Transcriptomics

Dataset Information

88

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| 2015-08-19

SECONDARY ACCESSION(S): SRP049713GSE63189PRJNA266932

REPOSITORIES: GEO, ArrayExpress, ENA

altmetric image

Publications

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]

Similar Datasets

2016-01-09 | E-GEOD-70390 | ArrayExpress
2016-01-17 | E-GEOD-64818 | ArrayExpress
2016-04-08 | E-GEOD-51878 | ArrayExpress
2017-12-06 | E-MTAB-6193 | ArrayExpress
2016-01-11 | E-GEOD-65263 | ArrayExpress
2016-07-10 | E-GEOD-83955 | ArrayExpress
2016-02-13 | E-GEOD-77675 | ArrayExpress
2018-08-21 | PXD008693 | Pride
2016-04-22 | E-GEOD-51878 | ExpressionAtlas
2014-07-31 | E-GEOD-55338 | ArrayExpress