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Sample GSM385226 Query DataSets for GSM385226
Status Public on Dec 22, 2010
Title US22502595_251269411255
Sample type RNA
 
Channel 1
Source name LCM Inf 4 week 4 B6
Organism Mus musculus
Characteristics cell type: Granuloma
protocol: Infected
biological replicate: 4
time: week 4
strain: wt C57BL/6
Extracted molecule total RNA
Extraction protocol RNA was isolated using Paradise reagents and spin columns according to manufacturer’s instructions. RNA was quantified and measured for purity using a NanoSpec (Nanometrics, Sunnyvale, CA, USA).
Label Cy3
Label protocol A total of 4 µg RNA was reverse transcribed using an oligo-dT-T7-promotor primer in a fluorescent linear amplification reaction (Agilent Technologies, Santa Clara, CA, USA). cRNA was labeled with Cyanine 3-CTP or Cyanine 5-CTP (NEB Life Science Products) in a T7 polymerase amplification reaction according to the supplier’s protocol.
 
Channel 2
Source name LCM control Naive week 5 pool
Organism Mus musculus
Characteristics cell type: Granuloma
protocol: control Naive
time: week 5
strain: wt C57BL/6
Extracted molecule total RNA
Extraction protocol RNA was isolated using Paradise reagents and spin columns according to manufacturer’s instructions. RNA was quantified and measured for purity using a NanoSpec (Nanometrics, Sunnyvale, CA, USA).
Label Cy5
Label protocol A total of 4 µg RNA was reverse transcribed using an oligo-dT-T7-promotor primer in a fluorescent linear amplification reaction (Agilent Technologies, Santa Clara, CA, USA). cRNA was labeled with Cyanine 3-CTP or Cyanine 5-CTP (NEB Life Science Products) in a T7 polymerase amplification reaction according to the supplier’s protocol.
 
 
Hybridization protocol 1.25 µg of each labeled cRNA was mixed, fragmented and hybridized to whole mouse genome 44k microarrays (Product no. G4122A) according to the supplier’s protocol (Agilent Technologies).
Scan protocol Scanning of microarrays was performed with 5 µm resolution using a DNA microarray laser scanner (Agilent Technologies).
Features were extracted with an image analysis tool Version A4.045 (Agilent Technologies) using default settings.
Description Granulomas were isolated from tissue sections using a PALM Zeiss laser capture microdissection apparatus (Carl Zeiss, Jena, Germany) immediately after staining. Adhesive caps were used to collect multiple microdissected granulomas from 3-8 lung sections from each of three mice. Granulomas from a single mouse were digested with proteinase K solution overnight at 55°C.
Data processing Data analysis was carried out on the Rosetta Inpharmatics (Seattle, WA, USA) platform (Resolver Built 3.0.0.3.22). Features detected as differentially regulated with a P-value ≤ 0.05 and at least ± 2-fold difference in signal intensity in both experiments were included in datasets. Datasets containing the GenBank accession numbers and fold changes were uploaded into Ingenuity pathway analysis software (Ingenuity Systems, Redwood City, CA, USA).
 
Submission date Mar 23, 2009
Last update date Dec 22, 2010
Contact name Hans-Joachim Mollenkopf
E-mail(s) mollenkopf@mpiib-berlin.mpg.de
Phone +49 30 28460 482
Organization name Max-Planck-Institute for Infection Biology
Lab Microarray/Genomics Core Facility
Street address Charitéplatz 1
City Berlin
ZIP/Postal code 10117
Country Germany
 
Platform ID GPL2872
Series (1)
GSE15335 Lymphoid function of the tuberculous granuloma

Data table header descriptions
ID_REF
VALUE -[INV_VALUE]; logRatio (base 10) represents Cy3/Cy5
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
INV_VALUE LogRatio (base 10) represents Cy5/Cy3 for each sample pair

Data table
ID_REF 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 INV_VALUE
1 1.86 1.53E-01 7.04E-34 0 128.087 1 1 9.27E+03 1.28E+02 9.84E+01 1.28E+01 2 3 0 0 116 116 7.00E+02 8.39E+01 689.5 84 7.25E+01 1.33E+01 1253 1253 5.10E+01 8.15E+01 51 81 5.80E+00 1.24E+01 0 0 0 0 -0.0876968 4.64E-05 0 0 0 0 0 0 0 0 0 634.541 1.18758 6.73434 1.23821 -0.0876968 1 0 8.47E-111 0.357753 1 1 1 0 65.7432 82.6917 5.79977 12.4108 0 9272.86 12.2565 98.4123 12.779 -0.0876968 1 -1.21E+01 0 0 65.7432 82.6917 -1.86E+00
2 0.00E+00 5.46E-01 1.00E+00 119.746 93.5169 1 1 1.20E+02 9.35E+01 1.53E+01 8.96E+00 0 1 0 0 117 117 6.75E+01 8.26E+01 68 83 8.18E+00 1.30E+01 1024 1024 5.09E+01 8.22E+01 50 82 5.90E+00 1.26E+01 0 0 0 0 0.13846 5.72E-06 0 0 0 0 0 0 0 0 0 1.74382 -0.0826635 0.756405 1.20583 0.13846 0 0 0.0268021 0.948125 1 1 0 0 65.7775 82.6895 5.90231 12.5797 0 35.3786 -0.614516 15.3459 8.96404 0.13846 1 -1.97E-01 0 1 65.7775 82.6895 0.00E+00
3 0.102 6.33E-02 1.09E-01 0 0 1 1 1.65E+03 1.30E+03 3.08E+01 3.06E+01 1 2 0 0 115 115 1.73E+02 2.16E+02 173 210 2.15E+01 3.34E+01 1113 1113 5.11E+01 8.27E+01 51 82 5.99E+00 1.32E+01 0 0 0 0 -0.105319 4.85E-05 0 0 0 0 0 0 0 0 0 107.142 132.852 2.0012 3.11761 -0.105319 1 1 2.31E-83 5.31E-73 1 1 1 1 65.8148 82.6871 5.98669 13.2037 1 1646.94 1303.49 30.7616 30.5887 -0.105319 1 -1.60E+00 0 0 65.8148 82.6871 -1.02E-01
4 -0.0329 5.12E-02 5.20E-01 0 0 1 1 3.92E+03 4.23E+03 4.77E+01 5.84E+01 2 0 1 0 117 117 3.19E+02 5.15E+02 319 508 3.34E+01 6.47E+01 1086 1086 5.08E+01 8.24E+01 50 82 5.70E+00 1.30E+01 0 0 0 0 -0.00353266 2.78E-05 0 0 0 0 0 0 0 0 0 253.533 432.811 3.08827 5.98582 -0.00353266 1 1 5.09E-105 7.51E-99 1 1 1 1 65.852 82.6847 5.70283 13.0126 1 3916.87 4225.25 47.7112 58.4356 -0.00353266 1 6.43E-01 0 0 65.852 82.6847 3.29E-02
5 0.23 5.65E-02 4.52E-05 0 0 1 1 3.35E+03 1.97E+03 4.96E+01 3.19E+01 2 5 0 0 113 113 2.82E+02 2.86E+02 281 286 3.40E+01 3.49E+01 1120 1120 5.08E+01 8.32E+01 51 83 6.04E+00 1.38E+01 0 0 0 0 0.109395 -1.91E-05 0 0 0 0 0 0 0 0 0 215.978 202.99 3.19866 3.28234 0.109395 1 1 6.27E-93 4.89E-90 1 1 1 1 65.8891 82.6825 6.04434 13.8353 0 3352.43 1972.35 49.6498 31.8928 0.109395 1 -4.08E+00 0 0 65.8891 82.6825 -2.30E-01
6 0.00E+00 5.31E-01 1.00E+00 86.4709 135.274 1 1 8.65E+01 1.35E+02 1.16E+01 1.22E+01 0 2 0 0 118 118 6.80E+01 8.46E+01 68 85.5 8.47E+00 1.31E+01 1054 1054 5.08E+01 8.34E+01 50 82 5.82E+00 1.33E+01 0 0 0 0 -0.0652358 1.33E-05 0 0 0 0 0 0 0 0 0 2.04141 1.90376 0.779549 1.20163 -0.0652358 0 0 0.0118674 0.135974 1 1 0 0 65.9247 82.681 5.81953 13.3271 0 30.3328 19.3237 11.5831 12.1968 -0.0652358 1 3.66E-01 0 0 65.9247 82.681 0.00E+00
7 1.88 1.55E-01 4.92E-34 0 128.895 1 1 9.83E+03 1.29E+02 8.28E+01 1.24E+01 3 1 0 1 113 113 7.25E+02 8.65E+01 720 86 5.91E+01 1.30E+01 1124 1124 5.07E+01 8.37E+01 50 83 6.08E+00 1.27E+01 0 0 0 0 -0.14288 -2.00E-05 0 0 0 0 1 0 0 0 0 659.349 3.86931 5.55649 1.22597 -0.14288 1 1 8.80E-120 0.00307575 1 1 1 0 65.9605 82.6794 6.07618 12.7353 0 9825.33 39.1615 82.8003 12.4081 -0.14288 1 -1.22E+01 0 0 65.9605 82.6794 -1.88E+00
8 -0.381 6.53E-02 5.52E-09 0 0 1 1 1.10E+03 2.64E+03 2.35E+01 4.35E+01 5 2 1 0 114 114 1.37E+02 3.53E+02 137 359 1.62E+01 4.76E+01 1047 1047 5.10E+01 8.30E+01 51 83 6.10E+00 1.19E+01 0 0 0 0 -0.112566 -6.45E-05 0 0 0 0 0 0 0 0 0 71.1967 270.357 1.52126 4.45471 -0.112566 1 1 5.17E-77 8.96E-89 1 1 1 1 65.9963 82.6778 6.10425 11.9289 0 1098.85 2641.91 23.4791 43.531 -0.112566 1 5.83E+00 0 0 65.9963 82.6778 3.81E-01
9 0.00E+00 5.09E-01 1.00E+00 0 137.067 1 1 9.34E+01 1.37E+02 1.03E+01 1.37E+01 1 0 1 0 116 116 7.28E+01 9.07E+01 73 88.5 7.99E+00 1.36E+01 1142 1142 5.15E+01 8.30E+01 51 83 6.16E+00 1.26E+01 0 0 0 0 -0.0090168 -3.55E-05 0 0 0 0 0 0 0 0 0 6.71758 7.97849 0.741961 1.26616 -0.0090168 1 1 7.86E-15 1.37E-08 1 1 0 0 66.0324 82.6767 6.16367 12.6401 1 93.4309 86.5169 10.3195 13.73 -0.0090168 1 3.27E-01 0 0 66.0324 82.6767 0.00E+00
10 0.306 5.55E-02 3.59E-08 0 0 1 1 6.33E+03 3.13E+03 7.72E+01 5.49E+01 1 1 0 0 116 116 4.77E+02 4.03E+02 476.5 405.5 5.39E+01 6.04E+01 1060 1060 5.16E+01 8.30E+01 51 82 6.00E+00 1.31E+01 0 0 0 0 0.147078 -7.58E-05 0 0 0 0 0 0 0 0 0 410.888 320.082 5.00844 5.60675 0.147078 1 1 4.48E-104 1.01E-86 1 1 1 1 66.0687 82.6762 6.00048 13.0835 0 6331.55 3132.81 77.1772 54.8761 0.147078 1 -5.51E+00 0 0 66.0687 82.6762 -3.06E-01
11 0.067 3.84E-01 8.61E-01 0 0 1 1 1.63E+02 1.40E+02 1.40E+01 1.44E+01 0 1 0 0 118 118 7.76E+01 9.59E+01 77 96 1.07E+01 1.48E+01 1064 1064 5.13E+01 8.25E+01 51 82 6.27E+00 1.28E+01 0 0 0 0 0.0447922 -1.36E-05 0 0 0 0 0 0 0 0 0 11.4966 13.2055 0.986005 1.35863 0.0447922 1 1 3.11E-21 2.37E-16 1 1 0 0 66.1051 82.6759 6.27004 12.7911 0 163.454 140.084 14.0186 14.4124 0.0447922 1 -1.75E-01 0 0 66.1051 82.6759 -6.70E-02
12 0.00E+00 4.79E-01 1.00E+00 0 143.576 1 1 1.01E+02 1.44E+02 1.12E+01 1.36E+01 1 1 1 0 117 117 7.34E+01 8.75E+01 72 86 8.69E+00 1.36E+01 1045 1045 5.10E+01 8.25E+01 51 82 5.85E+00 1.32E+01 0 0 0 0 -0.0580418 -4.37E-05 0 0 0 0 0 0 0 0 0 7.26049 4.87127 0.803769 1.25514 -0.0580418 1 1 7.46E-15 0.0003191 1 1 0 0 66.1412 82.6757 5.84636 13.2314 0 100.914 52.8587 11.1716 13.6197 -0.0580418 1 3.19E-01 0 0 66.1412 82.6757 0.00E+00
13 0.00E+00 5.31E-01 1.00E+00 85.0829 137.55 1 1 8.51E+01 1.38E+02 1.16E+01 1.45E+01 4 1 0 0 116 116 6.88E+01 8.53E+01 69 85 8.62E+00 1.51E+01 1143 1143 5.14E+01 8.24E+01 51 81 5.86E+00 1.32E+01 0 0 0 0 0.0454353 -2.73E-05 0 0 0 0 0 0 0 0 0 2.64172 2.66916 0.800262 1.40037 0.0454353 1 0 0.00159814 0.0686431 1 1 0 0 66.1772 82.6757 5.85955 13.2429 0 38.3588 27.7239 11.6201 14.5453 0.0454353 1 3.93E-01 0 0 66.1772 82.6757 0.00E+00
14 1.91 1.57E-01 2.99E-34 0 132.669 1 1 1.08E+04 1.33E+02 1.07E+02 1.12E+01 1 2 0 0 115 115 7.95E+02 8.57E+01 786 86 7.72E+01 1.19E+01 1066 1066 5.12E+01 8.21E+01 51 81 5.70E+00 1.31E+01 0 0 0 0 0.12353 4.53E-05 0 0 0 0 0 0 0 0 0 728.595 2.98488 7.19544 1.10742 0.12353 1 0 1.37E-113 0.0123073 1 1 1 0 66.2139 82.676 5.69691 13.0692 0 10824.9 30.3004 106.904 11.2417 0.12353 1 -1.22E+01 0 0 66.2139 82.676 -1.91E+00
15 0.00E+00 5.18E-01 1.00E+00 93.6627 132.152 1 1 9.37E+01 1.32E+02 1.18E+01 1.38E+01 0 2 0 0 118 118 7.19E+01 8.43E+01 71 81.5 8.91E+00 1.42E+01 1087 1087 5.23E+01 8.07E+01 52 80 6.52E+00 1.26E+01 0 0 0 0 -0.0903172 -1.97E-05 0 0 0 0 0 0 0 0 0 5.69746 1.66275 0.820554 1.31061 -0.0903172 1 0 4.33E-10 0.22531 1 1 0 0 66.2517 82.6762 6.51579 12.5955 0 81.8995 17.4456 11.7952 13.7509 -0.0903172 1 2.88E-01 0 0 66.2517 82.6762 0.00E+00
16 -0.0732 4.95E-02 1.39E-01 0 0 1 1 2.33E+04 2.75E+04 2.66E+02 2.68E+02 0 0 0 0 119 119 1.69E+03 2.70E+03 1643 2735 2.03E+02 2.78E+02 1001 1001 5.37E+01 8.52E+01 53 84 7.22E+00 1.41E+01 0 0 0 0 0.219437 0.000103945 0 0 0 0 0 0 0 1 0 1622.28 2617.76 18.5795 25.4866 0.219437 1 1 4.42E-109 2.54E-117 1 1 1 1 66.2892 82.6765 7.22272 14.0927 1 23263.3 27532.4 266.427 268.056 0.219437 1 1.48E+00 0 0 66.2892 82.6765 7.32E-02
17 0.164 5.62E-02 3.44E-03 0 0 1 1 2.83E+03 1.94E+03 4.20E+01 3.35E+01 1 0 0 0 120 120 2.49E+02 2.82E+02 246.5 283 2.96E+01 3.78E+01 1133 1133 5.20E+01 8.17E+01 51 81 6.39E+00 1.27E+01 0 0 0 0 0.152051 1.59E-06 0 0 0 0 0 0 0 0 0 182.54 199.464 2.7063 3.45041 0.152051 1 1 3.06E-97 3.89E-90 1 1 1 1 66.3271 82.6778 6.38741 12.7336 1 2831.5 1939.38 41.9794 33.5483 0.152051 1 -2.93E+00 0 0 66.3271 82.6778 -1.64E-01
18 0.00E+00 5.27E-01 1.00E+00 88.487 134.607 1 1 8.85E+01 1.35E+02 1.23E+01 1.45E+01 0 2 0 0 119 119 7.05E+01 8.48E+01 70 81 9.33E+00 1.51E+01 1102 1102 5.14E+01 8.17E+01 51 82 6.14E+00 1.29E+01 0 0 0 0 0.0468062 -2.75E-05 0 0 0 0 0 0 0 0 0 4.13951 2.15325 0.854946 1.38826 0.0468062 1 0 5.74E-06 0.137474 1 1 0 0 66.3647 82.6787 6.14349 12.855 0 59.623 22.5469 12.3141 14.5367 0.0468062 1 3.46E-01 0 0 66.3647 82.6787 0.00E+00
19 0.00E+00 5.27E-01 1.00E+00 84.2342 140.357 1 1 8.42E+01 1.40E+02 1.12E+01 1.32E+01 1 0 0 0 119 119 7.19E+01 8.52E+01 72 85 8.60E+00 1.36E+01 1145 1145 5.15E+01 8.22E+01 51 81 5.93E+00 1.32E+01 0 0 0 0 0.143123 1.02E-05 0 0 0 0 0 0 0 0 0 5.48846 2.52155 0.788465 1.24802 0.143123 1 0 3.52E-10 0.0558388 1 1 0 0 66.4023 82.6801 5.92669 13.2267 0 78.0057 26.7577 11.2062 13.2435 0.143123 1 4.21E-01 0 0 66.4023 82.6801 0.00E+00
20 0.159 5.06E-02 1.61E-03 0 0 1 1 2.86E+04 1.98E+04 2.76E+02 1.80E+02 1 0 0 1 116 116 2.06E+03 1.97E+03 2026.5 1976 2.07E+02 1.85E+02 1050 1050 5.18E+01 8.27E+01 52 83 6.04E+00 1.26E+01 0 0 0 0 -0.0172777 -4.97E-07 0 0 0 0 0 0 0 0 0 1993.22 1890.34 19.2218 17.1394 -0.0172777 1 1 1.86E-115 1.42E-118 1 1 1 1 66.4401 82.6816 6.03504 12.5925 1 28642.3 19840.2 276.215 179.887 -0.0172777 1 -3.15E+00 0 0 66.4401 82.6816 -1.59E-01

Total number of rows: 43790

Table truncated, full table size 18134 Kbytes.




Supplementary file Size Download File type/resource
GSM385226_US22502595_251269411255_S01.tif.gz 105.4 Mb (ftp)(http) TIFF
Processed data included within Sample table

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