Dataset Information

E-GEOD-38959

ABSTRACT: Gene expression profiling of triple negative breast cancer, normal ductal cells, and normal tissues

OTHER RELATED OMICS DATASETS IN: PRJNA169423

TISSUE(S): Heart, Lung, Liver, Breast, Kidney

DISEASE(S): Normal,Breast Cancer

PROVIDER: E-GEOD-38959 | ExpressionAtlas | 2015-08-19

REPOSITORIES: ExpressionAtlas

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Dataset's files

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			Action	DRS
	E-GEOD-38959-analysis-methods.tsv	Tabular
	E-GEOD-38959-atlasExperimentSummary.Rdata	Rdata
	E-GEOD-38959-configuration.xml	Xml
	E-GEOD-38959-percentile-ranks.tsv	Tabular
	E-GEOD-38959.condensed-sdrf.tsv	Tabular

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Project description:Twenty-four triple-negative breast cancer and 14 adjacent normal tissues were collected from breast cancer patients during surgeries at National Taiwan University Hospital (NTUH, Taipei, Taiwan). All triple-negative breast cancer samples were invasive ductal carcinomas (IDC) and were negative in immunohistochemical statuses of ER, PR, and HER2 receptors, as confirmed by professional pathologists. Treatment procedure of all patients followed the National Comprehensive Cancer Network (NCCN) guideline. All samples were neoadjuvant-free and were collected before systemic chemotherapy treatments. Written informed consent was obtained from all patients who participated in this study. Using human tissues for research in this study was approved by the institutional review board at NTUH. A novel set of 25-miRNA signature identified in this study was able to effectively distinguish between triple-negative breast cancer and adjacent normal tissues. Moreover, we documented the first evidence of seven polycistronic miRNA clusters preferentially harboring deregulated miRNA genes in triple-negative breast cancer. In the present study, a panel of 24 triple-negative breast cancer and 14 adjacent normal tissue samples were examined for the presence of deregulated miRNA genes using the high-throughput sequencing technology. Total RNA was extracted from the triple-negative breast cancer and adjacent normal samples for preparation of small RNA libraries. Each small RNA library was constructed from total RNA of each sample using the SOLiD Total RNA-Seq Kit (Applied Biosystems, Foster City, CA, USA). Upon completion of polymerase chain reaction (PCR) amplification, small RNA libraries were purified using the SOLiD Library Micro Column Purification Kit (Applied Biosystems) and hybridized to the template beads using the SOLiD EZ bead system (Applied Biosystems). The template beads were amplified and deposited onto subtract for ligation sequencing by SOLiD 4 System (Applied Biosystems).

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E-GEOD-38959

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