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Sample GSM26007 Query DataSets for GSM26007
Status Public on Jun 30, 2004
Title A404 SMC Differentiation Control 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 1.

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. Control cells were harvested and RNA was extracted at time 0 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 Channe. 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 24.0733 49.9121 -0.512125 0.0626349 2.93E-16 0 0 1 1 2730.72 839.754 45.1723 21.6381 1 0 0 0 62 62 2558.21 590.016 2496.5 592 298.202 104.973 268 268 62.8022 74.9552 62 75 6.68626 9.41659 0 0 0 0 0.620604 0.000412765 0 1 0 0 0 0 0 0 0 2289.52 517.868 37.8738 13.344 0.619991 1 1 3.71E-56 8.02E-45 1 1 1 1 0 268.691 72.1477 6.68626 9.41659 0 2730.72 839.754 45.1723 21.6381 0.619991 1
2 45.6303 48.4622 0 0.138183 1 9.43819 14.2108 1 1 9.43819 14.2108 2.65713 2.13501 2 0 1 0 55 55 267.745 79.1455 268 78 13.7265 10.5592 285 285 61.8912 75.7474 62 76 6.72488 10.3123 0 0 0 0 0.00779839 0.00015342 0 0 0 0 0 0 0 0 0 -0.0344824 6.20562 1.89326 1.54931 0.00701897 0 1 0.98553 0.000144105 1 1 0 0 0 267.78 72.9398 6.72488 10.3123 0 -0.0483952 8.55158 2.65713 2.13501 0.00701897 0
3 66.964 49.532 0.569652803 0.0646241 1.20E-18 0 0 1 1 3978.28 14768.9 44.1848 163.896 0 0 0 0 60 60 3429.02 9685.05 3349.5 9556.5 271.877 826.266 293 293 62.7031 75.4334 63 75 6.63923 10.0846 0 0 0 0 0.82293 3.07E-05 0 0 0 0 0 0 0 0 0 3160.42 9612.42 35.1013 106.672 0.822867 1 1 6.92E-65 6.74E-65 1 1 1 1 0 268.592 72.6259 6.63923 10.0846 0 3978.28 14768.9 44.1848 163.896 0.822867 1
4 88.1173 48.4901 -0.357772678 0.0557989 1.44E-10 0 0 1 1 6479.62 2843 90.0016 43.7671 0 1 0 0 59 59 5321.59 1958.22 5360 1959 538.968 222.909 292 292 63.9349 75.5685 64 75 6.77517 9.92266 0 0 0 0 0.772628 6.84E-05 0 0 0 0 0 0 0 0 0 5051.77 1885.46 70.1688 29.0261 0.772461 1 1 1.97E-58 6.65E-56 1 1 1 1 0 269.824 72.761 6.77517 9.92266 0 6479.62 2843 90.0016 43.7671 0.772461 1
5 109.117 49.1797 -1.011076531 0.0908235 8.73E-29 0 0 1 1 3343.24 325.905 37.388 11.3357 1 0 0 0 62 62 3168.95 266.452 3168.5 253.5 255.321 53.0285 278 278 63.3453 74.9748 63 76 6.36916 9.29128 0 0 0 0 0.282071 -2.19E-05 0 0 0 0 0 0 0 0 0 2899.72 194.284 32.428 6.75764 0.281091 1 1 2.04E-66 1.72E-37 1 1 1 1 0 269.234 72.1673 6.36916 9.29128 0 3343.24 325.905 37.388 11.3357 0.281091 1
6 130.022 48.3815 -0.07770486 0.0613595 0.205375 0 0 1 1 461.811 386.153 7.63636 11.7591 0 1 1 0 59 59 703.712 286.593 693 284 54.9834 49.5403 284 284 64.2641 76.7289 64 77 6.67869 9.8963 0 0 0 0 0.255251 -0.000163901 0 0 0 0 0 0 0 0 0 433.559 212.672 7.16919 6.47628 0.25381 1 1 2.43E-54 1.36E-39 1 1 1 1 0 270.153 73.9213 6.67869 9.8963 1 461.811 386.153 7.63636 11.7591 0.25381 1
7 151.835 48.9705 -0.511868 0.0623505 2.22E-16 0 0 1 1 3444.79 1059.97 38.2221 22.0486 4 0 0 0 60 60 3095.93 740.2 3078.5 735.5 242.828 107.568 277 277 64.4621 74.8412 64 74 6.70951 9.43725 0 0 0 0 0.432919 -0.000135857 0 0 0 0 1 0 0 0 0 2825.58 668.166 31.3516 13.8986 0.432522 1 1 6.47E-65 3.87E-49 1 1 1 1 0 270.351 72.0336 6.70951 9.43725 0 3444.79 1059.97 38.2221 22.0486 0.432522 1
8 172.418 48.3682 0.23675586 0.0949678 0.0126672 0 0 1 1 145.432 250.851 4.84445 9.59425 1 2 0 0 55 55 406.891 210.818 404 210 33.656 38.9164 282 282 64.2801 75.6596 64 75.5 6.42916 9.32286 0 0 0 0 0.160318 -0.000130349 0 0 0 0 0 0 0 0 0 136.722 137.966 4.5543 5.27677 0.158863 1 1 1.08E-35 8.83E-33 1 1 1 1 0 270.169 72.852 6.42916 9.32286 0 145.432 250.851 4.84445 9.59425 0.158863 1
9 194.54 48.3016 -0.230201883 0.458829 0.615866 0 0 1 1 43.3928 25.5397 3.18311 3.06052 1 2 0 0 55 55 305.891 89.3636 305 89 20.0487 12.8702 291 291 62.7801 76.7766 63 76 6.54479 10.6742 0 0 0 0 0.149507 -0.000140326 0 0 0 0 0 0 0 0 0 37.2221 15.3945 2.73046 1.84479 0.139241 1 1 1.83E-19 4.80E-12 1 1 1 0 0 268.669 73.9691 6.54479 10.6742 1 43.3928 25.5397 3.18311 3.06052 0.139241 1
10 215.044 48.2775 0.045282393 0.0540196 0.401882 0 0 1 1 656.146 728.254 11.1321 15.8081 0 1 0 0 60 60 860.7 491.35 866 487.5 77.6745 70.0798 279 279 63.3369 76.4409 63 77 6.32749 10.0708 0 0 0 0 0.387217 2.38E-05 0 0 0 0 0 0 0 0 0 591.474 417.717 10.0349 9.06733 0.386085 1 1 2.97E-54 2.93E-48 1 1 1 1 0 269.226 73.6333 6.32749 10.0708 1 656.146 728.254 11.1321 15.8081 0.386085 1
11 236.362 48.6382 0.116489879 0.0661745 0.0783497 0 0 1 1 307.741 402.416 7.28593 10.1243 0 2 0 0 58 58 559.897 292.276 562.5 288 52.367 41.959 274 274 63.0693 74.9964 63 74 6.7253 9.14294 0 0 0 0 0.0997863 0.000194819 0 0 0 0 0 0 0 0 0 290.938 220.087 6.88812 5.5371 0.0991169 1 1 6.29E-45 7.47E-44 1 1 1 1 0 268.958 72.1888 6.7253 9.14294 0 307.741 402.416 7.28593 10.1243 0.0991169 1
12 257.556 48.2787 0.232553577 0.227972 0.307682 0 0 1 1 52.3004 89.3426 3.25291 4.63745 0 1 0 0 57 57 315.175 124.211 318 124 21.6755 19.9237 284 284 62.6866 75.1725 63 75 6.69822 8.88492 0 0 0 0 0.114162 -0.000143972 0 0 0 0 0 0 0 0 0 46.6001 51.8455 2.89837 2.69111 0.110888 1 1 4.54E-23 1.65E-27 1 1 1 1 0 268.575 72.365 6.69822 8.88492 1 52.3004 89.3426 3.25291 4.63745 0.110888 1
13 278.795 48.3537 0.013957814 0.0576419 0.808671 0 0 1 1 501.606 517.989 9.10128 13.645 1 3 0 0 57 57 733.789 361.754 740 362 63.6825 57.2277 286 286 62.535 75.8776 62 76 6.50968 10.3417 0 0 0 0 0.353248 0.000329983 0 0 0 0 0 0 0 0 0 465.366 288.684 8.44373 7.60462 0.351739 1 1 1.24E-50 5.08E-42 1 1 1 1 0 268.424 73.0701 6.50968 10.3417 1 501.606 517.989 9.10128 13.645 0.351739 1
14 299.099 48.2874 -0.51613 0.0624668 1.43E-16 0 0 1 1 3782.93 1152.65 48.3029 22.41 2 1 0 0 59 59 3347.12 805.322 3346 808 301.883 109.279 278 278 63.0612 75.6942 62 75 6.91202 10.1883 0 0 0 0 0.479666 0.000179092 0 0 0 0 1 0 0 0 0 3078.17 732.435 39.304 14.2401 0.479198 1 1 1.54E-60 3.18E-50 1 1 1 1 0 268.95 72.8867 6.91202 10.1883 0 3782.93 1152.65 48.3029 22.41 0.479198 1
15 320.319 48.7545 -0.160532086 0.0584063 0.00598611 0 0 1 1 626.511 432.909 16.3769 14.2288 1 3 0 0 58 58 849.017 315.379 849.5 309 115.466 60.3178 279 279 62.9283 76.4839 63 77 6.40441 10.3437 0 0 0 0 0.470284 -0.000351749 0 0 0 0 0 0 0 0 0 580.2 241.703 15.1663 7.94429 0.468703 1 1 2.23E-42 3.18E-37 1 1 1 1 0 268.817 73.6763 6.40441 10.3437 0 626.511 432.909 16.3769 14.2288 0.468703 1
16 341.497 47.6872 -0.274322916 0.228919 0.230785 0 0 1 1 93.0083 49.4537 3.97835 3.85744 2 1 0 0 56 56 350.196 101.482 345.5 100 26.369 16.257 276 276 61.471 75.5797 61 76 6.1776 9.0303 0 0 0 0 0.186055 0.000207041 0 0 0 0 0 0 0 0 0 82.8367 28.71 3.54327 2.2394 0.179499 1 1 1.21E-30 4.26E-19 1 1 1 1 0 267.36 72.7722 6.1776 9.0303 1 93.0083 49.4537 3.97835 3.85744 0.179499 1
17 363.217 48.4535 -0.028791918 0.162615 0.859456 0 0 1 1 102.382 95.8146 4.17707 5.98936 0 3 0 0 55 55 361.6 126.455 356 129 28.0017 24.9346 275 275 62.5673 74.8073 63 74 7.13056 8.81786 0 0 0 0 -0.0533639 0.000126235 0 0 0 0 0 0 0 0 0 93.144 54.4548 3.80016 3.40397 -0.052368 1 1 2.03E-31 1.10E-22 1 1 1 1 0 268.456 71.9997 7.13056 8.81786 1 102.382 95.8146 4.17707 5.98936 -0.052368 1
18 384.591 47.8585 0.184638131 0.0535179 0.000560575 0 0 1 1 752.929 1151.84 7.92686 14.8496 5 1 2 0 51 51 927.098 751.569 925 761 49.502 62.4654 282 282 61.5603 74.5993 61.5 74 7.17138 9.12307 0 0 0 0 0.161344 0.000156491 0 0 0 0 0 0 0 0 0 659.649 679.777 6.94481 8.76377 0.16073 1 1 1.72E-58 4.28E-54 1 1 1 1 0 267.449 71.7918 7.17138 9.12307 0 752.929 1151.84 7.92686 14.8496 0.16073 1
19 405.671 47.9817 -0.337549815 0.0587366 9.09E-09 0 0 1 1 1072.02 492.78 14.0355 12.6909 0 0 2 0 59 59 1228.64 357.797 1229 358 96.6586 56.0042 272 272 61.1397 76.5588 61 77 6.47923 9.78685 0 0 0 0 0.362428 0.000144146 0 0 0 0 0 0 0 0 0 961.616 284.045 12.59 7.31524 0.361058 1 1 5.41E-60 1.34E-43 1 1 1 1 0 267.028 73.7513 6.47923 9.78685 0 1072.02 492.78 14.0355 12.6909 0.361058 1
20 425.919 47.6499 -0.15832798 0.16826 0.346715 0 0 1 1 114.156 79.2813 4.63684 4.3188 1 0 0 0 59 59 372.424 117.39 366 119 32.1442 18.4783 281 281 62.9253 75.032 63 75 7.46693 8.64678 0 0 0 0 0.115681 -2.98E-05 0 0 0 0 0 0 0 0 0 103.61 45.1653 4.20846 2.46035 0.112474 1 1 7.81E-33 4.54E-27 1 1 1 1 0 268.814 72.2245 7.46693 8.64678 1 114.156 79.2813 4.63684 4.3188 0.112474 1

Total number of rows: 21446

Table truncated, full table size 8135 Kbytes.




Supplementary data files not provided
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