|
| Status |
Public on Nov 27, 2012 |
| Title |
Hepatocytes from chimeric mouse 6 #18 |
| Sample type |
RNA |
| |
|
| Source name |
Hepatocytes from chimeric mouse 6
|
| Organism |
Mus musculus |
| Characteristics |
donor of hepatocytes: African American 6-years-old-female
gender: male
age: 15
weeks post-tarnsplantation: 12
human albumin level in mouse blood (mg/ml): 12.5
|
| Treatment protocol |
No treatment
|
| Growth protocol |
uPA/SCID mice were transplanted with human hepatocytes derived from a Caucasian 9-month-old male infant and an African American 6-year-old girl. Around 60 days after transplantation the mouse livers were replated with human hepatocytes.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cells or liver tissues with TRIzol regent (Invitrogen). Additionally, total RNA was purified with Rneasy Mini Kit (Qiagen) and treated with RNase-free DNase Set (Qiagen) to remove any contaminating genomic DNA.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, Rev. 3, 2009, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix Scanner 3000 7G.
|
| Data processing |
The data were digitalized using GeneChip Operating Software (GCOS) v.1.3 (Affymetrix).
Gene expression array data were normalized using MAS5 algorithm (Affymetrix). Then, to correct for bias between chips, quantile normalization (Bolstad, B. M. et al. Bioinformatics 19, 185-193 (2003)) was applied to all array data using R software.
The intensities were converted to a logarithmic scale (base 2). Signal reliability of each probe was determined based on the MAS5 Call algorithm (Affymetrix), and each probe was assigned to one of three flags (P: present, M: marginal, and A: absent).
|
| |
|
| Submission date |
Nov 21, 2011 |
| Last update date |
Nov 27, 2012 |
| Contact name |
Fuyuki Miya |
| E-mail(s) |
[email protected]
|
| Phone |
+81-3-5363-3890
|
| Organization name |
Keio University
|
| Department |
School of Medicine
|
| Lab |
Center for Medical Genetics
|
| Street address |
35 Shinanomachi, Shinjuku-ku
|
| City |
Tokyo |
| State/province |
Tokyo |
| ZIP/Postal code |
160-8582 |
| Country |
Japan |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE33846 |
Expression data of hepatocytes isolated from chimeric mouse livers repopulated with human hepatocytes and from normal human livers |
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