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Large field of view and spatial region of interest transcriptomics in frozen and FFPE tissue

ABSTRACT: Large field of view and spatial region of interest transcriptomics in frozen and FFPE tissue

PROVIDER: PRJNA1114766 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29131459_1.fastq.gz	Fastqsanger.gz
	SRR29131459_2.fastq.gz	Fastqsanger.gz
	SRR29131460_1.fastq.gz	Fastqsanger.gz
	SRR29131460_2.fastq.gz	Fastqsanger.gz
	SRR29131461_1.fastq.gz	Fastqsanger.gz

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Large field of view and spatial region of interest transcriptomics in frozen and FFPE tissue

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Project description: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

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