|
| Status |
Public on Sep 23, 2013 |
| Title |
swedish subject, 2 |
| Sample type |
RNA |
| |
|
| Source name |
vastus lateralis
|
| Organism |
Homo sapiens |
| Characteristics |
sample designation/group: ISCU myopathy patient
age at biopsy: 42
gender: M
tissue type: vastus lateralis
|
| Growth protocol |
Vastus lateralis muscle biopsies were performed with a 6G Bergstrom needle. Muscle samples were frozen and stored in liquid nitrogen until RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from biopsies and cell pellets was prepared using the mirVana™ RNA Isolation Kit (Ambion). RNA quality was verified using an Agilent 2100 Bioanalyzer.
|
| Label |
biotin
|
| Label protocol |
1-cycle target labeling at the NCI-Frederick Laboratory of Molecular Technology (http://ncifrederick.cancer.gov/atp/genetics-and-genomics/laboratory-of-molecular-technology/lmt-protocols-and-resources/)
|
| |
|
| Hybridization protocol |
please refer to http://ncifrederick.cancer.gov/atp/genetics-and-genomics/laboratory-of-molecular-technology/lmt-protocols-and-resources/
|
| Scan protocol |
please refer to http://ncifrederick.cancer.gov/atp/genetics-and-genomics/laboratory-of-molecular-technology/lmt-protocols-and-resources/
|
| Data processing |
R/Bioconductor software was used to identify differentially expressed genes in the dataset. The Robust Multi-Array Average expression measure (RMA) was applied for background correction, quantile normalization, and output of gene expression values in log2 scale. We used the LIMMA package to assess differentially expressed genes, and statistical significance was adjusted for multiple testing by controlling the Benjamini and Hochberg’s false discovery rate at 5%.
|
| |
|
| Submission date |
Jul 08, 2013 |
| Last update date |
Sep 24, 2013 |
| Contact name |
Chuming Chen |
| E-mail(s) |
chenc@udel.edu
|
| Phone |
302-831-3426
|
| Fax |
302 831-4841
|
| Organization name |
University of Delaware
|
| Department |
Computer and Information Sciences
|
| Lab |
Center for Bioinformatics and Computational Biology
|
| Street address |
15 Innovation Way, Suite 205
|
| City |
Newark |
| State/province |
DE |
| ZIP/Postal code |
19711 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE48574 |
Gene expression in human healthy control and ISCU myopathy patient muscle biopsies |
|
