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Sample GSM133003 Query DataSets for GSM133003
Status Public on Apr 20, 2007
Title US22502648_251357810004_S01_44k_CGH
Sample type genomic
 
Channel 1
Source name Neuralized EBs ChIP Biological Rep#1 Technical Rep#4
Organism Mus musculus
Characteristics Neuralized Embryoid bodies treated with 500nM retinoic acid and 1µm of HH Agonist (HH-Ag)
Biomaterial provider Steve Vokes
Treatment protocol Neuralized Embryoid bodies treated with 500nM retinoic acid and 1µm of HH Agonist (HH-Ag)
Extracted molecule genomic DNA
Extraction protocol Chromatin prep and shearing, crosslinks reversed, LMPCR amplification
Label Cy3
Label protocol 2 µg of amplified DNA was labeled with Cy3-dUTP (Perkin Elmer) using the Bioprime Array CGH kit (Invitrogen) per Agilent’s recommended protocol. 5 µg of amplified material was used for each channel during hybridization
 
Channel 2
Source name Neuralized EBs Input Biological Rep#1 Technical Rep#4
Organism Mus musculus
Characteristics Neuralized Embryoid bodies treated with 500nM retinoic acid and 1µm of HH Agonist (HH-Ag)
Biomaterial provider Steve Vokes
Treatment protocol Neuralized Embryoid bodies treated with 500nM retinoic acid and 1µm of HH Agonist (HH-Ag)
Extracted molecule genomic DNA
Extraction protocol Chromatin prep and shearing, crosslinks reversed, LMPCR amplification
Label Cy5
Label protocol 2 µg of amplified DNA was labeled with Cy5-dUTP (Perkin Elmer) using the Bioprime Array CGH kit (Invitrogen) per Agilent’s recommended protocol. 5 µg of amplified material was used for each channel during hybridization
 
 
Hybridization protocol Arrays were hybridized by competitive hybridization using 5µg of labeled material per channel using the Oligo CGH hybridization kit (Agilent Technologies). The hybridizations were done in Agilent SureHyb hybridization chambers and in an Agilent rotating hyb oven at a speed of 10rpm for 72 hours at 65º C. Samples were washed sequentially for 5 minutes at room temperature using Oligo aCGH wash buffer 1, 1 minute at 37º C using Oligo aCGH wash buffer 2, 1 minute in acetonitrile at room temperature and 30 seconds in stabilization and drying solution (all from Agilent technologies).
Scan protocol Finished arrays were scanned using an Agilent scanner. The settings were 10µm resolution and the PMT setting of both channels was at 100. Array images were extracted using Agilent’s Feature Extraction Software (version 8.5.1.1) using the standard CGH protocol included with the software. The settings included spatial detrending of the extracted array data and a linear median normalization
Description This is biological replicate #1 technical replicate #4. All control spots were removed from this dataset because they have redundant names. If needed, they are present in the attached original dataset.
Data processing The Value column is the Log Ratio of the two channels
 
Submission date Aug 31, 2006
Last update date Jan 29, 2022
Contact name Steven A. Vokes
E-mail(s) svokes@austin.utexas.edu
Organization name University of Texas at Austin
Department Molecular Biosciences
Street address 2500 Speedway, STOP A5000
City Austin
State/province Texas
ZIP/Postal code 78757
Country USA
 
Platform ID GPL4245
Series (1)
GSE5683 Identification of Gli-Act targets in the mouse ventral neural tube by ChIP

Data table header descriptions
ID_REF
PositionX
PositionY
VALUE l
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
gBGUsed
rBGUsed
gBGSDUsed
rBGSDUsed
IsNormalization
gDyeNormSignal
rDyeNormSignal
gDyeNormError
rDyeNormError
DyeNormCorrelation
ErrorModel
xDev
gSpatialDetrendIsInFilteredSet
rSpatialDetrendIsInFilteredSet
gSpatialDetrendSurfaceValue
rSpatialDetrendSurfaceValue
SpotExtentX
SpotExtentY
gNetSignal
rNetSignal
IsUsedBGAdjust

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 gBGUsed rBGUsed gBGSDUsed rBGSDUsed IsNormalization gDyeNormSignal rDyeNormSignal gDyeNormError rDyeNormError DyeNormCorrelation ErrorModel xDev gSpatialDetrendIsInFilteredSet rSpatialDetrendIsInFilteredSet gSpatialDetrendSurfaceValue rSpatialDetrendSurfaceValue SpotExtentX SpotExtentY gNetSignal rNetSignal IsUsedBGAdjust
110_058071295_058071355 1215.18 71.9579 3.10E-01 9.91E-02 1.72E-03 0 0 1 1 1.32E+02 2.69E+02 1.11E+01 8.76E+00 2 1 0 0 28 28 8.64E+01 1.33E+02 87 132 1.10E+01 1.40E+01 194 194 3.30E+01 4.15E+01 33 42 4.35E+00 4.08E+00 0 0 0 0 0.196514 0.0348111 0 0 0 0 0 0 0 0 0 24.7058 81.2405 2.08003 2.64292 0 1 1 2.20E-12 7.39E-23 1 1 1 1 61.7228 51.3666 4.34867 4.07724 0 131.769 269.332 11.0939 8.76191 0 1 3.13E+00 0 0 61.7228 51.3666 109.981 109.981 66.3806 112.401 0
102_140194858_140194918 1236.34 73.413 2.63E-01 1.23E-01 3.24E-02 0 0 1 1 1.05E+02 1.92E+02 1.09E+01 6.68E+00 0 0 0 1 30 30 8.27E+01 1.10E+02 83 109 1.12E+01 1.10E+01 200 200 3.26E+01 4.16E+01 32 42 4.37E+00 3.99E+00 0 0 0 0 -0.041696 0.07852 0 0 0 0 0 0 0 0 0 19.6695 57.9162 2.05238 2.01474 0 1 1 1.41E-10 2.39E-23 1 1 1 1 62.9972 51.5838 4.36933 3.99426 1 104.908 192.006 10.9464 6.67936 0 1 2.14E+00 0 0 62.9972 51.5838 107.047 107.047 62.6187 89.294 0
113_040296111_040296156 1257.53 72.5833 -5.85E-02 5.08E-02 2.49E-01 0 0 1 1 1.39E+03 1.21E+03 1.74E+01 1.84E+01 2 1 0 0 30 30 3.25E+02 4.18E+02 323.5 418.5 1.79E+01 3.04E+01 183 183 3.26E+01 4.18E+01 32 42 4.33E+00 4.40E+00 0 0 0 0 0.513422 0.129567 0 0 0 0 0 0 0 0 0 260.278 365.929 3.27045 5.55473 0 1 1 5.58E-36 2.72E-33 1 1 1 1 64.2883 51.8045 4.32503 4.39609 1 1388.2 1213.14 17.443 18.4153 0 1 -1.15E+00 0 0 64.2883 51.8045 108.23 108.23 304.519 397.527 0
102_146585229_146585289 1277.32 74.3333 -3.09E-01 6.24E-02 7.53E-07 0 0 1 1 7.17E+02 3.52E+02 2.59E+01 1.36E+01 0 1 0 0 29 29 2.00E+02 1.58E+02 197 153 2.62E+01 2.22E+01 180 180 3.29E+01 4.18E+01 33 42 4.13E+00 4.78E+00 0 0 0 0 0.474732 -0.0190068 0 0 0 0 0 0 0 0 0 134.388 106.217 4.86277 4.11373 0 1 1 5.86E-22 3.12E-21 1 1 1 1 65.5777 52.0242 4.12798 4.78487 0 716.76 352.135 25.9357 13.638 0 1 -4.95E+00 0 0 65.5777 52.0242 108.23 108.23 179.918 138.035 0
105_036339363_036339408 1299 72.5 -1.67E-01 5.43E-02 2.14E-03 0 0 1 1 9.79E+02 6.67E+02 2.55E+01 1.53E+01 1 0 0 0 29 29 2.50E+02 2.53E+02 244 254 2.57E+01 2.49E+01 204 204 3.29E+01 4.21E+01 33 42 3.65E+00 4.27E+00 0 0 0 0 0.202179 0.0320315 0 0 0 0 0 0 0 0 0 183.494 201.105 4.77996 4.62145 0 1 1 7.55E-26 2.11E-27 1 1 1 1 66.8509 52.24 3.65249 4.27411 0 978.669 666.71 25.494 15.3212 0 1 -3.07E+00 0 0 66.8509 52.24 104.642 104.642 230.297 233.139 0
102_051070802_051070862 1320.5 73.3778 5.52E-02 5.11E-02 2.80E-01 0 0 1 1 1.13E+03 1.28E+03 2.73E+01 3.50E+01 0 0 0 0 32 32 2.80E+02 4.39E+02 274.5 431 2.89E+01 5.98E+01 188 188 3.32E+01 4.22E+01 33 42 4.07E+00 4.34E+00 0 0 0 0 0.629465 0.0642368 0 0 0 0 0 0 0 0 0 211.405 386.2 5.11461 10.5723 0 1 1 8.49E-29 4.45E-27 1 1 1 1 68.1261 52.4559 4.07321 4.33731 0 1127.53 1280.35 27.2789 35.0497 0 1 1.08E+00 0 0 68.1261 52.4559 105.851 105.851 259.483 418.45 0
108_056346561_056346621 1341.11 72.3012 -6.08E-01 6.91E-02 1.29E-18 0 0 1 1 1.59E+03 3.91E+02 3.69E+01 1.55E+01 0 0 0 0 29 29 3.67E+02 1.71E+02 365 170 3.72E+01 2.52E+01 210 210 3.33E+01 4.19E+01 33 42 3.88E+00 4.30E+00 0 0 0 0 0.578524 0.0067362 0 0 0 0 0 0 0 0 0 297.758 118.016 6.91095 4.67598 0 1 1 3.43E-27 6.88E-21 1 1 1 1 69.4147 52.6739 3.8826 4.29916 0 1588.1 391.251 36.8597 15.502 0 1 -8.81E+00 0 0 69.4147 52.6739 102.179 102.179 347.124 150.484 0
102_051059490_051059540 1363.42 72.7802 -1.94E-01 5.80E-02 8.38E-04 0 0 1 1 7.21E+02 4.62E+02 1.57E+01 1.32E+01 0 0 0 0 29 29 2.06E+02 1.92E+02 200 193 1.59E+01 2.14E+01 199 199 3.29E+01 4.25E+01 33 43 4.39E+00 4.89E+00 0 0 0 0 0.394728 0.0529832 0 0 0 0 0 0 0 0 0 135.213 139.216 2.9488 3.98066 0 1 1 2.80E-28 7.24E-25 1 1 1 1 70.6835 52.8876 4.39122 4.8852 0 721.162 461.534 15.7275 13.1968 0 1 -3.34E+00 0 0 70.6835 52.8876 106.451 106.451 185.849 171.897 0
108_084255925_084255985 1383.08 73.0109 1.08E-01 5.40E-02 4.49E-02 0 0 1 1 6.70E+02 8.60E+02 2.90E+01 2.31E+01 0 0 0 0 29 29 1.98E+02 3.13E+02 192 306 2.93E+01 3.75E+01 196 196 3.36E+01 4.26E+01 34 42 4.50E+00 4.22E+00 0 0 0 0 0.666795 -0.0419806 0 0 0 0 0 0 0 1 0 125.675 259.452 5.43919 6.96306 0 1 1 7.63E-20 1.84E-25 1 1 1 1 71.946 53.0998 4.49607 4.21629 0 670.288 860.145 29.01 23.0842 0 1 2.01E+00 0 0 71.946 53.0998 109.4 109.4 177.573 292.346 0
113_058886906_058886959 1405.47 73.0494 1.47E-01 5.41E-02 6.54E-03 0 0 1 1 6.70E+02 9.41E+02 1.90E+01 1.94E+01 0 0 1 0 28 28 1.99E+02 3.37E+02 204 329.5 1.89E+01 3.10E+01 197 197 3.26E+01 4.20E+01 33 42 3.89E+00 4.38E+00 0 0 0 0 0.271018 0.0111521 0 0 0 0 0 0 0 0 0 125.688 283.796 3.56954 5.8539 0 1 1 2.84E-24 6.76E-28 1 1 1 1 73.2046 53.3108 3.88556 4.38275 0 670.361 940.853 19.0382 19.4071 0 1 2.72E+00 0 0 73.2046 53.3108 102.179 102.179 178.845 316.901 0
109_091291145_091291205 1426.55 72.5287 -2.95E-01 7.21E-02 4.16E-05 0 0 1 1 4.57E+02 2.32E+02 9.51E+00 7.56E+00 3 1 2 0 27 27 1.60E+02 1.23E+02 162 122 9.26E+00 1.18E+01 202 202 3.33E+01 4.23E+01 33 42 4.18E+00 4.62E+00 0 0 0 0 0.0337175 -0.153067 0 0 0 0 0 0 0 0 0 85.7256 69.8494 1.78234 2.27907 0 1 1 7.10E-28 1.95E-22 1 1 1 1 74.4596 53.5209 4.18188 4.61822 0 457.219 231.568 9.50616 7.55566 0 1 -4.10E+00 0 0 74.4596 53.5209 105.851 105.851 140.137 103.164 0
107_095544411_095544464 1447.32 74 -1.13E-01 5.95E-02 5.69E-02 0 0 1 1 5.58E+02 4.30E+02 1.68E+01 1.30E+01 1 0 1 0 30 30 1.80E+02 1.83E+02 182 184.5 1.72E+01 2.14E+01 190 190 3.35E+01 4.19E+01 33 42 4.34E+00 4.41E+00 0 0 0 0 0.157938 -0.0504739 0 0 0 0 0 0 0 0 0 104.622 129.67 3.14454 3.91596 0 1 1 6.20E-25 8.83E-25 1 1 1 1 75.7113 53.73 4.33603 4.40507 0 558.004 429.887 16.7715 12.9823 0 1 -1.90E+00 0 0 75.7113 53.73 109.981 109.981 160.285 163.194 0
112_053302210_053302270 1468.52 74.4925 6.93E-02 1.04E-01 5.04E-01 0 0 1 1 1.62E+02 1.89E+02 1.04E+01 8.05E+00 0 0 0 0 32 32 1.07E+02 1.11E+02 106 107 1.10E+01 1.37E+01 184 184 3.36E+01 4.20E+01 34 42 4.13E+00 4.45E+00 0 0 0 0 0.252266 -0.034777 0 0 0 0 0 0 0 0 0 30.2907 57.1557 1.94169 2.42897 0 1 1 1.65E-16 1.04E-21 1 1 1 1 76.9593 53.9381 4.12512 4.45435 1 161.556 189.485 10.356 8.05263 0 1 6.68E-01 0 0 76.9593 53.9381 93.0485 93.0485 87.202 90.8877 0
112_053279961_053280021 1489.79 74.8 -2.31E-01 1.13E-01 4.09E-02 0 0 1 1 2.05E+02 1.21E+02 9.74E+00 7.26E+00 0 0 0 0 30 30 1.17E+02 9.05E+01 115.5 91.5 1.00E+01 1.20E+01 178 178 3.33E+01 4.31E+01 33 43 3.93E+00 5.16E+00 0 0 0 0 -0.0442823 -0.143528 0 0 0 0 0 0 0 1 0 38.463 36.3549 1.82595 2.18918 0 1 1 1.40E-19 9.59E-17 1 1 1 1 78.2036 54.1451 3.92834 5.16002 0 205.143 120.525 9.73875 7.25767 0 1 -2.04E+00 0 0 78.2036 54.1451 109.4 109.4 96.6187 70.294 0
102_038304984_038305043 1511.23 74.4086 2.27E-01 5.92E-02 1.26E-04 0 0 1 1 4.25E+02 7.17E+02 1.44E+01 2.67E+01 0 0 1 0 28 28 1.59E+02 2.71E+02 157.5 264 1.43E+01 4.27E+01 188 188 3.34E+01 4.34E+01 33 43 4.23E+00 4.77E+00 0 0 0 0 0.316616 -0.0619762 0 0 0 0 0 0 0 1 0 79.6633 216.22 2.70084 8.06413 0 1 1 2.14E-22 4.90E-21 1 1 1 1 79.4438 54.351 4.23181 4.77289 0 424.886 716.822 14.405 26.7345 0 1 3.84E+00 0 0 79.4438 54.351 108.817 108.817 139.059 250.365 0
103_008649337_008649386 1531.79 74.4316 3.48E-01 5.99E-02 6.41E-09 0 0 1 1 4.55E+02 1.01E+03 1.72E+01 2.78E+01 0 0 0 0 29 29 1.66E+02 3.60E+02 164 353 1.73E+01 4.51E+01 188 188 3.32E+01 4.26E+01 33 42 3.90E+00 4.98E+00 0 0 0 0 0.428291 0.0152544 0 0 0 0 0 0 0 0 0 85.3911 305.893 3.21631 8.38242 0 1 1 1.43E-21 3.27E-25 1 1 1 1 80.6779 54.5555 3.90044 4.9815 0 455.435 1014.11 17.1543 27.7897 0 1 5.81E+00 0 0 80.6779 54.5555 110.558 110.558 146.021 340.242 0
115_038986106_038986166 1552.67 74.6269 6.12E-01 3.30E-01 6.35E-02 22.5346 0 1 1 2.25E+01 9.22E+01 9.15E+00 6.78E+00 2 2 0 1 25 25 8.18E+01 8.26E+01 81 84 8.58E+00 1.02E+01 187 187 3.35E+01 4.25E+01 33 42 4.23E+00 5.35E+00 0 0 0 0 0.127375 0.163028 0 0 0 0 0 0 0 0 0 -0.0682044 27.801 1.7153 2.0462 0 0 1 0.969089 4.39E-13 1 1 0 1 81.9082 54.759 4.22509 5.35442 0 -0.363769 92.1671 9.14861 6.78364 0 1 1.86E+00 0 0 81.9082 54.759 91.67 91.67 61.792 62.354 0
107_095530667_095530723 1575.71 73.6471 4.28E-01 8.19E-02 1.67E-07 0 0 1 1 1.63E+02 4.37E+02 1.46E+01 1.51E+01 0 0 0 0 30 30 1.14E+02 1.87E+02 116 182 1.50E+01 2.50E+01 199 199 3.26E+01 4.17E+01 33 42 4.16E+00 4.38E+00 0 0 0 0 -0.00420514 -0.018349 0 0 0 0 0 0 0 0 0 30.5604 131.838 2.7414 4.5666 0 1 1 4.54E-12 4.96E-23 1 1 1 1 83.1396 54.9619 4.16174 4.3757 0 162.994 437.075 14.6213 15.1394 0 1 5.23E+00 0 0 83.1396 54.9619 104.031 104.031 93.652 166.594 0
102_062443349_062443408 1594.75 76.0317 -2.11E-01 6.45E-02 1.06E-03 0 0 1 1 5.19E+02 3.19E+02 2.48E+01 1.27E+01 0 0 0 3 28 28 1.82E+02 1.51E+02 180.5 151.5 2.46E+01 2.03E+01 168 168 3.34E+01 4.26E+01 33 43 4.20E+00 4.56E+00 0 0 0 0 0.258439 -0.00952055 0 0 0 0 0 0 0 0 0 97.2449 96.1941 4.64517 3.82771 0 1 1 2.63E-18 1.93E-20 1 1 1 1 84.3623 55.1631 4.20124 4.55539 0 518.658 318.906 24.7751 12.6898 0 1 -3.27E+00 0 0 84.3623 55.1631 90.9728 90.9728 161.559 131.151 0
113_085860653_085860705 1616.89 74.5595 3.46E-02 4.98E-02 4.87E-01 0 0 1 1 1.93E+03 2.09E+03 6.63E+01 5.05E+01 0 0 0 0 28 28 4.47E+02 6.85E+02 454 669 6.57E+01 8.07E+01 191 191 3.26E+01 4.13E+01 32 41 4.49E+00 4.17E+00 0 0 0 0 0.601898 -0.0960312 0 0 0 0 0 0 0 0 0 361.598 629.994 12.4247 15.2416 0 1 1 6.10E-22 5.81E-26 1 1 1 1 85.5808 55.3631 4.49415 4.16653 0 1928.59 2088.58 66.2674 50.5297 0 1 6.94E-01 0 0 85.5808 55.3631 103.418 103.418 427.131 665.151 0

Total number of rows: 42850

Table truncated, full table size 19313 Kbytes.




Supplementary file Size Download File type/resource
GSM133003.txt.gz 10.7 Mb (ftp)(http) TXT

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