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Series GSE43986 Query DataSets for GSE43986
Status Public on Dec 01, 2014
Title The Estrogen receptor alpha regulated NEAT1 long non-coding RNA promotes prostate cancer progression [RNA-Seq]
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Prostate glands predominantly exhibit androgen dependence, but increasing evidence suggests that estrogen receptor signaling is involved in its development and pathogenesis. By integrating ChIP sequencing for estrogen receptor alpha (ERα) with transcriptome sequencing data from prostate cancer samples, we found ERα to significantly influence the noncoding transcriptome in prostate cancer. We identified one such long noncoding RNA, NEAT1, to play an important role in prostate cancer progression through direct regulation of transcription of its target genes. NEAT1, in an ERα dependent manner, promotes prostate tumorigenesis by interacting with and modulating chromatin state at promoters of prostate cancer specific signature genes. NEAT1 expression is positively correlated with PSMA in prostate adenocarcinoma and with B3GAT1 in neuroendocrine prostate cancer. This study identifies NEAT1 as a novel biomarker or therapeutic target in prostate cancer and also suggests that co-targeting ERα and androgen receptor (AR) may be effective for a subset of patients with advanced prostate cancer and with NEAT1 overexpression.
mRNA profiles of MEF cell lines prepared from E13.5 embryos of wild-type (WT) and NEAT1 knockout (KO; NEAT1−/−) mice were generated by deep sequencing, using Illumina HiSeq 2000. Strand specific mRNA profiles of VCaP and VCaP ERa cell lines were generated by deep sequencing, using Illumina GA IIx.
Overall design RNA sequencing of MEF (WT vs NEAT1 KO) and VCaP (control vs ERa)
Contributor(s) Chakravarty D, Sboner A, Rubin MA
Citation(s) 25415230
Submission date Feb 01, 2013
Last update date May 15, 2019
Contact name Dimple Chakravarty
Phone (646)962-6189
Organization name Weill Cornell Medical College
Department Pathology
Lab BB 1450
Street address Belfer Research Building 413 E 69 St., New York
State/province NY
ZIP/Postal code 10021
Country USA
Platforms (2)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (4)
GSM1076114 MEF WT [RNA-Seq]
GSM1076115 MEF NEAT1 KO [RNA-Seq]
GSM1076116 VCaP [RNA-Seq]
This SubSeries is part of SuperSeries:
GSE43988 The Estrogen receptor alpha regulated NEAT1 long non-coding RNA promotes prostate cancer progression
BioProject PRJNA188303
SRA SRP018377

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Supplementary file Size Download File type/resource
GSE43986_RAW.tar 4.1 Mb (http)(custom) TAR (of CSV, RPKM)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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