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Sample GSM26012 Query DataSets for GSM26012
Status Public on Jun 30, 2004
Title A404 SMC Differentiation RA48 Replicate 3
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 2.

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 48 hours of incubation (RA48 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 19.707 21.5051 -0.603282 0.0680339 7.49E-19 0 0 1 1 1839.58 458.603 23.2194 17.7024 0 2 0 0 56 56 1016.55 131.911 997.5 131 89.0009 15.477 252 252 34.3016 73.381 34 73 3.66695 8.39119 0 0 0 0 0.119558 0.000522563 0 0 0 0 0 0 0 0 0 942.433 55.3015 11.8955 2.13468 0.115815 1 1 2.07E-58 4.39E-35 1 1 1 1 0 74.1205 76.6092 3.66695 8.39119 0 1839.58 458.603 23.2194 17.7024 0.115815 1
2 40.8728 20.3873 0 0.0756766 1 0 61.4826 1 1 22.1695 61.4826 2.24527 8.36549 0 2 0 0 57 57 83.3333 76.807 83 77 7.082 8.08093 266 266 33.9586 71.703 34 72 3.88347 8.81199 0 0 0 0 -0.0668782 0.000442217 0 0 0 0 0 0 0 0 0 9.55576 1.87573 0.967783 1.19898 -0.0578186 1 0 1.92E-14 0.121348 1 1 0 0 0 73.7776 74.9313 3.88347 8.81199 0 22.1695 13.0872 2.24527 8.36549 -0.0578186 0
3 62.7433 21.6741 0.267652887 0.0529591 4.33E-07 0 0 1 1 4215.5 7807.32 50.6353 109.737 0 0 0 0 60 60 1834.17 1230.87 1844.5 1213 163.795 125.663 259 259 33.7954 72.7645 34 73 3.89501 8.93834 0 0 0 0 0.756256 0.000131326 0 0 0 0 0 0 0 0 0 1760.55 1154.87 21.1472 16.2326 0.755764 1 1 6.79E-63 5.34E-59 1 1 1 1 0 73.6143 75.9928 3.89501 8.93834 0 4215.5 7807.32 50.6353 109.737 0.755764 1
4 83.2709 21.2486 -0.369882032 0.0562356 4.79E-11 0 0 1 1 6230.51 2658.53 47.0125 49.5645 0 0 0 0 62 62 2719.95 462.919 2681 457 157.192 56.6109 248 248 34.1734 72.9556 34 73 4.19154 8.56424 0 0 0 0 0.496353 -0.000159665 0 0 0 0 0 0 0 0 0 2645.96 386.735 19.9651 7.21013 0.494895 1 1 8.55E-77 1.77E-53 1 1 1 1 0 73.9923 76.1839 4.19154 8.56424 0 6230.51 2658.53 47.0125 49.5645 0.494895 1
5 104.385 21.9324 -0.639803022 0.0683237 7.66E-21 0 0 1 1 5636.18 1291.76 57.9272 24.3711 0 1 0 0 60 60 2562.38 256.333 2564 255 198.13 26.1214 279 279 33.724 72.3871 33 73 3.99088 8.3984 0 0 0 0 0.365246 -7.74E-05 0 0 0 0 0 0 0 0 0 2488.84 180.718 25.5796 3.40954 0.361237 1 1 7.40E-67 3.92E-53 1 1 1 1 0 73.5429 75.6154 3.99088 8.3984 0 5636.18 1291.76 57.9272 24.3711 0.361237 1
6 125.903 20.7229 0.144041516 0.0524634 0.00604117 0 0 1 1 858.687 1196.4 11.6405 31.3963 2 1 0 0 59 59 506.407 222.068 502 215 45.095 29.2415 275 275 33.2582 72.3782 33 72 3.33346 8.77302 0 0 0 0 0.185292 -0.000152866 0 0 0 0 0 0 0 0 0 433.33 146.461 5.8743 3.8435 0.18342 1 1 3.84E-59 7.07E-44 1 1 1 1 0 73.0771 75.6065 3.33346 8.77302 0 858.687 1196.4 11.6405 31.3963 0.18342 1
7 147.32 20.4083 -0.599609 0.0670976 4.02E-19 0 0 1 1 2424.81 609.634 22.454 19.9097 2 1 0 1 55 55 1263.27 150.836 1248 151 81.66 18.1972 273 273 34.0513 70.8278 34 71 4.22061 8.53688 0 0 0 0 0.0264627 6.44E-05 0 0 0 0 0 0 0 0 0 1189.4 76.7802 11.014 2.50752 0.0258882 1 1 7.89E-65 7.32E-38 1 1 1 1 0 73.8702 74.0561 4.22061 8.53688 0 2424.81 609.634 22.454 19.9097 0.0258882 1
8 167.773 20.1333 -0.208575886 0.116405 0.0731605 0 0 1 1 185.175 114.553 5.99059 14.7488 0 0 0 0 63 63 173.54 87.3333 169 85 25.3516 12.7507 269 269 34.6803 70.8736 34 71 4.15848 9.29927 0 0 0 0 0.194928 0.000124874 0 0 0 0 0 0 0 0 0 99.0405 13.2314 3.20405 1.70356 0.183242 1 1 1.07E-39 2.63E-11 1 1 1 0 0 74.4992 74.1019 4.15848 9.29927 1 185.175 114.553 5.99059 14.7488 0.183242 1
9 189.452 20.5137 0.036060394 0.0788964 1 0 62.3544 1 1 57.3861 62.3544 3.04198 10.486 1 0 0 0 59 59 101.305 80.339 100 80 11.282 9.48976 268 268 33.4515 69.9813 33 70 3.70058 7.88516 0 0 0 0 -0.116447 -5.50E-05 0 0 0 0 0 0 0 0 0 28.0347 7.12936 1.48609 1.32603 -0.107234 1 1 4.33E-27 7.95E-07 1 1 1 0 0 73.2704 73.2096 3.70058 7.88516 1 57.3861 56.3777 3.04198 10.486 -0.107234 0
10 210.281 20.4221 -0.010213601 0.0570216 0.857851 0 0 1 1 537.101 524.617 10.1248 21.1112 0 1 0 0 58 58 369.741 133.603 371.5 130.5 42.3231 17.6674 279 279 34.8423 71.3835 35 71 4.02825 8.4129 0 0 0 0 0.252387 -0.000436034 0 0 0 0 0 0 1 0 0 295.08 58.9917 5.56253 2.37389 0.246405 1 1 2.38E-50 4.33E-34 1 1 1 1 0 74.6612 74.6118 4.02825 8.4129 1 537.101 524.617 10.1248 21.1112 0.246405 1
11 231.618 20.966 -0.024019155 0.0680569 0.724143 0 0 1 1 335.399 317.353 8.19582 16.7011 0 3 0 0 58 58 262.276 110 259.5 110.5 34.9635 13.4686 286 286 34.3322 71.8182 34 71 3.998 8.55663 0 0 0 0 0.110871 0.000143549 0 0 0 0 0 0 0 0 0 188.125 34.9535 4.59702 1.83947 0.106456 1 1 4.10E-44 1.33E-28 1 1 1 1 0 74.1511 75.0465 3.998 8.55663 1 335.399 317.353 8.19582 16.7011 0.106456 1
12 252.778 20.0819 0.113927245 0.181494 0.530189 0 0 1 1 76.9467 100.027 4.12414 14.2397 1 1 0 0 61 61 113.705 87.0656 114 86 16.2648 12.7644 256 256 34.6875 71.707 34 71 4.44355 8.92343 0 0 0 0 0.115696 0.000232015 0 0 0 0 0 0 0 0 0 39.1985 12.1303 2.10094 1.72685 0.108545 1 1 3.70E-27 8.57E-10 1 1 1 0 0 74.5064 74.9353 4.44355 8.92343 1 76.9467 100.027 4.12414 14.2397 0.108545 1
13 273.621 20.4356 0.025314509 0.0623656 0.68481 0 0 1 1 388.68 412.009 7.55476 18.2814 0 0 0 0 58 58 291.017 118.931 284.5 117 32.0944 14.9195 280 280 33.9857 70.1571 34 70 4.27795 8.30492 0 0 0 0 0.14403 0.000252078 0 0 0 0 0 0 0 0 0 217.213 45.5456 4.22195 2.02092 0.139366 1 1 9.84E-50 2.78E-32 1 1 1 1 0 73.8046 73.3854 4.27795 8.30492 1 388.68 412.009 7.55476 18.2814 0.139366 1
14 295.015 19.9706 -0.572122 0.0670302 1.40E-17 0 0 1 1 1582.56 423.875 16.8615 17.1881 1 2 0 0 58 58 897.172 123.379 888 119.5 66.8914 14.9547 254 254 32.6496 69.9016 32.5 69 4.00287 8.67018 0 0 0 0 0.180574 0.00036464 0 0 0 0 1 1 0 0 0 824.704 50.2495 8.78686 2.03761 0.173951 1 1 2.97E-64 5.11E-35 1 1 1 1 0 72.4685 73.1299 4.00287 8.67018 0 1582.56 423.875 16.8615 17.1881 0.173951 1
15 315.957 20.6851 -0.064008069 0.0635563 0.313887 0 0 1 1 412.42 355.903 8.36205 24.9647 2 1 0 0 58 58 304.362 112.69 305 111 35.5803 20.6688 267 267 33.7453 70.1723 34 70 4.36867 7.82902 0 0 0 0 0.339295 -0.000124442 0 0 0 0 0 0 0 0 0 230.798 39.2891 4.67956 2.75592 0.333581 1 1 1.13E-48 5.09E-21 1 1 1 1 0 73.5642 73.4006 4.36867 7.82902 1 412.42 355.903 8.36205 24.9647 0.333581 1
16 338.892 20.3616 -0.13273117 0.174183 0.446054 0 0 1 1 106.819 78.6896 4.32028 11.6155 1 1 0 0 58 58 127.828 83.0862 125 85 16.725 10.0163 259 259 33.3861 70.3514 33 70 3.86867 7.87475 0 0 0 0 -0.0466175 0.000128144 0 0 0 0 0 0 0 0 0 54.6226 9.50657 2.20921 1.40328 -0.0434273 1 1 1.28E-32 2.64E-09 1 1 1 0 0 73.205 73.5796 3.86867 7.87475 1 106.819 78.6896 4.32028 11.6155 -0.0434273 1
17 358.466 20.4709 0.064768668 0.239086 0.786468 0 0 1 1 60.8636 70.6523 3.27732 11.6574 1 1 1 1 56 56 103.214 82.9107 102 82 12.048 10.1539 257 257 33.2179 70.8794 33 71 3.52989 8.30833 0 0 0 0 0.0634736 -8.77E-05 0 0 0 0 0 0 0 0 0 30.1775 8.80305 1.62496 1.45247 0.0587444 1 1 7.28E-26 5.67E-08 1 1 1 0 0 73.0368 74.1077 3.52989 8.30833 1 60.8636 70.6523 3.27732 11.6574 0.0587444 1
18 380 20.5839 0.34249069 0.0556886 7.74E-10 0 0 1 1 1329.31 2924.94 14.5301 43.9925 0 2 0 0 58 58 683.414 467.983 680 468 50.7426 44.9079 285 285 33.6561 70.9439 33 71 3.98602 9.4312 0 0 0 0 0.198258 -1.17E-05 0 0 0 0 0 0 0 0 0 609.939 393.811 6.66701 5.9231 0.19725 1 1 1.15E-63 1.81E-56 1 1 1 1 0 73.4751 74.1721 3.98602 9.4312 0 1329.31 2924.94 14.5301 43.9925 0.19725 1
19 401.332 21.8919 -0.072671806 0.0523651 0.165199 0 0 1 1 963.22 814.805 15.1768 25.9068 1 0 0 0 59 59 569.678 172.475 562 174 60.0202 23.5103 262 262 33.729 71.5191 34 71 3.63769 8.66521 0 0 0 0 0.116112 -7.62E-05 0 0 0 0 0 0 0 0 0 496.13 97.7272 7.8172 3.10725 0.114328 1 1 2.32E-55 1.20E-39 1 1 1 1 0 73.5479 74.7474 3.63769 8.66521 1 963.22 814.805 15.1768 25.9068 0.114328 1
20 421.901 19.5848 -1.50949E-05 0.227733 0.999947 0 69.049 1 1 69.0514 69.049 4.25722 11.2764 3 0 0 0 56 56 107.286 79.9643 106 78 15.3939 9.95072 274 274 33.8577 71.1934 33 71 4.12064 8.76405 0 0 0 0 0.207073 -0.000331113 0 0 0 0 0 0 0 0 0 33.6091 5.54257 2.0721 1.43125 0.190975 1 1 6.05E-23 0.000231629 1 1 1 0 0 73.6766 74.4217 4.12064 8.76405 1 69.0514 43.6681 4.25722 11.2764 0.190975 1

Total number of rows: 21446

Table truncated, full table size 8138 Kbytes.




Supplementary data files not provided
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