|
| Status |
Public on Feb 05, 2014 |
| Title |
P14S1L3H1: AggressiveLocalizedAffected |
| Sample type |
RNA |
| |
|
| Source name |
periodontal tissue
|
| Organism |
Homo sapiens |
| Characteristics |
patient: 14
specimen: 1
biopsyid: 14.1
diagnosis: Aggressive
extent: Localized
condition: Affected
labelbatch: 3
hybridizebatch: 1
|
| Treatment protocol |
Gingival tissue samples comprising pocket/sulcus epithelium and the underlying connective tissue were obtained from patients with chronic or aggressive periodontitis in conjunction with periodontal surgery
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue samples were stored in liquid RNA stabilization reagent (RNAlater, Austin, TX) overnight at 4°C, snap-frozen and stored in liquid nitrogen. Specimens were homogenized in Trizol (Invitrogen Life Technologies, Carlsbad, CA), incubated with chloroform and centrifuged at 12,000g. RNA collected in the upper aqueous phase was precipitated by mixing with 75% isopropyl-alcohol and additional centrifugation and washings, and was quantified spectrophotometrically. RNA quality was assessed by determining the RNA Integrity Number (RIN).
|
| Label |
cyanine 3-pCp
|
| Label protocol |
miRNA profiling was carried out using the Agilent platform (Agilent Technologies). Total RNA (100 ng/specimen) was labeled to generate fluorescent miRNA by ligation of cyanine 3-pCp to the 3’end
|
| |
|
| Hybridization protocol |
Labeled RNA hybridized with microarrays carrying probes for 1,205 human and 144 human viral miRNAs (SurePrint G3 Human v16 miRNA 8x60K Microarray Kit).
|
| Scan protocol |
Array images were scanned with Agilent Technologies Scanner G2505C US83000178 using grid 031181_D_F_20110707 and protocol miRNA_105_Dec08.
|
| Description |
P14S1L3H1 (this sample failed QC and was excluded from the final analysis)
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using 031181_D_F_20110707.xml as design file to obtain background subtracted and Processed Signal intensities. Subsequent data analysis and normalization was performed within R/Bioconductor. Data was normalized and background corrected using rmaMicroRna function with background and normalize set to TRUE. Filtering was performed according to the recommended AgiMicroRna documentation having the following filterMicroRna parameters:
control = TRUE,
IsGeneDetected = TRUE,
wellaboveNEG = FALSE,
limIsGeneDetected = 75,
limNEG = 25
|
| |
|
| Submission date |
Feb 05, 2014 |
| Last update date |
Feb 06, 2014 |
| Contact name |
Paolo Guarnieri |
| E-mail(s) |
p.guarnieri@hotmail.com
|
| Organization name |
Columbia University
|
| Department |
Systems Biology
|
| Street address |
1130 St. Nicholas Avenue
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL15159 |
| Series (1) |
| GSE54710 |
MicroRNAs and their target genes in gingival tissues. |
|
