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Sample GSM132938 Query DataSets for GSM132938
Status Public on Apr 20, 2007
Title US22502648_251357810001_S01_44k_CGH
Sample type genomic
 
Channel 1
Source name Neuralized EBs Input Biological Rep#1 Technical Rep#1
Organism Mus musculus
Characteristics Mouse embryoid bodies treated to express neuronal progenitors
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 ChIP Biological Rep#1 Technical Rep#1
Organism Mus musculus
Characteristics Mouse embryoid bodies treated to express neuronal progenitors
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 #1. 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 Log Ratio value- used in all computational analyses
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 1226.11 105.258 -3.42E-01 1.33E-01 1.03E-02 0 0 1 1 1.89E+02 8.59E+01 1.41E+01 6.19E+00 0 0 0 0 29 29 1.20E+02 6.23E+01 120 61 1.57E+01 7.38E+00 197 197 2.82E+01 3.32E+01 28 33 3.58E+00 3.12E+00 0 0 0 0 0.398621 -0.0487305 0 0 0 0 0 0 1 1 0 39.1498 19.0183 2.91775 1.37023 0 1 1 8.75E-14 2.55E-14 1 1 1 1 80.6433 43.3266 3.58418 3.11732 0 188.921 85.8835 14.0799 6.18773 0 1 -2.57E+00 0 0 80.6433 43.3266 107.047 107.047 99.8151 42.7018 0
102_140194858_140194918 1247.13 106.287 1.91E-04 1.81E-01 9.99E-01 0 0 1 1 9.11E+01 9.11E+01 1.46E+01 7.29E+00 0 0 0 0 29 29 1.01E+02 6.38E+01 101 63 1.63E+01 8.69E+00 187 187 2.75E+01 3.25E+01 27 32 3.63E+00 3.49E+00 0 0 0 0 0.255356 0.189174 0 0 0 0 0 0 1 1 0 18.8725 20.1759 3.02558 1.61434 0 1 1 9.66E-07 3.68E-13 1 1 1 1 81.6792 43.6517 3.62986 3.48913 1 91.0711 91.1112 14.6003 7.29008 0 1 1.06E-03 0 0 81.6792 43.6517 104.642 104.642 80.5737 44.1846 0
113_040296111_040296156 1268.67 105.231 6.44E-02 5.42E-02 2.34E-01 0 0 1 1 6.60E+02 7.66E+02 2.51E+01 1.81E+01 0 0 0 1 29 29 2.19E+02 2.14E+02 225 218 2.80E+01 2.15E+01 188 188 2.75E+01 3.33E+01 27 33 3.54E+00 3.96E+00 0 0 0 0 0.438721 0.0748846 0 0 0 0 0 0 1 1 0 136.792 169.545 5.19891 4.00081 0 1 1 2.41E-21 4.08E-27 1 1 1 1 82.6908 43.9725 3.54422 3.96328 0 660.104 765.637 25.0879 18.067 0 1 1.19E+00 0 0 82.6908 43.9725 106.451 106.451 199.505 193.874 0
102_146585229_146585289 1288.57 106.378 2.77E-01 7.41E-02 1.81E-04 0 0 1 1 2.20E+02 4.16E+02 1.15E+01 1.26E+01 0 0 0 0 32 32 1.29E+02 1.36E+02 129.5 138 1.35E+01 1.58E+01 177 177 2.76E+01 3.26E+01 27 32 3.36E+00 3.51E+00 0 0 0 0 0.160995 -0.00520908 0 0 0 0 0 0 1 1 0 45.5508 92.1769 2.38231 2.7893 0 1 1 6.79E-19 5.41E-26 1 1 1 1 83.6992 44.2918 3.35907 3.51319 0 219.81 416.256 11.4961 12.596 0 1 3.74E+00 0 0 83.6992 44.2918 105.851 105.851 109.272 116.826 0
105_036339363_036339408 1309.51 104.833 1.42E-01 5.91E-02 1.66E-02 0 0 1 1 4.30E+02 5.96E+02 1.33E+01 1.87E+01 1 0 4 0 23 23 1.74E+02 1.77E+02 173 175 1.33E+01 1.99E+01 205 205 2.77E+01 3.34E+01 27 33 3.28E+00 3.69E+00 0 0 0 0 0.403644 0.121913 0 0 0 0 0 0 1 1 0 89.1452 131.995 2.76361 4.14354 0 1 1 3.52E-20 5.43E-20 1 1 1 1 84.7244 44.6133 3.27815 3.69045 0 430.179 596.07 13.3361 18.7116 0 1 2.40E+00 0 0 84.7244 44.6133 102.179 102.179 153.892 156.966 0
102_051070802_051070862 1331.45 105.866 3.91E-02 5.44E-02 4.72E-01 0 0 1 1 6.56E+02 7.18E+02 3.44E+01 3.11E+01 0 0 0 0 29 29 2.22E+02 2.04E+02 226 216 3.84E+01 3.70E+01 181 181 2.76E+01 3.35E+01 27 34 3.46E+00 3.32E+00 0 0 0 0 0.829113 0.0600127 0 0 0 0 0 0 1 1 0 135.948 158.964 7.13524 6.87634 0 1 1 1.38E-17 8.30E-20 1 1 1 1 85.7412 44.9325 3.45788 3.31599 0 656.033 717.856 34.4318 31.0525 0 1 7.19E-01 0 0 85.7412 44.9325 102.179 102.179 201.712 184.254 0
108_056346561_056346621 1352.21 104.548 6.87E-01 7.79E-02 1.14E-18 0 0 1 1 1.98E+02 9.62E+02 1.85E+01 3.74E+01 0 0 0 0 29 29 1.28E+02 2.58E+02 126 260 2.06E+01 4.45E+01 213 213 2.75E+01 3.36E+01 27 34 3.25E+00 3.82E+00 0 0 0 0 0.731062 0.061049 0 0 0 0 0 0 1 1 0 40.9955 213.1 3.82463 8.2716 0 1 1 1.95E-11 4.59E-21 1 1 1 1 86.7286 45.2444 3.2483 3.8161 0 197.828 962.327 18.4562 37.3532 0 1 8.82E+00 0 0 86.7286 45.2444 102.8 102.8 107.746 238.702 0
102_051059490_051059540 1374.55 105.424 1.98E-01 6.50E-02 2.26E-03 0 0 1 1 3.13E+02 4.95E+02 1.38E+01 1.62E+01 0 0 4 0 28 28 1.53E+02 1.55E+02 151 156 1.51E+01 1.90E+01 188 188 2.80E+01 3.37E+01 28 34 3.60E+00 3.49E+00 0 0 0 0 0.301514 -0.0419012 0 0 0 0 0 0 1 1 0 64.9397 109.583 2.86054 3.59221 0 1 1 2.78E-19 1.38E-22 1 1 1 1 87.7389 45.5602 3.59862 3.48837 0 313.373 494.857 13.8038 16.2219 0 1 3.05E+00 0 0 87.7389 45.5602 104.642 104.642 132.701 135.5 0
108_084255925_084255985 1393.58 104.69 -7.00E-02 6.06E-02 2.48E-01 0 0 1 1 4.90E+02 4.17E+02 2.52E+01 1.92E+01 0 0 0 0 30 30 1.90E+02 1.38E+02 195 138.5 2.86E+01 2.33E+01 190 190 2.73E+01 3.37E+01 27 33 3.06E+00 3.73E+00 0 0 0 0 0.721048 0.1197 0 0 0 0 0 0 1 1 0 101.482 92.2908 5.22762 4.25781 0 1 1 3.44E-18 1.55E-19 1 1 1 1 88.7517 45.8759 3.06188 3.726 1 489.71 416.77 25.2264 19.2276 0 1 -1.16E+00 0 0 88.7517 45.8759 103.418 103.418 170.255 118.524 0
113_058886906_058886959 1416.58 105.655 -9.97E-02 6.50E-02 1.25E-01 0 0 1 1 4.23E+02 3.36E+02 2.80E+01 1.48E+01 0 0 0 0 31 31 1.77E+02 1.21E+02 180 120 3.23E+01 1.82E+01 183 183 2.78E+01 3.38E+01 28 34 3.38E+00 3.64E+00 0 0 0 0 0.468769 0.0496795 0 0 0 0 0 0 1 1 0 87.6561 74.4547 5.80411 3.2757 0 1 1 1.40E-15 1.35E-20 1 1 1 1 89.7632 46.1905 3.37559 3.6415 0 422.994 336.225 28.0083 14.7925 0 1 -1.53E+00 0 0 89.7632 46.1905 104.031 104.031 157.441 101.002 0
109_091291145_091291205 1438.66 105.784 3.08E-01 8.30E-02 2.05E-04 0 0 1 1 1.73E+02 3.52E+02 1.27E+01 1.57E+01 0 1 3 0 25 25 1.27E+02 1.24E+02 123 126 1.32E+01 1.74E+01 178 178 2.83E+01 3.36E+01 28 33 3.56E+00 3.90E+00 0 0 0 0 -0.508202 0.130602 0 0 0 0 0 0 1 1 0 35.9082 77.9764 2.63611 3.47617 0 1 1 7.02E-13 9.79E-18 1 1 1 1 90.7718 46.5036 3.56043 3.90341 0 173.279 352.129 12.7208 15.6978 0 1 3.71E+00 0 0 90.7718 46.5036 113.401 113.401 106.702 104.837 0
107_095544411_095544464 1458.62 106.041 1.49E-01 7.79E-02 5.64E-02 0 0 1 1 2.24E+02 3.15E+02 1.58E+01 1.42E+01 1 0 0 0 29 29 1.38E+02 1.17E+02 134 115 1.76E+01 1.69E+01 187 187 2.77E+01 3.35E+01 27 33 3.37E+00 3.71E+00 0 0 0 0 0.482863 0.120862 0 0 0 0 0 0 1 1 0 46.3957 69.8056 3.26538 3.14526 0 1 1 2.21E-14 1.89E-19 1 1 1 1 91.7767 46.8151 3.37216 3.71038 0 223.887 315.231 15.7574 14.2035 0 1 1.91E+00 0 0 91.7767 46.8151 111.704 111.704 118.194 96.9777 0
112_053302210_053302270 1479.93 105.684 4.25E-01 1.89E-01 2.43E-02 0 0 1 1 5.20E+01 1.38E+02 1.41E+01 9.02E+00 0 0 0 0 29 29 1.04E+02 7.78E+01 102 75 1.58E+01 1.08E+01 195 195 2.77E+01 3.37E+01 28 34 3.52E+00 3.72E+00 0 0 0 0 0.10741 0.0807582 0 0 0 0 0 0 1 1 0 10.7743 30.6683 2.92879 1.99777 0 1 1 0.00100674 2.31E-15 1 1 1 1 92.7775 47.1248 3.51928 3.72277 1 51.9923 138.493 14.1332 9.02161 0 1 2.25E+00 0 0 92.7775 47.1248 110.558 110.558 83.5737 58.1501 0
112_053279961_053280021 1500.57 105.838 3.93E-01 1.55E-01 1.13E-02 0 0 1 1 6.77E+01 1.67E+02 1.05E+01 1.17E+01 0 0 0 0 29 29 1.08E+02 8.44E+01 107 83 1.17E+01 1.39E+01 185 185 2.81E+01 3.47E+01 28 34 3.91E+00 4.26E+00 0 0 0 0 0.180913 -0.0174938 0 0 0 0 0 0 1 1 0 14.0194 37.0157 2.16862 2.58243 0 1 1 5.23E-07 1.44E-14 1 1 1 1 93.7737 47.4326 3.91042 4.26004 1 67.6519 167.157 10.4649 11.6618 0 1 2.53E+00 0 0 93.7737 47.4326 112.838 112.838 87.8151 64.8053 0
102_038304984_038305043 1522.2 105.256 -1.35E-01 6.55E-02 3.97E-02 0 0 1 1 4.38E+02 3.21E+02 2.38E+01 1.57E+01 0 0 0 0 30 30 1.86E+02 1.19E+02 189 117 2.71E+01 1.91E+01 188 188 2.84E+01 3.43E+01 29 34 3.64E+00 3.91E+00 0 0 0 0 0.708351 -0.00306712 0 0 0 0 0 0 1 1 0 90.7674 71.1281 4.94097 3.4799 0 1 1 1.47E-17 6.98E-19 1 1 1 1 94.7659 47.7386 3.63903 3.91194 0 438.007 321.203 23.8432 15.7147 0 1 -2.06E+00 0 0 94.7659 47.7386 102.179 102.179 165.555 99.2237 0
103_008649337_008649386 1542.71 105.58 -2.31E-01 6.29E-02 2.38E-04 0 0 1 1 5.78E+02 3.40E+02 2.73E+01 1.62E+01 0 0 0 0 30 30 2.16E+02 1.23E+02 223.5 120.5 3.09E+01 1.97E+01 183 183 2.81E+01 3.43E+01 28 34 3.49E+00 3.87E+00 0 0 0 0 0.403211 -0.0286812 0 0 0 0 0 0 1 1 0 119.871 75.2548 5.65024 3.59538 0 1 1 3.03E-19 3.69E-19 1 1 1 1 95.7621 48.0452 3.49169 3.86904 0 578.451 339.838 27.2658 16.2362 0 1 -3.67E+00 0 0 95.7621 48.0452 113.401 113.401 195.655 103.657 0
115_038986106_038986166 1564.31 105.398 5.62E-01 4.15E-01 1.76E-01 18.9119 0 1 1 1.89E+01 6.90E+01 1.22E+01 7.18E+00 1 2 0 0 27 27 9.61E+01 6.36E+01 97 62 1.32E+01 8.26E+00 194 194 2.81E+01 3.42E+01 28 34 3.92E+00 3.84E+00 0 0 0 0 0.400458 -0.0134201 0 0 0 0 0 0 1 1 0 -0.605041 15.2797 2.53168 1.58981 0 0 1 0.814066 3.66E-10 1 1 0 1 96.7532 48.35 3.91908 3.84106 0 -2.91969 69.0005 12.2169 7.17932 0 1 1.35E+00 0 0 96.7532 48.35 107.641 107.641 76.1701 43.9866 0
107_095530667_095530723 1586.81 104.814 -2.56E-01 1.11E-01 2.06E-02 0 0 1 1 2.16E+02 1.20E+02 2.12E+01 7.61E+00 0 2 0 0 28 28 1.42E+02 7.51E+01 150 73 2.32E+01 8.92E+00 205 205 2.87E+01 3.46E+01 28 34 3.48E+00 4.18E+00 0 0 0 0 0.236017 -0.0756989 0 0 0 0 0 0 1 1 0 44.7226 26.5004 4.39168 1.68617 0 1 1 9.28E-11 1.88E-15 1 1 1 1 97.706 48.6424 3.47759 4.17954 0 215.813 119.672 21.1925 7.61446 0 1 -2.31E+00 0 0 97.706 48.6424 104.031 104.031 122.451 55.4999 0
102_062443349_062443408 1606.18 105.83 3.83E-01 8.87E-02 1.56E-05 0 0 1 1 1.45E+02 3.50E+02 1.30E+01 1.73E+01 1 1 0 0 29 29 1.29E+02 1.26E+02 129 126 1.45E+01 2.06E+01 189 189 2.78E+01 3.52E+01 28 35 3.57E+00 4.10E+00 0 0 0 0 0.157536 -0.0276975 0 0 0 0 0 0 1 1 0 30.0155 77.4747 2.68691 3.83095 0 1 1 6.96E-12 2.40E-18 1 1 1 1 98.6742 48.9391 3.57187 4.10355 0 144.843 349.863 12.9659 17.2999 0 1 4.32E+00 0 0 98.6742 48.9391 112.838 112.838 108.712 106.771 0
113_085860653_085860705 1627.54 105.342 -4.11E-02 5.07E-02 4.17E-01 0 0 1 1 1.39E+03 1.27E+03 4.18E+01 4.80E+01 1 1 2 0 28 28 3.88E+02 3.29E+02 389 326.5 4.58E+01 5.62E+01 184 184 2.86E+01 3.44E+01 29 34 3.73E+00 3.59E+00 0 0 0 0 0.288102 -0.187082 0 0 0 0 0 0 1 1 0 288.161 280.127 8.66199 10.6201 0 1 1 1.77E-23 8.00E-21 1 1 1 1 99.6251 49.2299 3.72836 3.59184 1 1390.55 1265.01 41.7993 47.9586 0 1 -8.11E-01 0 0 99.6251 49.2299 100.293 100.293 367.808 309.714 0

Total number of rows: 42850

Table truncated, full table size 19310 Kbytes.




Supplementary file Size Download File type/resource
GSM132938.txt.gz 10.7 Mb (ftp)(http) TXT

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