NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1373814 Query DataSets for GSM1373814
Status Public on Aug 29, 2014
Title Chimeric liver_human_PB_1000ppm_10
Sample type RNA
 
Source name Chimeric Liver, 7days, 1000ppm, replicate 1
Organisms Homo sapiens; Mus musculus
Characteristics background strain: CD-1
tissue: Liver (human hepatocytes)
gender: male
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.
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).
Label Cy3
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.
 
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.
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%).
Description Gene expression after 7 days of administration
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.
 
Submission date Apr 24, 2014
Last update date Aug 29, 2014
Contact name Kayo Sumida
E-mail(s) sumida@sc.sumitomo-chem.co.jp
Phone 81-6-6466-5325
Organization name Sumitomo Chemical Co., Ltd.
Department Environmental Health Science Laboratory
Lab Biochemistry and Metabolism Group
Street address 1-98, Kasugadenaka 3-chome, Konohana-ku
City Osaka
ZIP/Postal code 554-8558
Country Japan
 
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

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
1 463.717
2 0.022
3 0.011
4 30.370
5 0.014
6 0.011
7 0.036
8 0.066
9 2.285
10 0.182
11 0.418
12 43.398
13 0.363
14 0.012
15 0.012
16 0.012
17 1.971
18 0.275
19 0.023
20 35.186

Total number of rows: 62976

Table truncated, full table size 732 Kbytes.




Supplementary file Size Download File type/resource
GSM1373814_249H-10.txt.gz 3.0 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.