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Status |
Public on Aug 29, 2014 |
Title |
Chimeric liver_human_PB_1000ppm_10 |
Sample type |
RNA |
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Source name |
Chimeric Liver, 7days, 1000ppm, replicate 1
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Organisms |
Homo sapiens; Mus musculus |
Characteristics |
background strain: CD-1 tissue: Liver (human hepatocytes) gender: male
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Treatment protocol |
Male chimeric mice (4-5 animals/dose) also fed diets containing 0 (control) or 1000 ppm NaPB for 7 days. Liver samples were used for gene expression analysis.
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was prepared using the Isogen solution (Nippon Gene, Tokyo, Japan) and RNeasy Mini Kits (QIAGEN, Valencia, CA) from liver following the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA).
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Label |
Cy3
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Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Low Input Quick Amp Labeling kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.
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Hybridization protocol |
600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE v2 8x60K Microarrays for 17 hours at 65 °C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
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Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).
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Description |
Gene expression after 7 days of administration
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Data processing |
The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
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Submission date |
Apr 24, 2014 |
Last update date |
Aug 29, 2014 |
Contact name |
Kayo Sumida |
E-mail(s) |
sumida@sc.sumitomo-chem.co.jp
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Phone |
81-6-6466-5325
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Organization name |
Sumitomo Chemical Co., Ltd.
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Department |
Environmental Health Science Laboratory
|
Lab |
Biochemistry and Metabolism Group
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Street address |
1-98, Kasugadenaka 3-chome, Konohana-ku
|
City |
Osaka |
ZIP/Postal code |
554-8558 |
Country |
Japan |
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Platform ID |
GPL16699 |
Series (2) |
GSE57056 |
Human hepatocytes support the hypertrophic but not the hyperplastic response to the murine nongenotoxic hepatocarcinogen sodium phenobarbital in an in vivo study using a chimeric mouse with humanized liver [Chimeric Liver Experiments] |
GSE57058 |
Human hepatocytes support the hypertrophic but not the hyperplastic response to the murine nongenotoxic hepatocarcinogen sodium phenobarbital in an in vivo study using a chimeric mouse with humanized liver |
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