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Sample GSM26025 Query DataSets for GSM26025
Status Public on Jun 30, 2004
Title A404 SMC Differentiation Puromycin Replicate 5
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 4.

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 was changed at time 0 to basal medium supplemented with 1 umol/L all trans-retinoic acid for 96 hours, followed by 48 hours of treatment with puromycin and harvesting (Puro 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 33.8722 44.8722 -0.429002 0.0597778 7.15E-13 0 0 1 1 1862.45 693.558 18.6575 18.5533 1 0 0 0 61 61 2427.36 383.967 2424 389 161.448 63.8428 273 273 81.2674 78.0513 81 78 7.9158 10.3411 0 0 0 0 0.492002 -0.000402198 0 0 0 0 0 0 0 0 0 2064.03 306.463 20.6769 8.19815 0.490434 1 1 1.85E-68 1.30E-43 1 1 1 1 0 363.33 77.5038 7.9158 10.3411 0 1862.45 693.558 18.6575 18.5533 0.490434 1
2 55.1318 44.1318 -0.420288 0.436116 0.335193 0 21.0646 1 1 55.4422 21.0646 2.21699 3.25934 1 1 1 0 59 59 422.847 85.6441 425 87 18.1894 10.4035 282 282 80.4823 76.8156 80.5 76 7.63594 9.48391 0 0 0 0 -0.0394697 2.86E-05 0 0 0 0 0 0 0 0 0 60.3022 9.37596 2.41132 1.46745 -0.035774 1 1 3.34E-34 1.05E-08 1 1 1 0 0 362.545 76.2681 7.63594 9.48391 0 55.4422 20.8248 2.21699 3.25934 -0.035774 1
3 76.2364 44.7905 0.234524192 0.0522013 7.03E-06 0 0 1 1 2845.52 4882.99 22.4335 47.3528 0 0 0 0 62 62 3385.48 2327.53 3365 2280 187.512 171.909 274 274 82.2117 75.9526 82 75 7.69323 9.50581 0 0 0 0 0.65896 0.000197384 0 0 0 0 0 0 0 0 0 3021.21 2252.13 23.8186 21.84 0.658606 1 1 1.16E-75 3.13E-70 1 1 1 1 0 364.275 75.4051 7.69323 9.50581 0 2845.52 4882.99 22.4335 47.3528 0.658606 1
4 98.16 43.84 -0.007683325 0.0492073 0.875911 0 0 1 1 5932.39 5828.36 45.9781 59.9773 3 1 0 0 58 58 6870.97 2680 6865.5 2677.5 384.006 203.904 284 284 82.7359 78.1268 82 77 8.53991 9.99813 0 0 0 0 0.713933 -2.62E-05 0 0 0 0 0 0 0 0 0 6506.17 2602.42 50.425 26.7805 0.713722 1 1 5.04E-72 4.47E-65 1 1 1 1 0 364.799 77.5793 8.53991 9.99813 1 5932.39 5828.36 45.9781 59.9773 0.713722 1
5 119.139 44.8489 0.52284394 0.0624387 5.58E-17 0 0 1 1 3119.62 10397.9 28.9943 81.2842 0 0 0 0 62 62 3776.5 4734.66 3738.5 4710.5 249.636 286.558 268 268 82.8433 79.1754 82 79 8.33508 10.033 0 0 0 0 0.73846 -0.000606728 0 0 0 0 0 0 0 0 0 3411.59 4656.03 31.7079 36.398 0.73826 1 1 2.65E-71 7.14E-76 1 1 1 1 0 364.906 78.6279 8.33508 10.033 0 3119.62 10397.9 28.9943 81.2842 0.73826 1
6 139.998 45.166 0.087114852 0.0574694 0.129558 0 0 1 1 476.16 581.926 6.31813 10.9148 0 1 0 0 62 62 927.532 317.081 920 316 58.6022 35.3532 257 257 83.2062 76.2996 83 76 8.3334 9.20893 0 0 0 0 0.110797 -0.000742105 0 0 0 0 0 0 0 0 0 562.263 241.329 7.46062 4.52645 0.109628 1 1 2.25E-62 3.86E-54 1 1 1 1 0 365.269 75.7521 8.3334 9.20893 1 476.16 581.926 6.31813 10.9148 0.109628 1
7 162.103 45.2401 -0.535105 0.0644298 9.96E-17 0 0 1 1 1948.06 568.194 21.5454 15.4488 1 0 0 0 62 62 2537.66 326.016 2534 334 189.105 53.2349 277 277 83.6173 77.0072 84 76 8.6459 9.57427 0 0 0 0 0.426799 -0.000165952 0 0 0 0 0 0 0 0 0 2171.98 249.556 24.022 6.78526 0.425163 1 1 9.62E-67 9.14E-44 1 1 1 1 0 365.68 76.4597 8.6459 9.57427 0 1948.06 568.194 21.5454 15.4488 0.425163 1
8 183.051 44.1324 0.002226326 0.0920641 0.980707 0 0 1 1 196.713 197.724 3.75867 7.7672 1 1 0 1 61 61 610.639 154.361 616 154 36.1631 23.5719 279 279 85.0072 76.7097 85 76 7.84425 9.56076 0 0 0 0 0.333378 -0.000430025 0 0 0 0 0 0 0 0 0 243.569 78.1985 4.65396 3.07187 0.32586 1 1 1.50E-52 2.58E-35 1 1 1 1 0 367.07 76.1622 7.84425 9.56076 1 196.713 197.724 3.75867 7.7672 0.32586 1
9 203.911 44.9908 -0.473910406 0.220594 0.0316865 0 0 1 1 118.871 39.9177 3.07926 3.29255 2 3 0 1 55 55 508.927 92.7091 514 91 26.8451 8.98079 278 278 85.8633 76.777 85 77 8.13221 10.295 0 0 0 0 0.145776 0.000389875 0 0 0 0 0 0 0 0 0 141.001 16.4796 3.65251 1.3593 0.128729 1 1 4.96E-42 3.41E-20 1 1 1 0 0 367.926 76.2295 8.13221 10.295 1 118.871 39.9177 3.07926 3.29255 0.128729 1
10 224.425 44.8701 -0.061770933 0.0512987 0.228524 0 0 1 1 1173.7 1018.09 16.3026 18.122 0 2 0 3 54 54 1672.65 524.944 1667.5 522.5 133.118 58.4696 287 287 85.899 76.993 86 77 8.5616 11.0352 0 0 0 0 0.325863 -6.47E-06 0 0 0 0 0 0 1 0 0 1304.69 448.499 18.122 7.98332 0.32465 1 1 1.30E-54 2.14E-49 1 1 1 1 0 367.962 76.4455 8.5616 11.0352 1 1173.7 1018.09 16.3026 18.122 0.32465 1
11 246.206 44.9972 -0.075450662 0.0625738 0.227899 0 0 1 1 436.143 366.588 5.7826 9.87422 2 1 0 0 60 60 892.55 224.417 887.5 219 53.7724 30.8162 277 277 85.6534 75.7834 85 76 7.97385 9.40109 0 0 0 0 0.311131 6.06E-05 0 0 0 0 0 0 0 0 0 524.834 149.181 6.9585 4.01825 0.307312 1 1 8.16E-61 9.00E-44 1 1 1 1 0 367.716 75.2359 7.97385 9.40109 1 436.143 366.588 5.7826 9.87422 0.307312 1
12 267.46 44.8328 -0.222669369 0.165935 0.179626 0 0 1 1 124.486 74.5506 4.21342 4.80345 1 3 0 0 54 54 520.667 106.352 514 106.5 37.7224 13.5356 293 293 86.1536 77.0887 86 76 8.94505 9.32034 0 0 0 0 0.180341 7.71E-05 0 0 0 0 0 0 1 0 0 152.45 29.8106 5.1599 1.92076 0.172056 1 1 4.65E-35 3.94E-23 1 1 1 1 0 368.217 76.5412 8.94505 9.32034 1 124.486 74.5506 4.21342 4.80345 0.172056 1
13 288.978 45.1323 0.013311384 0.053909 0.80497 0 0 1 1 682.374 703.613 10.2152 19.271 0 1 0 0 62 62 1157.02 375.339 1149 377 92.8269 64.1601 277 277 86.8159 77.5668 87 77 7.8799 10.0235 0 0 0 0 0.469582 0.000203346 0 0 0 0 0 0 1 0 0 788.137 298.319 11.7985 8.17057 0.467928 1 1 6.75E-59 1.79E-43 1 1 1 1 0 368.879 77.0193 7.8799 10.0235 1 682.374 703.613 10.2152 19.271 0.467928 1
14 308.814 45.6894 -0.554172 0.0653108 2.15E-17 0 0 1 1 1980.56 552.86 20.2907 17.1674 0 0 0 0 62 62 2579.34 320.468 2604.5 319 178.161 59.1535 266 266 88.1165 78.297 88 79 8.68948 9.88262 0 0 0 0 0.32112 0.000210924 0 0 0 0 0 0 1 0 0 2209.16 242.718 22.6327 7.5369 0.319992 1 1 9.08E-69 2.48E-40 1 1 1 1 0 370.18 77.7495 8.68948 9.88262 0 1980.56 552.86 20.2907 17.1674 0.319992 1
15 329.817 45.1834 -0.247705478 0.0566194 1.21E-05 0 0 1 1 936.096 529.194 16.2832 14.1932 0 0 0 0 62 62 1451.92 301.371 1459.5 300.5 147.851 47.2483 284 284 90.0458 77.2641 90 78 8.00715 9.2027 0 0 0 0 0.598236 0.00019326 0 0 0 0 0 0 1 0 0 1079.81 224.654 18.7831 6.02534 0.595584 1 1 6.85E-55 3.53E-44 1 1 1 1 0 372.109 76.7166 8.00715 9.2027 0 936.096 529.194 16.2832 14.1932 0.595584 1
16 351.841 45.2114 -0.227948274 0.110009 0.0382587 0 0 1 1 203.444 120.364 3.32551 7.26234 0 0 1 0 62 62 622.968 123.565 618 121.5 32.2729 22.0087 277 277 88.3105 76.639 89 77 8.30385 10.4188 0 0 0 0 0.0175901 0.000455837 0 0 0 0 0 0 1 0 0 252.594 47.473 4.12892 2.86435 0.0170511 1 1 1.06E-57 1.94E-25 1 1 1 1 0 370.373 76.0915 8.30385 10.4188 0 203.444 120.364 3.32551 7.26234 0.0170511 1
17 372.883 45.8087 -0.297529862 0.143473 0.038101 0 0 1 1 159.443 80.3666 3.38503 5.3212 1 1 0 0 61 61 567.82 108.836 564 109 32.4523 15.8358 265 265 88.7509 77.5321 89 77 7.78099 9.44441 0 0 0 0 0.265164 2.82E-05 0 0 0 0 0 0 1 0 0 197.006 31.8515 4.18249 2.10894 0.253264 1 1 5.09E-50 9.81E-24 1 1 1 1 0 370.814 76.9846 7.78099 9.44441 0 159.443 80.3666 3.38503 5.3212 0.253264 1
18 393.813 44.895 0.254079434 0.0556528 4.98E-06 0 0 1 1 614.976 1103.92 5.92557 19.0119 1 2 1 0 59 59 1073.47 551.814 1074 554 51.6274 62.6585 279 279 91.4086 77.4373 91 77 9.40217 9.96192 0 0 0 0 0.198814 0.000269129 0 0 0 0 0 0 1 0 0 700.003 474.924 6.74485 8.17921 0.197594 1 1 2.53E-68 1.66E-53 1 1 1 1 0 373.472 76.8898 9.40217 9.96192 0 614.976 1103.92 5.92557 19.0119 0.197594 1
19 415.847 44.9686 -0.300514459 0.0599493 5.36E-07 0 0 1 1 806.552 403.755 11.1817 11.8945 0 3 0 0 61 61 1319.3 246.115 1314 243 102.363 38.4483 281 281 90.9181 78.1459 90 79 9.78613 10.7539 0 0 0 0 0.392282 0.000192671 0 0 0 0 0 0 1 0 0 946.314 168.516 13.1193 4.96442 0.388609 1 1 3.47E-60 8.77E-42 1 1 1 1 0 372.981 77.5984 9.78613 10.7539 0 806.552 403.755 11.1817 11.8945 0.388609 1
20 435.939 45.3764 -0.038779336 0.104824 0.711406 0 0 1 1 173.421 158.607 4.55998 6.36074 1 0 1 0 59 59 588.407 139.458 586 141 43.2726 18.7491 287 287 91.0836 77.4321 90 77 9.26381 9.8649 0 0 0 0 0.160403 -0.000114964 0 0 0 0 0 0 1 0 0 215.26 62.5731 5.66009 2.50942 0.155292 1 1 2.98E-43 6.59E-35 1 1 1 1 0 373.147 76.8846 9.26381 9.8649 1 173.421 158.607 4.55998 6.36074 0.155292 1

Total number of rows: 21446

Table truncated, full table size 8135 Kbytes.




Supplementary data files not provided
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