Dataset Information


Identification and functional characterization of long noncoding RNAs in breast cancer

ABSTRACT: In this study, we have integrated RNA-seq data from subcellular fractionated RNA (i.e., cytoplasm, nucleoplasm, and chromatin-associated) with GRO-seq data using a novel bioinformatics pipeline. This has yielded a comprehensive catalog of polyadenylated lncRNAs in MCF-7 cells, about half of which have not been annotated previously and about a quarter of which are estrogen-regulated. Knockdown of selected lncRNAs, such as lncRNA152 and lncRNA67 followed by RNA-seq suggest that these lncRNAs regulate the expression of cell cycle genes. characterization of long noncoding RNAs

ORGANISM(S): Homo sapiens  

SUBMITTER: W. Lee Kraus   W L Kraus  Shrikanth S Gadad  Dae S Kim  Miao Sun 

PROVIDER: E-GEOD-63189 | ArrayExpress | 2015-07-30



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Discovery, Annotation, and Functional Analysis of Long Noncoding RNAs Controlling Cell-Cycle Gene Expression and Proliferation in Breast Cancer Cells.

Sun Miao M   Gadad Shrikanth S SS   Kim Dae-Seok DS   Kraus W Lee WL  

Molecular cell 20150730 4

We describe a computational approach that integrates GRO-seq and RNA-seq data to annotate long noncoding RNAs (lncRNAs), with increased sensitivity for low-abundance lncRNAs. We used this approach to characterize the lncRNA transcriptome in MCF-7 human breast cancer cells, including >700 previously unannotated lncRNAs. We then used information about the (1) transcription of lncRNA genes from GRO-seq, (2) steady-state levels of lncRNA transcripts in cell lines and patient samples from RNA-seq, an  ...[more]

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