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Series GSE12458 Query DataSets for GSE12458
Status Public on Nov 01, 2008
Title An array based analysis of miRNA expression comparing matched frozen and FFPE human tissue samples
Organism Homo sapiens
Experiment type Non-coding RNA profiling by array
Summary MicroRNAs (miRNAs) are small non-coding RNAs that repress gene expression at the post transcriptional level via an antisense RNA-RNA interaction. Generally, miRNAs derived from snap frozen or fresh samples are used for array based profiling. Since tissues in most pathology departments are available only in formalin fixed and paraffin embedded state, we sought to evaluate the miRNA derived from formalin fixed and paraffin embedded (FFPE) samples for microarray analysis. In this study, miRNAs extracted from matched snap frozen and FFPE samples were profiled using the Agilent miRNA array platform. Each miRNA sample was hybridized to arrays containing probes interrogating 470 human miRNAs. A total of seven cases were compared in either duplicate or triplicate. Intrachip and interchip analyses demonstrated that the processes of miRNA extraction, labeling and hybridization from both frozen and FFPE samples are highly reproducible and add little variation to the results, as technical replicates showed high correlations (Kendall tau=0.722-0.853, Spearman rank correlation coefficient=0.891-0.954). Our results showed consistent high correlation between matched frozen and FFPE samples (Kendall tau=0.669-0.815, Spearman rank correlation coefficient=0.847-0.948), supporting the use of FFPE-derived miRNAs for profiling.

Keywords: formalin-fixed and paraffin-embedded (FFPE) miRNA profiling
 
Overall design 7 matched frozen and FFPE lymphoid hyperplasia tissues were profiled and compared. Triplicate arrays were performed for two pairs of hyperplasia samples and duplicate arrays for three pairs of hyperplasia samples.
 
Contributor(s) Feilotter H, Tron VA
Citation(s) 18832457
Submission date Aug 15, 2008
Last update date Mar 20, 2012
Contact name Harriet Feilotter
Organization name Queen's University
Department Pathology and molecular department
Lab microarray facility
Street address 88 Stuart St
City Kingston
State/province Ontario
ZIP/Postal code K7L 3N6
Country Canada
 
Platforms (1)
GPL9081 Agilent-016436 Human miRNA Microarray 1.0 G4472A (miRNA ID version)
Samples (28)
GSM313069 Hyperplasia tissue Frozen 2817 extraction 1
GSM313070 Hyperplasia tissue Frozen 17176 extraction 1
GSM313071 Hyperplasia tissue Frozen 2248 extraction 1
Relations
BioProject PRJNA113021

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE12458_RAW.tar 41.6 Mb (http)(custom) TAR (of TXT)
GSE12458_miRNA_QC_metrics(2).pdf 93.5 Kb (ftp)(http) PDF
Processed data included within Sample table

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