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Sample GSM26022 Query DataSets for GSM26022
Status Public on Jun 30, 2004
Title A404 SMC Differentiation Puromycin Replicate 2
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 50.9012 52.3579 -0.709561 0.073347 3.89E-22 0 0 1 1 2122.85 414.342 29.1144 14.1189 2 0 0 0 58 58 1311.45 158.724 1266.5 159 128.696 22.2267 288 288 37.0556 72.0313 37 72 4.26929 7.89141 0 0 0 0 0.0703854 0.000165365 0 0 0 0 0 0 0 0 0 1232.28 86.7286 16.9004 2.95533 0.0695014 1 1 5.43E-58 2.95E-37 1 1 1 1 0 79.1686 71.9956 4.26929 7.89141 0 2122.85 414.342 29.1144 14.1189 0.0695014 1
2 72.1792 52.4717 0 0.079456 1 0 33.1097 1 1 22.6554 33.1097 1.93522 5.43544 3 0 0 0 55 55 90.0545 74.7455 91 76 7.24292 8.8427 288 288 36.2292 70.8472 36 71 3.68388 7.78171 0 0 0 0 0.0302913 0.000100057 0 0 0 0 0 0 0 0 0 11.7124 3.93389 1.00047 1.27748 0.027607 1 1 4.53E-17 0.00295044 1 1 1 0 0 78.3422 70.8116 3.68388 7.78171 0 22.6554 16.738 1.93522 5.43544 0.027607 0
3 93.6124 52.5 0.19115057 0.0511223 0.000184688 0 0 1 1 6104.64 9480.05 71.0794 108.449 0 0 0 0 58 58 2839.52 2618.59 2806.5 2601.5 244.798 221.871 282 282 36.6738 71.5567 37 71 4.27439 8.74014 0 0 0 0 0.813707 -1.55E-05 0 0 0 0 0 0 0 0 0 2760.73 2547.07 32.1446 29.1377 0.813552 1 1 5.39E-62 1.87E-62 1 1 1 1 0 78.7868 71.5211 4.27439 8.74014 0 6104.64 9480.05 71.0794 108.449 0.813552 1
4 114.924 51.0765 0.117381699 0.0499117 0.0186835 0 0 1 1 7238.03 9484.23 67.7673 95.5077 2 4 0 0 57 57 3349.44 2622.96 3294 2612 231.164 193.867 286 286 36.979 72.5175 37 73 3.78542 8.93395 0 0 0 0 0.692317 -3.81E-05 0 0 0 0 0 0 0 0 0 3270.35 2550.48 30.6192 25.6838 0.692152 1 1 2.04E-66 1.08E-64 1 1 1 1 0 79.092 72.4818 3.78542 8.93395 1 7238.03 9484.23 67.7673 95.5077 0.692152 1
5 136.035 51.6155 0.103063731 0.0497432 0.0382729 0 0 1 1 7304.53 9260.96 79.9062 120.88 1 0 0 0 60 60 3379.78 2562.12 3358.5 2507.5 279.666 251.75 283 283 37.1166 71.8339 37 72 4.17233 9.02031 0 0 0 0 0.807935 -7.58E-05 0 0 0 0 0 0 0 0 0 3300.55 2490.32 36.1056 32.5052 0.807806 1 1 2.89E-65 8.50E-61 1 1 1 1 0 79.2296 71.7983 4.17233 9.02031 1 7304.53 9260.96 79.9062 120.88 0.807806 1
6 157.051 51.8657 0.237149397 0.0535446 9.47E-06 0 0 1 1 936.278 1616.42 11.4476 28.1702 3 0 1 0 60 60 600.133 423.567 600 421.5 49.3591 47.3785 269 269 36.5539 70.9665 37 71 3.50185 9.78437 0 0 0 0 0.2645 0.000463535 0 0 0 0 0 0 0 0 0 521.466 352.636 6.37581 6.14556 0.263105 1 1 1.54E-62 3.27E-54 1 1 1 1 0 78.6669 70.9309 3.50185 9.78437 0 936.278 1616.42 11.4476 28.1702 0.263105 1
7 178.348 51.9509 -0.744761 0.0750512 3.29E-23 0 0 1 1 2377.49 427.915 33.6291 16.7673 0 0 0 0 61 61 1445 161.918 1464 159 150.889 27.3443 267 267 36.9888 71.4532 37 71 3.25655 9.20815 0 0 0 0 0.379028 6.38E-07 0 0 0 0 1 0 0 0 0 1365.9 90.5005 19.3204 3.54614 0.374192 1 1 1.69E-59 5.69E-35 1 1 1 1 0 79.1018 71.4175 3.25655 9.20815 0 2377.49 427.915 33.6291 16.7673 0.374192 1
8 200.087 51.524 0.048084431 0.124017 0.698224 0 0 1 1 127.579 142.516 3.82932 9.41423 4 0 1 0 55 55 153.145 99.3091 153 97 16.5724 14.0183 284 284 36.2148 69.8169 36 69.5 3.74916 8.11021 0 0 0 0 -0.102308 0.000398215 0 0 0 0 0 0 0 0 0 74.8177 29.5279 2.24567 1.95053 -0.0986478 1 1 3.48E-38 2.34E-22 1 1 1 1 0 78.3278 69.7812 3.74916 8.11021 1 127.579 142.516 3.82932 9.41423 -0.0986478 1
9 220.673 51.5364 0.607731593 0.145906 1 7.90225 32.0245 1 1 7.90225 32.0245 2.46157 4.52605 3 2 0 0 54 54 80.0185 74.8519 79.5 75 8.35417 7.76399 275 275 37.1636 70.7236 37 71 3.71996 8.26588 0 0 0 0 0.052986 -8.83E-05 0 0 0 0 0 0 0 0 0 0.741884 4.16388 1.15878 1.16822 0.047007 0 1 0.52458 0.000624691 1 1 0 0 0 79.2766 70.688 3.71996 8.26588 0 1.57597 16.1321 2.46157 4.52605 0.047007 0
10 241.671 50.9874 0.035003685 0.0541959 0.518362 0 0 1 1 648.803 703.261 13.1508 18.1028 0 4 0 0 57 57 469.754 213.439 465 209 59.7543 27.2999 274 274 37.0182 71.5474 37 71.5 3.60449 8.63078 0 0 0 0 0.20975 0.000294476 0 0 0 0 0 0 0 0 0 390.623 141.927 7.91765 3.65336 0.207526 1 1 6.82E-48 2.14E-43 1 1 1 1 0 79.1312 71.5118 3.60449 8.63078 1 648.803 703.261 13.1508 18.1028 0.207526 1
11 263 50.732 0.165002682 0.0639612 0.00988799 0 0 1 1 322.541 471.615 7.34136 13.1861 2 6 0 1 54 54 277.37 165.296 272.5 162.5 33.1288 18.6453 271 271 36.9114 72.1476 37 72 3.92045 9.74035 0 0 0 0 0.254569 -5.60E-05 0 0 0 0 0 0 0 0 0 198.346 93.1844 4.51455 2.60538 0.247572 1 1 1.53E-43 1.22E-41 1 1 1 1 0 79.0244 72.1119 3.92045 9.74035 0 322.541 471.615 7.34136 13.1861 0.247572 1
12 285.021 50.7628 -0.091974225 0.154293 0.551115 0 0 1 1 116.613 94.3567 5.95062 8.06148 0 2 0 0 60 60 146.467 91.0667 143 92 26.5103 12.5521 281 281 37.121 71.2171 37 71 4.01065 8.5544 0 0 0 0 0.119806 0.000115069 0 0 0 0 0 0 0 0 0 67.2327 19.8852 3.43082 1.69892 0.113998 1 1 1.17E-27 3.01E-18 1 1 1 0 0 79.234 71.1814 4.01065 8.5544 1 116.613 94.3567 5.95062 8.06148 0.113998 1
13 305.606 50.9307 0.016988797 0.0648496 0.793344 0 0 1 1 355.899 370.097 7.67654 15.9953 3 3 1 0 53 53 298.642 143.811 293 141 34.3484 22.6181 275 275 37.4764 70.7855 37 71 4.17526 9.35636 0 0 0 0 0.0892461 0.000131169 0 0 0 0 0 0 0 0 0 219.052 73.0615 4.72483 3.15765 0.0876864 1 1 3.74E-44 3.56E-30 1 1 1 1 0 79.5894 70.7498 4.17526 9.35636 1 355.899 370.097 7.67654 15.9953 0.0876864 1
14 325.702 51.4172 -0.752985 0.0753237 1.58E-23 0 0 1 1 2602.04 459.546 35.4927 20.2937 1 0 0 0 58 58 1556.4 169.017 1524 163.5 153.4 32.8599 272 272 37.511 70.6691 37 71 3.79452 8.39922 0 0 0 0 0.281741 -0.000283494 0 0 0 0 1 0 0 0 0 1476.77 98.3838 20.1437 4.34467 0.27978 1 1 4.07E-58 1.15E-30 1 1 1 1 0 79.624 70.6335 3.79452 8.39922 0 2602.04 459.546 35.4927 20.2937 0.27978 1
15 347.064 51.289 -0.165571343 0.0685021 0.0156485 0 0 1 1 399.959 273.177 9.78407 12.8497 0 1 0 1 58 58 325.672 125.052 322 125.5 45.8535 18.9593 278 278 37.2446 71.1906 37 72 3.95707 7.99208 0 0 0 0 0.342241 -0.000104694 0 0 0 0 0 0 0 0 0 246.315 53.8967 6.02553 2.5352 0.335806 1 1 5.09E-44 5.63E-30 1 1 1 1 0 79.3576 71.155 3.95707 7.99208 0 399.959 273.177 9.78407 12.8497 0.335806 1
16 368.555 50.8387 0.152690566 0.156635 0.329653 0 0 1 1 86.3953 122.795 3.59147 10.2014 0 1 0 0 57 57 128.825 97.193 132 94 15.5151 15.7814 284 284 36.9577 71.3204 37 72 3.93924 8.64859 0 0 0 0 0.269111 1.40E-06 0 0 0 0 0 0 0 0 0 49.7538 25.9082 2.06828 2.15237 0.259675 1 1 1.10E-31 5.67E-18 1 1 1 1 0 79.0707 71.2848 3.93924 8.64859 1 86.3953 122.795 3.59147 10.2014 0.259675 1
17 390.292 50.8486 -0.165921633 0.20999 0.429445 0 0 1 1 90.648 61.8638 5.34691 7.5779 0 0 0 0 62 62 130.516 84.4355 122.5 84.5 23.6981 12.1785 276 276 37.2029 71.163 37 71 4.16245 8.55563 0 0 0 0 0.371489 -6.71E-06 0 0 0 0 0 0 0 0 0 51.2002 13.3081 3.02007 1.63015 0.351249 1 1 6.25E-25 5.79E-12 1 1 1 0 0 79.3159 71.1274 4.16245 8.55563 1 90.648 61.8638 5.34691 7.5779 0.351249 1
18 411.02 49.7232 0.292491535 0.0542269 6.90E-08 0 0 1 1 1304.67 2558.54 17.6834 31.9477 0 1 0 0 60 60 759.817 668.817 750 663.5 71.4035 57.5127 277 277 37.3827 72.6787 38 73 3.82187 8.93665 0 0 0 0 0.325631 -0.000279543 0 0 0 0 0 0 0 0 0 680.321 596.174 9.22101 7.44425 0.324681 1 1 7.15E-60 2.14E-62 1 1 1 1 0 79.4957 72.643 3.82187 8.93665 0 1304.67 2558.54 17.6834 31.9477 0.324681 1
19 432.217 50.1838 -0.443305636 0.0657876 1.60E-11 0 0 1 1 837.852 301.899 12.2668 11.0196 0 2 0 0 61 61 592.541 131.705 589 130 58.551 16.5634 281 281 38.1637 71.7438 38 72 3.70447 9.15649 0 0 0 0 0.221605 3.70E-05 0 0 0 0 0 0 0 0 0 512.264 59.9968 7.49994 2.18994 0.214507 1 1 1.12E-58 1.62E-38 1 1 1 1 0 80.2767 71.7081 3.70447 9.15649 0 837.852 301.899 12.2668 11.0196 0.214507 1
20 453.27 50.0454 -0.111580034 0.14041 0.426811 0 0 1 1 132.629 102.579 5.93818 8.59395 0 1 0 0 60 60 156.983 92.6333 157.5 93 26.6226 13.2229 276 276 37.8877 71.1957 38 70.5 4.30877 9.43175 0 0 0 0 -0.00950262 1.95E-05 0 0 0 0 0 0 0 0 0 76.9827 21.4733 3.44673 1.799 -0.00899101 1 1 1.14E-30 8.65E-19 1 1 1 0 0 80.0007 71.16 4.30877 9.43175 1 132.629 102.579 5.93818 8.59395 -0.00899101 1

Total number of rows: 21446

Table truncated, full table size 8127 Kbytes.




Supplementary data files not provided
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