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Sample GSM1322473 Query DataSets for GSM1322473
Status Public on Feb 05, 2014
Title P5S2L1H1: ChronicLocalizedAffected
Sample type RNA
Source name periodontal tissue
Organism Homo sapiens
Characteristics patient: 5
specimen: 2
biopsyid: 5.2
diagnosis: Chronic
extent: Localized
condition: Affected
labelbatch: 1
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 P5S2L1H1
Data processing The scanned images were analyzed with Feature Extraction Software (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
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.

Data table header descriptions
VALUE RMA Normalized signal intensity as computed with AgiMicroRna bioconductor package.

Data table
A_25_P00015345 2.353111066
A_25_P00015343 2.332752554
Blank 1.93453491
dmr_285 10.12973714
dmr_3 14.11744727
dmr_308 2.451412094
dmr_316 2.688438091
dmr_31a 9.264059545
dmr_6 13.21933542
A_25_P00013722 2.415833253
A_25_P00013718 2.334644688
A_25_P00011668 2.451291209
A_25_P00013809 2.505549621
A_25_P00011834 2.364698874
A_25_P00013749 2.374408955
A_25_P00013752 4.381286409
A_25_P00011853 5.985016945
A_25_P00013814 2.284593517
A_25_P00014783 2.31527813
A_25_P00011886 2.317916321

Total number of rows: 1368

Table truncated, full table size 35 Kbytes.

Supplementary file Size Download File type/resource
GSM1322473_US83000178_253118110699_S01_miRNA_105_Dec08_1_2.txt.gz 8.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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