|
| Status |
Public on Dec 31, 2011 |
| Title |
Lepromatous Patient 5 |
| Sample type |
RNA |
| |
|
| Source name |
leprosy skin lesion biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
leprosy type: lepromatous
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A, samples were skin biopsy specimens from leprosy patients.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from the OCT embedded and sections biopsies using guanidinium-isothiocyanate (CTC) buffer as previously described (Bleharski et al., 2003).
|
| Label |
biotin
|
| Label protocol |
Samples were processed by Ausragen through the Discovarray miRNA profiling service. Total RNA is dephosphorylated with calf intestinal phosphatase and the pCp-Biotin labeling molecule is ligated to the 3’ ends of the RNA molecules. Labeled RNA is purified using BioSpin6 (Bio-Rad, Hercules CA).
|
| |
|
| Hybridization protocol |
Samples were processed by Ausragen through the Discovarray miRNA profiling service. Hybridization, washing, staining, imaging, and signal extraction were performed according to Affymetrix-recommended procedures, except that the 20X GeneChip Eukaryotic Hybridization Control cocktail was omitted from the hybridization.
|
| Scan protocol |
Samples were processed by Ausragen through the Discovarray miRNA profiling service. The signal processing implemented for the Ambion miRCHIP is a multi-step process involving probe specific signal detection calls, background estimate and correction, constant variance stabilization and either array scaling or global normalization. For each probe, an estimated background value is subtracted that is derived from the median signal of a set of G-C-matched anti-genomic controls. Arrays within a specific analysis experiment were normalized together according to the variance stabilization method described by Huber et al. (Huber et al., 2002). Detection calls were based on a Wilcoxon rank-sum test of the miRNA probe signal compared to the distribution of signals from GC-content matched anti-genomic probes.
|
| Description |
L-lep5
|
| Data processing |
Samples were analyzed by Ausragen through the Discovarray miRNA profiling service, and normalized using Variation Stabilization Normalization (VSN).
|
| |
|
| Submission date |
Oct 24, 2011 |
| Last update date |
Dec 31, 2011 |
| Contact name |
Philip T. Liu |
| E-mail(s) |
ptliu@mednet.ucla.edu
|
| Phone |
310-206-8457
|
| Organization name |
University of California at Los Angeles
|
| Department |
Department of Orthopaedic Surgery
|
| Lab |
Liu Lab
|
| Street address |
615 Charles E Young Drive South, 410 OHRC
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL14777 |
| Series (1) |
| GSE33192 |
miRNA expression profile in leprosy skin biopsy specimens |
|
