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Sample GSM90304 Query DataSets for GSM90304
Status Public on Jan 04, 2006
Title C57BL/6 vs. C57BL/6 Cholesterol
Sample type RNA
 
Channel 1
Source name C57BL/6
Organism Mus musculus
Characteristics Female C57BL/6 mice (6 weeks old, Charles River, Sulzfeld, Germany). The stomach was removed, and the stomach mucosa was scraped off with a sterile scalpel blade on liquid nitrogen until ~2/3 of the tissue was removed.
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name C57BL/6 Cholesterol
Organism Mus musculus
Characteristics Female C57BL/6 mice (6 weeks old, Charles River, Sulzfeld, Germany) were treated with 2% or 0% cholesterol diet (custom product (Altromin, Lage, Germany). The stomach was removed, and the stomach mucosa was scraped off with a sterile scalpel blade on liquid nitrogen until ~2/3 of the tissue was removed.
Extracted molecule total RNA
Label Cy5
 
 
Description Total RNA was prepared using the RNeasy protocol with on-column DNAse digestion (Qiagen, Hilden, Germany) and confirmed to be intact and free of contaminating DNA using an Agilent 2100 bioanalyzer and a RNA 6000 Nano LabChip kit (Agilent Technologies, Palo Alto, CA). A custom tailored 'in situ' synthesized 60-mer oligonucleotide microarray (Agilent) comprising 8014 murine genes with immunological focus was used for expression profiling. RNA was amplified and labeled using a reverse-transcriptase/T7 polymerase linear amplification labeling kit (Agilent), and 1.5 mg of respective cRNAs labeled either with Cy3 or Cy5 were hybridized for 16 h at 65°C. Slides were used and processed according to the manufacturer's manuals.
Data processing Features were extracted with an Image Analysis software (Version A.7.5.1, Agilent). Intensities were normalized by local background correction and by rank consistency filtering with a combination of linear and LOWESS normalization. Data analysis was performed with Rosetta Resolver Biosoftware (Build 5.1.0.0.163, Rosetta Biosoftware, Seattle, WA).
 
Submission date Jan 02, 2006
Last update date Jan 04, 2006
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 GPL1868
Series (1)
GSE3878 Sugar turns benefit of cholesterol into immune evasion in Helicobacter pylori infected C57BL/6 mice

Data table header descriptions
ID_REF
Fold Change
P-value
Intensity1
Intensity2
Log(Intensity)
Ratio
VALUE
Log(Error)
X Dev

Data table
ID_REF Fold Change P-value Intensity1 Intensity2 Log(Intensity) Ratio VALUE Log(Error) X Dev
633390 -1.15913 0.9529 89.43199 77.15418 1.91943 0.86271 -0.06413 1.08578 -0.05907
633391 -1.04605 0.77732 1897.35498 1813.83301 3.26837 0.95598 -0.01955 0.06913 -0.28282
633392 -1.05515 0.68136 3260.46289 3090.04004 3.50162 0.94773 -0.02332 0.05678 -0.41061
633393 -1.04962 0.67032 18869.91992 17977.91992 4.26525 0.95273 -0.02103 0.0494 -0.4257
633394 1 1 61.88551 81.22634 1.85064 1 0 1.26903 0
633395 4.31428 0.71788 22.65265 97.72981 1.67257 4.31428 0.63491 1.75735 0.36129
633396 1.5134 0.33963 401.1008 607.02753 2.69323 1.5134 0.17995 0.18845 0.9549
633397 -1.02227 0.98806 143.0968 139.9798 2.15085 0.97822 -0.00956 0.63907 -0.01497
633398 1.04752 0.6859 10574.50977 11077.0498 4.03434 1.04752 0.02016 0.04986 0.40442
633399 1.38966 0.62375 265.38062 368.78989 2.49532 1.38966 0.14291 0.29133 0.49054
633400 1.20626 0.90364 122.2062 147.41251 2.12781 1.20626 0.08144 0.67273 0.12106
633401 1.23081 0.83338 190.539 234.5177 2.32508 1.23081 0.09019 0.42872 0.21037
633402 -1.07281 0.79292 886.35773 826.19891 2.93235 0.93213 -0.03052 0.11628 -0.26252
633403 -1.43388 0.86115 120.2241 83.84537 2.00174 0.69741 -0.15651 0.89479 -0.17491
633404 -1.14535 0.2356 15982.26953 13954.09961 4.17417 0.8731 -0.05894 0.04969 -1.18607
633405 1.07985 0.9321 223.3297 241.16229 2.36563 1.07985 0.03336 0.39159 0.0852
633406 -1.07268 0.74337 1181.78198 1101.70605 3.0573 0.93224 -0.03047 0.09308 -0.32739
633407 -1.60478 0.79917 140.47189 87.53329 2.04488 0.62314 -0.20542 0.80737 -0.25443
633408 1.20653 0.93505 82.03199 98.97382 1.95475 1.20653 0.08154 1.00059 0.08149
633409 -1.02565 0.90122 1238.547 1207.57495 3.08741 0.97499 -0.011 0.08861 -0.12412

Total number of rows: 8014

Table truncated, full table size 615 Kbytes.




Supplementary data files not provided

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