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Sample GSM14728 Query DataSets for GSM14728
Status Public on Jan 09, 2004
Title 43h-CHX replication 2
Sample type RNA
 
Channel 1
Source name 43h-CHX, 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-CHX replication 2
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
1 111.712 78.0313 -2 0.160092 8.16727e-036 0 0 1 1 422885 241.529 7718.75 13.8099 0 0 0 0 76 76 20747.1 417.487 20168.5 415.5 3236.73 11.4292 229 229 370.729 393.729 371 394 4.33024 8.58937 0 0 0 0 0.324281 0.335522 1 0 0 0 0 0 0 1 0 20341.1 23.0711 371.278 1.31913 0.322316 1 1 3.02211e-062 1.62087e-028 151 151 1 1 0 406.007 394.416 3.65252 1.79529 0 422885 241.529 7718.75 13.8099 0.322316 1
2 132.5 77.902 -2 0.160058 7.9048e-036 0 0 1 1 365995 132.939 6810.54 10.8812 0 0 0 0 74 74 16526 408.284 15848 409 2580.4 9.68337 224 224 370.799 392.201 371 392.5 4.44698 7.7448 0 0 0 0 0.173451 0.335522 1 0 0 0 0 0 0 0 0 16120 13.868 299.965 1.13511 0.172051 1 1 1.89717e-060 1.46343e-019 151 151 1 1 0 406.007 394.416 3.65252 1.79529 0 365995 132.939 6810.54 10.8812 0.172051 1
3 153.67 78.53 0.158562 0.208381 0.446702 62.9251 0 1 1 62.9251 90.6539 14.1477 12.3183 1 2 2 0 71 71 406.859 401.592 407 401 6.45046 8.1233 225 225 370.898 391.538 371 391 3.99478 7.76264 0 0 0 0 -0.202862 0.335522 0 0 0 0 0 0 0 0 0 0.851795 7.17578 0.821209 0.975065 -0.168777 0 1 0.302348 2.19993e-010 151 151 0 1 0 406.007 394.416 3.65252 1.79529 0 14.6746 90.6539 14.1477 12.3183 -0.168777 1
4 174.97 79.05 -0.236685 0.183245 0.196484 0 0 1 1 113.368 65.7362 18.0341 10.8631 0 0 0 0 69 69 411.435 400.725 411 402 6.73332 8.57473 228 228 371.167 390.189 371 390 4.32881 7.83949 0 0 0 0 -0.226368 0.335522 0 0 0 0 0 0 0 0 0 5.42742 6.30887 0.863375 1.04256 -0.194246 1 1 1.26414e-008 6.17013e-008 151 151 0 1 0 406.007 394.416 3.65252 1.79529 0 113.368 65.7362 18.0341 10.8631 -0.194246 1
5 196.3 79.258 -2 0.160066 7.9637e-036 0 0 1 1 445878 183.111 8019.03 11.6753 0 1 0 0 75 75 21295.8 412.373 20475 413 3253.65 9.83482 224 224 371.107 388.728 371 389 4.43257 7.8118 0 0 0 0 0.102796 0.335522 1 0 0 0 0 0 0 0 0 20889.8 17.9576 375.699 1.14499 0.101989 1 1 4.12394e-062 1.32372e-025 151 151 1 1 0 406.007 394.416 3.65252 1.79529 0 445878 183.111 8019.03 11.6753 0.101989 1
6 216.917 78.4189 -2 0.160036 7.73504e-036 0 0 1 1 399986 90.1087 7429.69 9.88489 0 3 0 0 72 72 17389.1 404.167 16507 405.5 2676.76 8.99139 223 223 370.812 387.695 371 387 4.25541 7.66919 0 0 0 0 0.202426 0.335522 1 0 0 0 0 0 0 0 0 16983.1 9.7509 315.46 1.06967 0.200572 1 1 2.63097e-059 1.03973e-013 151 151 1 1 0 406.007 394.416 3.65252 1.79529 0 399986 90.1087 7429.69 9.88489 0.200572 1
7 238.235 79.3333 0.528625 0.303416 0.0814657 26.4767 0 1 1 26.4767 89.4312 6.10269 30.0941 0 2 2 0 71 71 405.746 397.394 405 398 6.63695 8.35546 224 224 370.304 388.991 371 389.5 4.37038 6.83108 0 0 0 0 0.00620804 0.335522 0 0 0 0 0 0 0 0 0 -0.260881 2.9786 0.841879 1.00232 0.0230132 0 1 0.757365 0.00400734 151 151 0 0 0 406.007 394.416 3.65252 1.79529 0 -1.8911 89.4312 6.10269 30.0941 0.0230132 1
8 259.705 79.3619 -0.241715 0.193912 0.212573 0 0 1 1 107.213 61.4516 23.5389 10.3074 0 1 0 1 72 72 411.208 400.236 411.5 400 9.35518 8.1905 207 207 371.324 388.382 371 388 3.85496 7.29105 0 0 0 0 -0.124726 0.335522 0 0 0 0 0 0 0 0 0 5.20097 5.82034 1.14188 0.976254 -0.105999 1 1 1.81799e-005 7.79039e-008 151 151 0 1 0 406.007 394.416 3.65252 1.79529 0 107.213 61.4516 23.5389 10.3074 -0.105999 1
9 280.917 79.6447 -2 0.160071 8.00517e-036 0 0 1 1 447961 198.765 8369.31 13.7556 0 0 0 0 76 76 21608.8 413.711 21179.5 413.5 3453.41 11.571 224 224 370.902 389.353 371 390 4.33043 8.35189 0 0 0 0 0.0891093 0.335522 1 0 0 0 0 0 0 0 0 21202.8 19.2948 396.134 1.3353 0.0886019 1 1 1.66333e-061 1.31223e-023 151 151 1 1 0 406.007 394.416 3.65252 1.79529 0 447961 198.765 8369.31 13.7556 0.0886019 1
10 301.649 79.3371 -2 0.160046 7.81375e-036 0 0 1 1 397088 115.018 7597.39 11.636 0 1 0 1 73 73 17761.5 406.507 17140 404 2837.11 10.3764 228 228 370.158 388.996 370 389 4.37973 7.88323 0 0 0 0 0.109725 0.335522 1 0 0 0 0 0 0 0 0 17355.5 12.0911 332.058 1.22322 0.108975 1 1 5.27767e-059 3.57331e-015 151 151 1 1 0 406.007 394.416 3.65252 1.79529 0 397088 115.018 7597.39 11.636 0.108975 1
11 323.118 79.9412 0.640399 0.262807 0.0148193 26.4767 0 1 1 26.4767 115.681 5.84788 36.3951 2 0 1 0 67 67 404.164 398.269 404 397 6.13879 9.84975 232 232 370.612 388.629 371 389 3.90198 7.60329 0 0 0 0 0.229794 0.335522 0 0 0 0 0 0 0 0 0 -1.84318 3.85289 0.806728 1.21218 0.22697 0 1 0.024748 0.00222916 151 151 0 0 0 406.007 394.416 3.65252 1.79529 0 -13.361 115.681 5.84788 36.3951 0.22697 1
12 344.371 80.4095 -0.168863 0.207208 0.415105 0 0 1 1 92.2394 62.525 16.8911 10.9557 0 0 1 0 75 75 410.547 400.253 410 398 6.72288 8.7674 212 212 370.193 389.764 370 390 3.93253 7.17295 0 0 0 0 0.144579 0.335522 0 0 0 0 0 0 0 0 0 4.53931 5.83757 0.831251 1.02286 0.150772 1 1 3.69738e-007 2.03661e-007 151 151 0 1 0 406.007 394.416 3.65252 1.79529 0 92.2394 62.525 16.8911 10.9557 0.150772 1
13 365.62 80.6219 -2 0.160075 8.03896e-036 0 0 1 1 447545 210.569 7069.33 12.4989 0 0 0 0 75 75 21731.4 414.72 21412 413 2917.21 10.3605 212 212 371.962 391.377 372 391 4.00929 8.21218 0 0 0 0 0.130037 0.335522 1 0 0 0 0 0 0 0 0 21325.4 20.3042 336.851 1.20521 0.129114 1 1 3.38288e-066 2.05813e-027 151 151 1 1 0 406.007 394.416 3.65252 1.79529 0 447545 210.569 7069.33 12.4989 0.129114 1
14 385.815 80.3565 -2 0.160063 7.9416e-036 0 0 1 1 393358 154.537 7729.6 10.1707 0 3 0 1 73 73 18202.8 410.11 17749 409 2987.94 8.7362 229 229 371.507 391.306 372 391 4.30179 7.50573 0 0 0 0 0.160259 0.335522 1 0 0 0 0 0 0 0 0 17796.8 15.6938 349.712 1.03288 0.158688 1 1 3.42972e-058 1.36816e-024 151 151 1 1 0 406.007 394.416 3.65252 1.79529 0 393358 154.537 7729.6 10.1707 0.158688 1
15 407.051 81.6364 0.599072 0.277101 0.0306238 26.4767 0 1 1 26.4767 105.181 5.96974 32.8151 1 1 0 0 74 74 403.527 397.919 404 398 6.60681 9.31747 220 220 371.609 392.136 372 392 3.80722 6.65727 0 0 0 0 0.136002 0.335522 0 0 0 0 0 0 0 0 0 -2.48033 3.50315 0.823538 1.09294 0.141884 0 1 0.0033239 0.00197704 151 151 0 0 0 406.007 394.416 3.65252 1.79529 0 -17.9797 105.181 5.96974 32.8151 0.141884 1
16 428.088 81.8039 0.0108051 0.224577 0.961626 69.2013 0 1 1 69.2013 70.9445 17.2448 13.1809 1 0 0 0 71 71 408.282 400.592 409 402 7.24901 9.58954 225 225 370.747 392.729 371 393 4.32009 7.04972 0 0 0 0 0.00804949 0.335522 0 0 0 0 0 0 0 1 0 2.27433 6.17578 0.9102 1.14741 0.0214976 0 1 0.0143407 8.68176e-007 151 151 0 1 0 406.007 394.416 3.65252 1.79529 0 43.0899 70.9445 17.2448 13.1809 0.0214976 1
17 449.675 82.3009 -2 0.160096 8.20308e-036 0 0 1 1 455029 272.583 7855.28 13.2564 0 1 0 2 71 71 22791.9 419.873 22198 420 3256.31 10.3592 226 226 371.204 392.133 371 392 4.64693 7.58303 0 0 0 0 0.151479 0.335522 1 0 0 0 0 0 0 0 0 22385.9 25.4575 386.453 1.23806 0.150451 1 1 7.0036e-061 7.45876e-032 151 151 1 1 0 406.007 394.416 3.65252 1.79529 0 455029 272.583 7855.28 13.2564 0.150451 1
18 471.039 81.6773 -2 0.160062 7.93483e-036 0 0 1 1 407336 157.835 7972.97 10.3703 0 2 0 0 74 74 18958.8 410.338 18403 410 3123.86 8.91094 224 224 371.036 392.183 371 392 3.94225 7.56422 0 0 0 0 0.156875 0.335522 1 0 0 0 0 0 0 0 0 18552.8 15.9221 363.142 1.04613 0.155375 1 1 6.9236e-059 9.04361e-025 151 151 1 1 0 406.007 394.416 3.65252 1.79529 0 407336 157.835 7972.97 10.3703 0.155375 1
19 491.902 82.3431 0.891444 0.193791 4.22444e-006 26.4767 0 1 1 26.4767 206.209 7.32074 30.1531 1 0 0 0 74 74 404.095 401.284 405 401.5 8.30278 8.54724 224 224 371.205 391.817 371 392 3.66449 7.88979 0 0 0 0 0.121226 0.335522 0 0 0 0 0 0 0 0 0 -1.91277 6.86802 1.00991 1.00428 0.12899 0 1 0.0615439 1.74894e-009 151 151 0 1 0 406.007 394.416 3.65252 1.79529 0 -13.8654 206.209 7.32074 30.1531 0.12899 1
20 513.22 82.63 -0.0838355 0.167571 0.616865 0 0 1 1 105.468 86.9535 23.3771 11.3421 0 1 0 0 75 75 410.947 402.947 412 403 9.1251 9.5534 223 223 371.327 392.417 371 392 4.67266 8.62957 0 0 0 0 -0.0370816 0.335522 0 0 0 0 0 0 0 1 0 4.93931 8.5309 1.0948 1.11276 -0.0234198 1 1 2.02605e-005 4.57745e-011 151 151 0 1 0 406.007 394.416 3.65252 1.79529 0 105.468 86.9535 23.3771 11.3421 -0.0234198 1

Total number of rows: 22575

Table truncated, full table size 8828 Kbytes.




Supplementary data files not provided
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