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Status |
Public on Jan 01, 2011 |
Title |
PFOS_2 |
Sample type |
RNA |
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Source name |
ApoE3L.CETP mice liver
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Organism |
Mus musculus |
Characteristics |
diet group: PFOS tissue: liver gender: male background strain: C57Bl/6 mouse model: E3L.CETP
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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
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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).
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Label |
biotin
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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.
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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
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Scan protocol |
Probe arrays were scanned with a Hewlett-Packard Gene Array Scanner (ServiceXS, Leiden, The Netherlands).
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Description |
gene expression data of ApoE3L.CETP mice liver samples
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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.
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Submission date |
Jul 14, 2010 |
Last update date |
Jan 01, 2011 |
Contact name |
MJ van Erk |
E-mail(s) |
marjan.vanerk@tno.nl
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Organization name |
TNO Quality of Life
|
Street address |
PO Box 360
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City |
Zeist |
ZIP/Postal code |
3700AJ |
Country |
Netherlands |
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Platform ID |
GPL10288 |
Series (1) |
GSE22940 |
PFOS and PFHxS decrease lipoprotein production |
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