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Sample GSM1322531 Query DataSets for GSM1322531
Status Public on Feb 05, 2014
Title P38S3L8H3: AggressiveGeneralizedControl
Sample type RNA
Source name periodontal tissue
Organism Homo sapiens
Characteristics patient: 38
specimen: 3
biopsyid: 38.3
diagnosis: Aggressive
extent: Generalized
condition: Control
labelbatch: 8
hybridizebatch: 3
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 P38S3L8H3 (this sample failed QC and was excluded from the final analysis)
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 2.678302099
A_25_P00015343 2.245971814
Blank 1.934448782
dmr_285 7.224841824
dmr_3 13.99506089
dmr_308 2.305435694
dmr_316 3.562106223
dmr_31a 9.301187408
dmr_6 12.58813288
A_25_P00013722 6.515837626
A_25_P00013718 2.387900199
A_25_P00011668 2.420258566
A_25_P00013809 6.705830695
A_25_P00011834 2.699234982
A_25_P00013749 2.371537401
A_25_P00013752 3.055292747
A_25_P00011853 2.496257797
A_25_P00013814 2.357652103
A_25_P00014783 2.253025697
A_25_P00011886 2.679725511

Total number of rows: 1368

Table truncated, full table size 35 Kbytes.

Supplementary file Size Download File type/resource
GSM1322531_US83000178_253118110685_S01_miRNA_105_Dec08_1_3.txt.gz 8.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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