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Sample GSM566447 Query DataSets for GSM566447
Status Public on Jan 01, 2011
Title PFBS_5
Sample type RNA
 
Source name ApoE3L.CETP mice liver
Organism Mus musculus
Characteristics diet group: PFBS
tissue: liver
gender: male
background strain: C57Bl/6
mouse model: E3L.CETP
Treatment protocol Male E3L.CETP mice were fed a cholesterol-rich Western-type diet for 4-6 weeks. Mice were randomized and fed the same diet without (time-matched control group) or with different PFAS (0.03% PFBS, 0.006% PFHxS or 0.003% PFOS) for another 4 weeks. Livers were isolated for hepatic lipid analysis and hepatic gene expression analysis using an Affymetrix technology platform and Affymetrix GeneChip® mouse genome 430 2.0 arrays
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from individual livers using RNA-Bee (Bio-Connect, Huissen, The Netherlands) and glass beads according to the manufacturer's instructions. The RNA was further purified using the nucleospin RNA II kit (Machery-Nagel, Düren, Germany) according to the manufacturer's instructions. The integrity of each RNA sample obtained was examined by Agilent Lab-on-a-chip technology using a RNA 6000 Nano LabChip kit and a Bioanalyzer 2100 (Agilent Technologies, Amstelveen, The Netherlands).
Label biotin
Label protocol The Affymetrix 3’ IVT-Express labeling Kit (#901229) and the protocols optimized by Affymetrix were used to synthesize Biotin-labeled cRNA (from 100 ng of total RNA) for microarray hybridization. For the hybridization 15 μg cRNA was used for further fragmentation and finally 10 μg for the hybridizations. The quality of intermediate products (that is, biotin-labeled cRNA and fragmented cRNA) was again checked.
 
Hybridization protocol Briefly, fragmented cRNA was mixed with spiked controls and hybridized with murine GeneChip® 430 2.0 arrays. The hybridization, probe array washing and staining, and washing procedures were executed as described in the Affymetrix protocols
Scan protocol Probe arrays were scanned with a Hewlett-Packard Gene Array Scanner (ServiceXS, Leiden, The Netherlands).
Description gene expression data of ApoE3L.CETP mice liver samples
Data processing Raw signal intensities (from CEL-files) were normalized using the GCRMA algorithm (gc-rma slow). For annotation of probes and summarization of signals from probes representing one gene the custom MNBI CDF-file was used (based on EntrezGene, version 11.0.2; GPL10288) (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/cdfreadme.htm).
gcRMA slow normalized data, log2 transformed. Genes were filtered for expression above 5 in 3 or more samples (dataset including 6 arrays from fenofibrate treatment (GSM530353-358), GSE21211), resulting in a set of 11587 genes that was used for further analysis.
 
Submission date Jul 14, 2010
Last update date Jan 01, 2011
Contact name MJ van Erk
E-mail(s) marjan.vanerk@tno.nl
Organization name TNO Quality of Life
Street address PO Box 360
City Zeist
ZIP/Postal code 3700AJ
Country Netherlands
 
Platform ID GPL10288
Series (1)
GSE22940 PFOS and PFHxS decrease lipoprotein production

Data table header descriptions
ID_REF
VALUE gcRMA slow normalized data, log2 transformed

Data table
ID_REF VALUE
100009600_at 2.15
100017_at 6.42
100019_at 2.89
100034251_at 9.58
100036521_at 9.31
100037258_at 10.52
100038570_at 2.03
100038887_at 12.31
100038959_at 2.39
100039235_at 2.72
100039284_at 2.27
100039307_at 2.95
100039359_at 2.34
100039495_at 2.72
100039590_at 2.69
100039599_at 2.97
100039652_at 2.17
100039684_at 2.98
100039773_at 4.21
100039795_at 2.98

Total number of rows: 11587

Table truncated, full table size 162 Kbytes.




Supplementary file Size Download File type/resource
GSM566447.CEL.gz 3.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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