|
| Status |
Public on Jun 01, 2008 |
| Title |
MLS003B |
| Sample type |
RNA |
| |
|
| Source name |
human oral tissue
|
| Organism |
Homo sapiens |
| Characteristics |
pretreated oral tissue
|
| Treatment protocol |
Patients applied a 10% freeze dried black raspberry gel to treatment site four times daily for six weeks. Pretreatment-baseline-no gel yet applied.
|
| Growth protocol |
Tissue was immediately placed in RNA later and stored at -80 degrees until RNA processing by routine methods.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extration was performed by using Absolutely RNA Miniprep Kit according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
The Ovation™ Biotin RNA Amplification and Labeling System (NuGen Technologies, Inc., San Carlos, CA) was used to prepare amplified, biotin-labeled cDNA from total RNA for following manufacturer’s instructions. Briefly, first strand cDNA was synthesized from 25 ng of total RNA using a unique first strand DNA/RNA chimeric primer and reverse transcriptase. Following double strand cDNA generation, amplification of cDNA was achieved by utilizing an isothermal DNA amplification process that involves repeated SPIA™ DNA/RNA primer binding, DNA duplication, strand displacement and RNA cleavage. The amplified SPIA™ cDNA was purified and subjected to a two-step fragmentation and labeling process. The fragmented/biotinylated cDNA content was measured in a ND-1000 spectrophotometer and the quality was analyzed on an RNA 6000 Nano LabChip (Agilent) using Agilent Bioanalyzer 2100.
|
| |
|
| Hybridization protocol |
Following fragmentation, labeled cRNA was hybridized to the human genoma gene chip U133A 2.0 Plus. Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).
|
| Scan protocol |
GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)
|
| Description |
Gene expression data from pretreated oral tissue
|
| Data processing |
CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals were generated using the RMA algorithm in ArrayAssist 3.4 (Stratagene) and were used to determine differential gene expression by pair-wise comparisons. The genes that were altered by two-fold either ways were sorted and used for further interpretation of the microarray data.
|
| |
|
| Submission date |
Jan 14, 2008 |
| Last update date |
Jan 16, 2008 |
| Contact name |
Ping Pei |
| E-mail(s) |
pei.4@osu.edu
|
| Phone |
614-292-4028
|
| Fax |
614-2920-9384
|
| Organization name |
OSU
|
| Department |
Oral Pathology
|
| Lab |
Dr. Mallery
|
| Street address |
305 West 12th Ave
|
| City |
Columbus |
| State/province |
OH |
| ZIP/Postal code |
43210 |
| Country |
USA |
| |
|
| Platform ID |
GPL571 |
| Series (1) |
| GSE10174 |
Bioadhesive black rasberry gel effect on gene expression and proinflammatory proteins in human premalignant oral lesions |
|
