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Sample GSM14727 Query DataSets for GSM14727
Status Public on Jan 09, 2004
Title 43h-DMSO replication 3
Sample type RNA
 
Channel 1
Source name 43h-DMSO, early 2-cell embryo
Organism Mus musculus
Extracted molecule total RNA
 
Channel 2
Source name Universal Reference
Organism Mus musculus
Extracted molecule total RNA
 
 
Description 43h-DMSO replication 3
Keywords = preimplantation
Keywords = development
 
Submission date Dec 30, 2003
Last update date May 28, 2005
Contact name Minoru S.H. Ko
E-mail(s) [email protected]
Phone 410-558-8359
Organization name NIH
Department National Institute on Aging
Lab Lab of Genetics
Street address 251 Bayview Blvd, Suite 100, 10C
City Baltimore
State/province MD
ZIP/Postal code 21224
Country USA
 
Platform ID GPL870
Series (1)
GSE936 Dynamics of global gene expression changes during mouse preimplantation development

Data table header descriptions
ID_REF Feature number
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 74.51 60.3307 -2 0.160815 1.65227e-035 0 0 1 1 36167.2 180.072 501.869 9.0408 1 3 0 0 72 72 3233.96 418.264 3188 418.5 329.658 9.32359 218 218 372.927 392.803 373 392 4.64343 8.92635 0 0 0 0 0.233803 0.346602 0 0 0 0 0 0 0 1 0 2799.97 22.2186 38.8533 1.11552 0.230995 1 1 3.7575e-068 9.25885e-032 144 144 1 1 0 433.993 396.045 5.56005 2.30936 0 36167.2 180.072 501.869 9.0408 0.230995 1
2 97 58.661 -2 0.160388 1.09117e-035 0 0 1 1 23781.6 53.3244 381.861 8.6947 3 1 0 0 72 72 2189.81 402.944 2130 403 239.194 9.40466 229 229 372.786 392.087 373 392 4.68504 8.70981 0 0 0 0 0.159402 0.346602 0 0 0 0 0 0 0 1 0 1755.81 6.8992 28.1931 1.12493 0.158005 1 1 9.89419e-064 3.67657e-008 144 144 1 1 0 433.993 396.045 5.56005 2.30936 0 23781.6 53.3244 381.861 8.6947 0.158005 1
3 116.617 60.4522 0 0.118099 1 69.6793 0 1 1 69.6793 26.4227 13.7171 5.99077 0 2 0 3 72 72 425.014 399.208 424.5 400 8.41443 5.86212 215 215 371.814 391.135 372 391 4.33771 8.23064 0 0 0 0 0.162982 0.346602 0 0 0 0 0 0 0 0 0 -8.97925 3.16309 1.09456 0.717161 0.181615 0 1 6.99827e-013 3.09891e-005 144 144 0 0 0 433.993 396.045 5.56005 2.30936 0 -112.529 26.4227 13.7171 5.99077 0.181615 0
4 138.422 60.2759 0 0.107856 1 72.1601 0 1 1 72.1601 63.6975 12.7999 10.0168 2 1 2 1 69 69 435.304 403.942 436 404 7.23209 10.1907 216 216 374.093 390.407 374 390 5.3301 7.8094 0 0 0 0 -0.141628 0.346602 0 0 0 0 0 0 0 0 0 1.31121 7.89678 0.986254 1.24181 -0.0982811 0 1 0.186492 1.68906e-008 144 144 0 1 0 433.993 396.045 5.56005 2.30936 0 17.0173 63.6975 12.7999 10.0168 -0.0982811 0
5 159.108 60.7227 -2 0.160847 1.70557e-035 0 0 1 1 36373.4 188.474 453.316 10.8269 4 0 0 0 71 71 3257.35 419.239 3209 420 296.466 11.1092 206 206 373.752 388.379 373 389 4.94081 7.54255 0 0 0 0 0.190016 0.346602 0 0 0 0 0 0 0 0 0 2823.36 23.1942 35.1871 1.33239 0.188666 1 1 1.17122e-070 1.0711e-027 144 144 1 1 0 433.993 396.045 5.56005 2.30936 0 36373.4 188.474 453.316 10.8269 0.188666 1
6 181.52 59.4148 -2 0.160463 1.17432e-035 0 0 1 1 25244.4 68.8877 457.246 8.94259 1 1 0 0 74 74 2300.34 404.946 2240 404 290.771 9.8006 213 213 373.042 387.728 373 387 4.73676 7.93791 0 0 0 0 0.149792 0.346602 1 0 0 0 0 0 0 0 0 1866.34 8.9007 33.8047 1.15544 0.148477 1 1 2.66783e-061 3.73141e-011 144 144 1 1 0 433.993 396.045 5.56005 2.30936 0 25244.4 68.8877 457.246 8.94259 0.148477 1
7 201.375 60.8583 0 0.218967 1 69.6793 19.2912 1 1 69.6793 19.2912 13.2813 9.01614 0 0 1 0 75 75 425.693 395.973 426 395 8.25436 9.19749 202 202 372.376 387.5 373 388 4.45285 7.82727 0 0 0 0 -0.0269869 0.346602 0 0 0 0 0 0 0 0 0 -8.2998 -0.0719144 1.05978 1.07933 0.00313686 0 0 3.25965e-012 0.947046 144 144 0 0 0 433.993 396.045 5.56005 2.30936 0 -104.014 -0.600733 13.2813 9.01614 0.00313686 0
8 222.51 60.5499 0.0688456 0.204189 0.735992 71.5191 0 1 1 71.5191 83.8046 13.8643 10.5135 3 0 0 0 73 73 434.055 406.342 435 408 8.3148 10.9141 201 201 372.328 387.607 372 387 4.44203 8.10554 0 0 0 0 -0.158309 0.346602 0 0 0 0 0 0 0 0 0 0.0616599 10.2972 1.07784 1.29181 -0.119143 0 1 0.954489 1.3233e-011 144 144 0 1 0 433.993 396.045 5.56005 2.30936 0 0.793132 83.8046 13.8643 10.5135 -0.119143 1
9 243.569 60.6379 -2 0.160771 1.58413e-035 0 0 1 1 38606.3 182.223 552.945 11.4616 1 0 0 0 75 75 3434.71 418.44 3366 417 372.181 12.0844 218 218 372.972 386.647 373 386.5 4.64095 8.68013 0 0 0 0 0.307001 0.346602 0 0 0 0 0 0 0 0 0 3000.71 22.3948 42.9782 1.4086 0.304615 1 1 2.64372e-069 5.23024e-026 144 144 1 1 0 433.993 396.045 5.56005 2.30936 0 38606.3 182.223 552.945 11.4616 0.304615 1
10 265.91 60.0178 -2 0.160366 1.06849e-035 0 0 1 1 25167.1 53.5312 363.457 8.60373 0 0 0 0 69 69 2292.14 402.971 2260 402 222.875 9.10716 223 223 373.103 386.816 373 386 4.87623 7.32866 0 0 0 0 0.175719 0.346602 0 0 0 0 0 0 0 0 0 1858.15 6.92577 26.835 1.11314 0.174081 1 1 8.11985e-065 2.87438e-008 144 144 1 1 0 433.993 396.045 5.56005 2.30936 0 25167.1 53.5312 363.457 8.60373 0.174081 1
11 286.155 61.2759 0 0.196433 1 69.6793 19.2912 1 1 69.6793 19.2912 13.8664 8.5558 2 2 0 1 70 70 425.714 397.171 426 398 8.40659 8.41664 203 203 373.251 386.453 373 386 4.45449 7.79829 0 0 0 0 0.170916 0.346602 0 0 0 0 0 0 0 0 0 -8.27885 1.12618 1.10647 1.02422 0.179715 0 0 2.99027e-011 0.275089 144 144 0 0 0 433.993 396.045 5.56005 2.30936 0 -103.752 9.4075 13.8664 8.5558 0.179715 0
12 306.978 61.3099 0.0111351 0.21635 0.958953 71.9456 0 1 1 71.9456 73.8141 16.3116 7.91092 0 4 0 1 71 71 437.38 405.169 437 405 9.87835 8.07816 216 216 373.412 387.792 374 389 4.78288 8.28998 0 0 0 0 0.202551 0.346602 0 0 0 0 0 0 0 0 0 3.38715 9.12377 1.26059 0.977827 0.209762 1 1 0.00854975 3.22798e-014 144 144 0 1 0 433.993 396.045 5.56005 2.30936 0 43.8288 73.8141 16.3116 7.91092 0.209762 1
13 328.152 61.7004 -2 0.160908 1.80793e-035 0 0 1 1 38625.6 214.785 532.488 12.3241 0 0 0 0 76 76 3462.74 422.211 3406 423 363.979 12.9803 219 219 373.877 388.205 374 387 5.00993 7.78193 0 0 0 0 0.167006 0.346602 0 0 0 0 0 0 0 0 0 3028.74 26.1653 41.7539 1.50133 0.166111 1 1 3.12335e-071 1.54968e-028 144 144 1 1 0 433.993 396.045 5.56005 2.30936 0 38625.6 214.785 532.488 12.3241 0.166111 1
14 350.416 60.4643 -2 0.16054 1.26593e-035 0 0 1 1 25486.7 81.8012 359.151 10.1118 7 0 0 0 70 70 2323.39 406.586 2252 408 222.726 10.7818 228 228 373.259 388.145 373 387 4.80993 7.85615 0 0 0 0 0.187551 0.346602 0 0 0 0 0 0 0 0 0 1889.39 10.5405 26.6248 1.30296 0.186357 1 1 2.94116e-066 1.03427e-011 144 144 1 1 0 433.993 396.045 5.56005 2.30936 0 25486.7 81.8012 359.151 10.1118 0.186357 1
15 370.655 62.437 0 0.212204 1 69.6793 19.2912 1 1 69.6793 19.2912 14.4439 8.94387 1 1 0 0 74 74 425.743 397.784 426 397.5 9.07814 9.06033 211 211 372.441 388.758 372 389 4.49021 8.2389 0 0 0 0 0.0829223 0.346602 0 0 0 0 0 0 0 0 0 -8.24989 1.73854 1.15255 1.07068 0.099735 0 0 1.29696e-010 0.108464 144 144 0 0 0 433.993 396.045 5.56005 2.30936 0 -103.389 14.5228 14.4439 8.94387 0.099735 0
16 392 61.8964 0.163094 0.188476 0.386857 69.6793 0 1 1 69.6793 101.437 14.9133 12.7007 0 0 0 0 69 69 433.797 408.188 433 408 9.10491 12.5279 227 227 372.586 388.361 372 388 4.86866 8.1285 0 0 0 0 0.0614503 0.346602 0 0 0 0 0 0 0 0 0 -0.196033 12.1432 1.19001 1.52042 0.0732274 0 1 0.869512 1.89459e-011 144 144 0 1 0 433.993 396.045 5.56005 2.30936 0 -2.45671 101.437 14.9133 12.7007 0.0732274 1
17 412.924 62.0351 -2 0.160955 1.89259e-035 0 0 1 1 37623.7 220.033 426.259 11.0243 0 0 0 1 68 68 3383.84 422.853 3374 424 275.565 10.9616 221 221 374.054 389.964 374 390 4.81916 8.34149 0 0 0 0 0.248106 0.346602 0 0 0 0 0 0 0 0 0 2949.85 26.8077 33.4203 1.34315 0.246211 1 1 4.45662e-071 1.44868e-030 144 144 1 1 0 433.993 396.045 5.56005 2.30936 0 37623.7 220.033 426.259 11.0243 0.246211 1
18 434.849 61.0183 -2 0.16051 1.2289e-035 0 0 1 1 25824.2 78.1074 383.463 10.1191 0 2 0 0 69 69 2347.23 406.116 2289 406 235.957 10.7191 218 218 373.894 390.376 374 390 5.23484 8.50512 0 0 0 0 0.221737 0.346602 0 0 0 0 0 0 0 0 0 1913.24 10.0707 28.4096 1.30469 0.220116 1 1 5.28039e-064 5.5326e-011 144 144 1 1 0 433.993 396.045 5.56005 2.30936 0 25824.2 78.1074 383.463 10.1191 0.220116 1
19 455.844 63.25 0 0.168734 1 69.6793 0 1 1 69.6793 23.0804 13.6951 7.74823 0 1 0 0 73 73 431.342 398.808 431 399 8.45613 7.75252 203 203 379.729 390.685 378 390 9.312 7.78925 0 0 0 0 -0.0311872 0.346602 0 0 0 0 0 0 1 0 0 -2.65067 2.76297 1.0928 0.927548 0.00285974 0 1 0.0169985 0.00384854 144 144 0 0 0 433.993 396.045 5.56005 2.30936 0 -33.2185 23.0804 13.6951 7.74823 0.00285974 0
20 476.847 62.4698 0.0898879 0.198467 0.650613 71.9151 0 1 1 71.9151 88.452 16.0568 12.2706 0 0 0 0 76 76 437.066 406.974 437 405.5 10.0404 13.1098 230 230 375.852 390.209 375 390 5.90129 7.54607 0 0 0 0 0.118935 0.346602 0 0 0 0 0 0 0 0 0 3.07265 10.9284 1.24142 1.51606 0.12587 0 1 0.0150029 3.25178e-010 144 144 0 1 0 433.993 396.045 5.56005 2.30936 0 39.7425 88.452 16.0568 12.2706 0.12587 1

Total number of rows: 22575

Table truncated, full table size 8797 Kbytes.




Supplementary data files not provided
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