1 1 1 1 0 483.684 87.0142 9.8749 10.4764 1 452.472 504.674 7.03833 9.38096 0.456089 1
7 164.076 35.8488 -0.506462 0.0631938 1.11E-15 0 0 1 1 1869.52 582.461 28.3906 11.6208 0 1 0 1 61 61 2605.15 524.115 2552 514 251.49 67.7852 282 282 102.39 88.2943 102 89 10.2129 11.0116 0 0 0 0 0.52827 0.000186009 0 0 0 0 0 0 0 0 0 2120.74 436.25 32.2057 8.70374 0.526675 1 1 1.08E-57 4.32E-51 1 1 1 1 0 484.41 87.8645 10.2129 11.0116 0 1869.52 582.461 28.3906 11.6208 0.526675 1
8 185.802 35.0663 -0.0757662 0.0976562 0.437847 0 0 1 1 198.697 166.888 4.39866 4.88366 1 3 1 0 59 59 740.271 198 743 197 43.2705 24.2814 277 277 102.372 88.3249 102 89 9.88277 10.3715 0 0 0 0 0.356046 -6.30E-05 0 0 0 0 0 0 0 0 0 255.88 110.105 5.66455 3.22201 0.347397 1 1 1.23E-47 3.45E-42 1 1 1 1 0 484.392 87.895 9.88277 10.3715 1 198.697 166.888 4.39866 4.88366 0.347397 1
9 206.159 35.5573 -0.545582754 0.281734 0.0528043 0 0 1 1 98.243 27.9717 4.1444 2.9176 0 0 0 1 57 57 596.702 108.719 594 109 34.6338 16.0865 284 284 104.944 87.8732 105 88 10.4822 10.4549 0 0 0 0 0.0518667 -0.000154181 0 0 0 0 0 0 0 0 0 109.738 21.2759 4.62933 2.21919 0.0493415 1 1 1.50E-31 4.10E-14 1 1 1 0 0 486.963 87.4434 10.4822 10.4549 1 98.243 27.9717 4.1444 2.9176 0.0493415 1
10 227.712 35.2224 0.040110236 0.0529638 0.44886 0 0 1 1 749.541 822.064 11.484 15.5838 0 0 0 0 61 61 1368 684.672 1365 673 104.962 88.1621 282 282 107.936 88.8759 107.5 89 10.248 9.63694 0 0 0 0 0.266018 0.000294506 0 0 0 0 0 0 0 0 0 878.044 596.226 13.4529 11.3026 0.265402 1 1 1.31E-57 3.57E-52 1 1 1 1 0 489.956 88.446 10.248 9.63694 1 749.541 822.064 11.484 15.5838 0.265402 1
11 249.096 35.2519 0.0213089 0.0630705 0.73547 0 0 1 1 379.147 398.214 6.18174 10.2781 1 0 1 0 60 60 966.367 357.25 968.5 360 60.1681 53.4915 279 279 106.753 89.0896 107 89 9.12699 10.1646 0 0 0 0 0.374271 1.82E-05 0 0 0 0 0 0 0 0 0 477.594 268.59 7.78687 6.93249 0.371907 1 1 1.51E-55 4.00E-44 1 1 1 1 0 488.772 88.6597 9.12699 10.1646 1 379.147 398.214 6.18174 10.2781 0.371907 1
12 270.357 34.8488 -0.186286988 0.193919 0.336737 0 0 1 1 100.924 65.7215 3.77185 4.65247 0 0 5 0 55 55 609.4 135.582 608 137 33.3237 23.9944 287 287 106.296 89.4704 106 90 9.09504 10.5419 0 0 0 0 0.351277 9.81E-05 0 0 0 0 0 0 0 0 0 121.084 46.5413 4.52532 3.2947 0.342521 1 1 2.02E-33 1.94E-20 1 1 1 1 0 488.316 89.0405 9.09504 10.5419 1 100.924 65.7215 3.77185 4.65247 0.342521 1
13 291.951 35.3756 0.059141577 0.0578697 0.306789 0 0 1 1 473.567 542.654 8.6573 11.8709 0 0 0 0 61 61 1069.51 462.689 1071 454 83.0385 63.8403 284 284 105.13 88.1972 105 88 9.2458 11.3559 0 0 0 0 0.447017 1.11E-05 0 0 0 0 0 0 0 0 0 582.358 374.921 10.6461 8.20164 0.444914 1 1 4.12E-53 8.43E-49 1 1 1 1 0 487.15 87.7673 9.2458 11.3559 1 473.567 542.654 8.6573 11.8709 0.444914 1
14 312.378 35.3099 -0.531675 0.0644165 1.54E-16 0 0 1 1 1853.6 544.931 17.1007 15.8432 0 0 1 0 58 58 2596.57 495.448 2595 484.5 148.289 89.8418 279 279 103.104 89.4301 103 90 9.41337 11.5208 0 0 0 0 0.344859 0.000305358 0 1 0 0 0 1 0 0 0 2111.45 406.448 19.4795 11.817 0.344128 1 1 8.32E-68 5.37E-40 1 1 1 1 0 485.124 89.0002 9.41337 11.5208 0 1853.6 544.931 17.1007 15.8432 0.344128 1
15 333.392 35.927 -0.205927222 0.0628303 0.00104727 0 0 1 1 533.391 331.985 16.9273 12.5365 7 3 0 0 52 52 1152.65 315.346 1125 316.5 152.778 61.1638 283 283 102.795 90.4982 103 91 9.54313 10.9779 0 0 0 0 0.504477 -0.000254536 0 1 0 0 0 0 0 0 0 667.839 225.278 21.1941 8.50696 0.50281 1 1 3.89E-35 1.06E-31 1 1 1 1 0 484.815 90.0684 9.54313 10.9779 0 533.391 331.985 16.9273 12.5365 0.50281 1
16 354.278 34.9162 0.065658688 0.143636 0.647588 0 0 1 1 105.446 122.656 3.95359 5.25822 4 4 0 0 55 55 615.964 172.164 616 172 36.4818 25.9285 284 284 101.694 89.5035 101.5 90 10.51 11.488 0 0 0 0 0.243391 -0.000155109 0 0 0 0 0 0 0 0 0 132.25 83.09 4.95859 3.56204 0.236992 1 1 2.02E-33 3.27E-31 1 1 1 1 0 483.713 89.0736 10.51 11.488 1 105.446 122.656 3.95359 5.25822 0.236992 1
17 375.419 36.0044 -0.095364749 0.186748 0.60959 0 0 1 1 94.9939 76.266 3.88982 4.54918 2 3 2 0 54 54 598.796 141.389 601 140.5 34.2419 23.1112 285 285 102.046 88.1684 101 88 10.1045 9.98589 0 0 0 0 0.491487 0.000364247 0 0 0 0 0 0 0 0 0 114.731 53.6503 4.69801 3.20018 0.479091 1 1 4.07E-31 1.17E-23 1 1 1 1 0 484.065 87.7385 10.1045 9.98589 1 94.9939 76.266 3.88982 4.54918 0.479091 1
18 397.019 35.132 0.332249988 0.0571828 6.24E-09 0 0 1 1 629.743 1353.36 5.04793 16.7784 3 0 4 0 56 56 1206.23 1088.75 1198.5 1089.5 43.238 92.6372 274 274 100.047 89.2591 100 89 9.2349 10.8727 0 0 0 0 0.112502 0.000230422 0 0 0 0 0 0 0 0 0 724.165 999.921 5.8048 12.3966 0.111826 1 1 3.34E-70 4.66E-59 1 1 1 1 0 482.067 88.8292 9.2349 10.8727 0 629.743 1353.36 5.04793 16.7784 0.111826 1
19 418.246 35.9538 -0.216278829 0.0589436 0.000243268 0 0 1 1 684.934 416.265 12.8912 7.01829 1 3 0 2 57 57 1316.75 378 1311 373 118.958 36.545 276 276 97.0471 89.2536 97 89 9.24188 9.69578 0 0 0 0 0.300962 -0.000275437 0 0 0 0 0 0 0 0 0 837.688 289.176 15.7662 4.87556 0.298611 1 1 1.07E-49 2.30E-53 1 1 1 1 0 479.067 88.8237 9.24188 9.69578 0 684.934 416.265 12.8912 7.01829 0.298611 1
20 439.918 34.5434 -0.031646102 0.196296 0.871924 0 0 1 1 83.7793 77.8916 3.76475 4.29261 1 1 0 0 58 58 578.81 143.5 579 138.5 34.1223 22.7482 285 285 96.4 88.7018 97 89 8.87479 9.86594 0 0 0 0 0.0498026 -0.000143221 0 0 0 0 0 0 0 0 0 100.391 55.2281 4.51121 3.04362 0.0485397 1 1 2.92E-30 2.31E-26 1 1 1 1 0 478.42 88.2719 8.87479 9.86594 1 83.7793 77.8916 3.76475 4.29261 0.0485397 1

Total number of rows: 21446

Table truncated, full table size 8150 Kbytes.




Supplementary data files not provided
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