|
| Status |
Public on May 20, 2014 |
| Title |
Normal symmetry, sleep apnea, class II, open bite |
| Sample type |
RNA |
| |
|
| Source name |
subject 4_left_normal facial symmetry_sleep apnea
|
| Organism |
Homo sapiens |
| Characteristics |
subject id: Orthognathic surgical subject 4
race/ethnicity: French caucasian
gender: Female
age: 41
facial symmetry: normal facial symmetry
malocclusion classification: class II open bite
tissue: masseter muscle
|
| Treatment protocol |
Specimens of the deep portion of masseter muscles were collected from patients at orthognathic surgery for correction of malocclusion with jaw discrepancies. Muscles were positioned vertically with mounting medium and snap frozen in the operating room before transfer and storage at -80C. Muscle sections were taken for immunohistochemistry. RNA was isolated from remaining muscle.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Muscle was homogenized in QIAzol Lysis Reagent and total RNA was isolated using a Qiagen miRNeasy Mini Kit according to the manufacturer’s instructions. Quantity and quality of total RNA sampleswere evaluated by Agilent Bioanalyzer and Nanodrop spectrophotometry.
|
| Label |
biotin
|
| Label protocol |
Total RNA (250ng) was converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers. Second-strand cDNA was in vitro transcribed with T7 RNA polymerase. Resulting cRNA was converted to cDNA, fragmented, and biotinylated by terminal transferase end labeling according to the Ambion WT Expression Manual.
|
| |
|
| Hybridization protocol |
Labeled cDNA (5.5g) were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Human Transcriptome 2.0 GeneChips. Following low and high stringency washes, chips were stained with streptavidin-phycoerythrin.
|
| Scan protocol |
A GeneChip 3000 7G scanner was used to collect fluorescence signal.
|
| Description |
4L_Open_II
|
| Data processing |
Affymetrix Command Console was used with default settings to generate .cel files. Cel files were RMA normalized using Partek Genomics Suite, v6.6.
|
| |
|
| Submission date |
May 19, 2014 |
| Last update date |
May 20, 2014 |
| Contact name |
michael joseph horton |
| E-mail(s) |
mjhorton@temple.edu
|
| Phone |
215-707-2129
|
| Organization name |
temple university school of dentistry
|
| Department |
orthodontics
|
| Lab |
craniofacial biology research laboratory room 384
|
| Street address |
3223 n broad st
|
| City |
philadelphia |
| State/province |
pennsylvania |
| ZIP/Postal code |
19140 |
| Country |
USA |
| |
|
| Platform ID |
GPL17586 |
| Series (1) |
| GSE57775 |
Masseter muscle gene expression in human malocclusion subjects with and without posterior facial asymmetry |
|
