|
| Status |
Public on Dec 22, 2009 |
| Title |
Sample 2 from patient 42, Affected site |
| Sample type |
RNA |
| |
|
| Source name |
Patient 42 gingival tissue sample collected as Affected
|
| Organism |
Homo sapiens |
| Characteristics |
gingival tissue phenotype: Diseased (BoP + interproximal PPD of>3 mm + concomitant CAL of>2 mm)
tissue: Gingival
|
| Treatment protocol |
After collection gingival tissue specimens were thoroughly rinsed with sterile normal saline solution and transferred into Eppendorf tubes containing 5 volumes of a RNA stabilization reagent (RNAlater, Ambion, Austin, TX, USA). Specimens were stored in RNAlater overnight at 4.0 C and thereafter snap-frozen and stored in liquid nitrogen. All further processing occurred simultaneously for gingival biopsies originating from the same donor.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Gingival tissue specimens were homogenized in Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA collected in the upper aqueous phase was precipitated by mixing with isopropyl alcohol and additional centrifugation and washed in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer's instructions. The purified RNA was quantitated spectrophotometrically, and 7.5 micrograms of total RNA was reverse transcribed using GeneChip Expression 3' amplification one-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Synthesis of Biotin-Labeled cRNA was performed using the GeneChip Expression 3'-Amplification Reagents for IVT labeling kit (Affymetrix). The cRNA yield was determined spectrophotometrically at 260 nm. Finally, the cRNA was fragmented by incubation in fragmentation buffer at 94 0C for 35 min and stored at ?80 0C until hybridizations.
|
| |
|
| Hybridization protocol |
According to the manufacturer's instructions.
|
| Scan protocol |
According to the manufacturer's instructions.
|
| Description |
A total of 120 patients undergoing periodontal surgery contributed with a minimum of two interproximal gingival papillae (range 2-4) from a maxillary posterior. Prior to tissue harvesting, subgingival plaque samples were collected from the mesial and distal aspects of each papilla. Gingival tissue RNA was extracted, reverse-transcribed, labeled, and hybridized with whole-genome microarrays (310 in total)
|
| Data processing |
All CEL files in the series were processed using RMA in R using justRMA with default parameters.
|
| |
|
| Submission date |
May 15, 2009 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Ryan T Demmer |
| E-mail(s) |
rtd2106@columbia.edu
|
| Organization name |
Columbia University
|
| Department |
Epidemiology
|
| Street address |
722 W 168th St.
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE16134 |
Bacterial Correlates of Gingival Gene Expression |
|
| Relations |
| Reanalyzed by |
GSE119087 |
