|
| Status |
Public on Aug 06, 2009 |
| Title |
Global gene expression of NASH patients, P53 |
| Sample type |
RNA |
| |
|
| Source name |
patient liver biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: non-alcoholic steatohepatitis (NASH)
tissue: liver
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were stored in RNAlater at -80 freezer before total RNA extraction with Qiagen RNeasy kit.
|
| Label |
Biotin
|
| Label protocol |
Complementary DNA was prepared from total RNA.
In vitro transcription was then performed with biotin labeled substrate to produce biotin labeled cRNA.
|
| |
|
| Hybridization protocol |
1, Fragmentation of cRNA.
2, Denature cRNA at 90C for 5 min.
3, Hybridization was performed at 37 C, for 18-24 hours.
4, Detection with Cy5-streptavidin conjugate.
|
| Scan protocol |
Microarray scanning and data acquisition were done at the gene expression facility, Roswell Park Cancer Institute, following their routine standard procedure.
|
| Description |
The human studies have been approved by the Institutional Review Board (IRB) of the State University of New York at Buffalo and Women and Children’s Hospital of Buffalo. Liver biopsies were obtained, with prior informed consent, from parents of patients suspected of having NASH as part of regular medical care. Patients from 7 to 18 years of age signed an assent to the research. Diagnosis of NASH was based on hepatic fat infiltration, inflammation and fibrosis as revealed by liver biopsy. Only children and adolescents were included in this study to ensure that our patients were not sustained alcohol users. All NASH patients included in this study exhibited significant insulin resistance (IR). IR was calculated based on the “homeostasis model assessment (HOMA)” method
|
| Data processing |
Data were median-normalized for comparison. Medium normalization were done by our collaborators at Roswell Park cancer institute and verified using MS Excel2003.
|
| |
|
| Submission date |
Aug 02, 2009 |
| Last update date |
Oct 20, 2010 |
| Contact name |
Susan Baker |
| E-mail(s) |
sbaker@upa.chob.edu, lixinzhu@buffalo.edu
|
| Organization name |
SUNY at Buffalo
|
| Department |
Pediatrics
|
| Lab |
Digestive Diseases and Nutrition Center Research Laboratory
|
| Street address |
3435 Main street, 422 BRB
|
| City |
Buffalo |
| State/province |
NY |
| ZIP/Postal code |
14214 |
| Country |
USA |
| |
|
| Platform ID |
GPL2895 |
| Series (2) |
| GSE17470 |
Global gene expression of NASH patients |
| GSE24807 |
Increased hemoglobin expression in NASH livers |
|
