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ABSTRACT: Bulk 3-prime RNA-sequencing of macrodissected neuroendocrine and exocrine tumor components of FFPE-embedded mouse gastric neuroendocrine carcinomas

PROVIDER: PRJEB61968 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR11422919_1.fastq.gz	Fastqsanger.gz
	ERR11422919_2.fastq.gz	Fastqsanger.gz
	ERR11422920_1.fastq.gz	Fastqsanger.gz
	ERR11422920_2.fastq.gz	Fastqsanger.gz
	ERR11422921_1.fastq.gz	Fastqsanger.gz

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miRNA profiles in formalin-fixed and paraffin embedded (FFPE) breast cancer tissues

Project description:We describe a miRNA profiling analysis of matched ductal carcinoma in situ and invasive duct carcinoma components of FFPE breast carcinomas with the purpose to identify potential prognostic markers

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Pulmonary Carcinoids and Low-Grade Gastrointestinal Neuroendocrine Tumors Show Common MicroRNA Expression Profiles, Different from Adenocarcinomas and Small Cell Carcinomas

Project description:Background: It is still uncertain whether carcinoids of the lung and gastrointestinal (GI) tract have a common origin or whether they are closer in origin to carcinomas of the same organs. MicroRNA (miRNA) expression may clarify their nature and origin. Methods: First, to verify whether formalin-fixed paraffin-embedded (FFPE) samples retain the expression signature of the tissue, miRNA expression was compared between FFPE and frozen samples. Second, we selected surgically resected FFPE samples of pulmonary and GI carcinoids, as well as other types of tumors and normal tissues from each organ, and we compared the comprehensive expression patterns of miRNAs by microarray. These data were analyzed by hierarchical clustering and consensus clustering with non-negative matrix factorization (NMF). Results: The miRNA expression profiles of FFPE and frozen samples correlated quite well. In the first hierarchical clustering, most of the carcinoids formed one major cluster with loose subpartitioning into each organ type, while the second major cluster mainly comprised adenocarcinomas and normal tissues. The NMF approach largely supported hierarchical clustering. In the additional cluster analysis comparing carcinoids to small-cell lung carcinomas (SCLCs), carcinoids formed a distinct cluster, while SCLCs grouped together with pulmonary adenocarcinomas and normal lung tissues in another major cluster. Furthermore, we found some miRNAs that exhibited significant expression in carcinoids. Conclusion: Carcinoids had a characteristic pattern of miRNA expression, suggesting a common origin for pulmonary and GI carcinoids. The expression profiles were different in carcinoids and SCLCs, indicating distinct histogenesis of these neuroendocrine tumors.

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single cell chromatin accessiblity profiling in formlin fixed paraffin embedded samples

Project description:We evaluated the performance of ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) on formalin-fixed paraffin-embedded (FFPE) spleen samples from C57BL/6J mice. Nuclei were isolated from FFPE mouse spleen tissue, and ATAC-seq was performed at both the bulk and single-cell levels, with and without reverse crosslinking. The resulting datasets were compared to ATAC-seq and scATAC-seq profiles obtained from fresh spleen samples. Our analysis revealed a markedly reduced library complexity in FFPE-derived samples compared to fresh tissue, across both bulk and single-cell experiments. These findings highlight the technical limitations of applying standard ATAC-seq protocols to FFPE samples. Based on our results, we conclude that conventional ATAC-seq approaches are not well-suited for chromatin accessibility profiling in FFPE-preserved tissues.

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