Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

15 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RMST associates with SOX2 to regulate neurogenesis

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Homo sapiens

SUBMITTER: Shi Yan Ng

PROVIDER: E-GEOD-49405 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RMST associates with SOX2 to regulate neurogenesis [Illumina expression data]

Project description:We report that knockdown of the lncRNA RMST changes the gene expression profile of neural stem cells. RMST and SOX2 regulates a common subset of downstream targets. Examination of genome wide transcriptomic changes upon knockdown of the lncRNA RMST.

2013-08-01 | E-GEOD-49403 | biostudies-arrayexpress

RMST associates with SOX2 to regulate neurogenesis [ChIP-Seq]

Project description:We report that knockdown of the lncRNA RMST changes the chromatin binding profile of the transcription factor SOX2. Examination of SOX2 chromatin binding profile under normal and RMST-depleted conditions in differentiating neural stem cells.

2013-08-01 | E-GEOD-49404 | biostudies-arrayexpress

The cistrome and transcriptome landscape of androgen receptor splice variants in castration-resistant prostate cancer cells

Project description:The spliced variant forms of androgen receptor (AR-Vs) have been identified recently in castration-resistant prostate cancer (CRPC) cell lines and clinical samples. Here we identified the cistrome and transcriptome landscape of AR-Vs in CRPC cell lines and determine the clinical significance of AR variants regulated gene.The AR variants binding sites can be identified in 22Rv1 cell line in the absence of androgen. Knocking down full-length AR (AR-FL) doesn't affect AR-Vs binding sites in genome-wide. A set of genes were identified to be regulated uniquely by AR-Vs, but not by AR-FL in androgen-depleted condition. Integrated analysis showed that some genes may be modulated by AR-Vs directly. Unsupervised clustering analysis demonstrated that AR variants gene signature can separate not only the benign and malignant prostate tissue, but also the localized prostate cancer and metastatic CRPC specimens. Some genes modulated uniquely by AR variants were also identified to correlate with the Gleason Pattern of prostate cancer and PSA failure. We conclude that AR spliced variants bind to DNA independent of full-length AR, and can modulate a unique set of genes which is not regulated by full-length AR in the absence of androgen. AR variants gene signature correlate with CRPC and prostate cnacer disease progress. Androgen receptor (AR) binding sites in human prostate cancer 22Rv1 cell lines were studied using ChIP-seq. ChIP enriched and input DNA were sequenced using Illumina HiSeq 2000.

2014-09-10 | E-GEOD-58478 | biostudies-arrayexpress

Activation of P-TEFb by androgen receptor-regulated enhancer RNAs in androgen deprivation conditions [ChIP-Seq]

Project description:Androgen receptor (AR) is required for castration resistant prostate cancer (CRPC) progression, but the function and disease relevance of AR-bound enhancers remain poorly understood. Here, we identify a group of AR-regulated enhancer RNAs (e.g. PSA eRNA) that are upregulated in CRPC cells, patient-derived xenografts (PDX) and patient tissues. PSA eRNA binds to CYCLIN T1, activates P-TEFb and promotes in cis and trans gene transcription by increasing serine-2 phosphorylation of RNA polymerase II (Pol II-Ser2p). To avoid the total Pol II changing by PSA eRNA. We measured the total Pol II using N20 and 8WG16 antibodies with or without PSA eRNA knocking down. To avoid the AR binding changes by PSA eRNA, we also measured the AR binding using AR N20 antibodies with or without PSA eRNA knocking down. Androgen receptor (AR) binding sites in human prostate cancer cell lines, C4-2, were studied using ChIP-seq. Total Pol II Ser-2p and AR binding sites in human prostate cancer cell lines C4-2 with or without PSA eRNA knockdown, were studied using ChIP-seq. ChIP enriched DNA were sequenced using Illumina HiSeq 2500and input DNA were sequenced using Illumina HiSeq 2000.

2016-02-12 | E-GEOD-71704 | biostudies-arrayexpress

Activation of P-TEFb by enhancer RNAs associated with lethal prostate cancer [ChIP-seq]

Project description:Castration resistant prostate cancer (CRPC) is a lethal disease. Sustained aberrant activation of androgen receptor (AR) becomes a central mechanism that contributes to endocrine therapy resistance. Here, we demonstrate that AR-bound enhancer RNAs (AR-eRNAs), including eRNA of the KLK3 (or PSA) gene, are upregulated in human CRPC cells and patient tissues. By enhancing C-termine domain (CTD) serine-2 phosphorylation of RNA polymerase II (Pol II-Ser2p), PSA eRNA acts in cis to promote PSA mRNA transcription and in trans to induce mRNA expression of a large set of genes involved in androgen action, cell cycle progression and tumorgenesis. Accordingly, we demonstrate that PSA eRNA binds in vitro and in vivo to CYCLIN T1, a regulatory subunit of the positive transcription elongation factor b (P-TEFb) complex that mediates Pol II-Ser2p. To identify the PSA eRNAâ??s functions on the Pol II-Ser2p and CYCLINT1 in the CRPC C4-2 cells, we detected the Pol II-Ser2p and CYCLINT1 ChIP-seq with or without PSA eRNA knockdown in the C4-2 cells. Moreover, to rule out the AR binding changes and identify the AR binding sites around the new genes, we detected the AR ChIP-seq in LNCaP and C4-2 cells with or without the androgen. Androgen receptor (AR) binding sites in human prostate cancer cell lines, LNCaP and C4-2, were studied using ChIP-seq. Pol II Ser-2p and CYCLINT1 binding sites in human prostate cancer cell lines C4-2 with or without PSA eRNA knockdown, were studied using ChIP-seq. ChIP enriched and input DNA were sequenced using Illumina HiSeq 2000.

2016-02-12 | E-GEOD-65066 | biostudies-arrayexpress

Activation of the P-TEFb Complex by Lethal Prostate Cancer-Associated Enhancer RNAs

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-02-12 | E-GEOD-55032 | biostudies-arrayexpress

Co-regulated gene expression by estrogen receptor-a and liver receptor homolog-1 is a feature of the estrogen response in breast cancer cells

Project description:Our findings establish a key role for LRH-1 in the regulation of ERa target genes in breast cancer cells and identify a mechanism in which co-operative binding of LRH-1 and ERa at estrogen response elements controls the expression of estrogen responsive g Examination of ERα, with or without LRH-1 knockdown, and HA-LRH-1 in MCF-7 cells

2013-08-01 | E-GEOD-49390 | biostudies-arrayexpress

The histone demethylase Jmjd3 sequentially associates with the transcription factors Tbx3 and Eomes to drive endoderm differentiation

Project description:Here we show that T-box proteins team up with chromatin modifying enzymes to drive the expression of the key lineage regulator, Eomes during endodermal differentiation of embryonic stem (ES) cells. The Eomes locus is maintained in a transcriptionally poised configuration in ES cells. During early differentiation steps, the ES cell factor Tbx3 associates with the histone demethylase Jmjd3 at the enhancer element of the Eomes locus to allow enhancer-promoter interactions. This spatial reorganization of the chromatin primes the cells to respond to Activin signaling, which promotes the binding of Jmjd3 and Eomes to its own bivalent promoter region to further stimulate Eomes expression in a positive feedback loop. Examination of the binding of pluripotency factors to mouse embryonic stem cells and embryoid bodies

2013-04-18 | E-GEOD-44764 | biostudies-arrayexpress

HEB associates with PRC2 and SMAD2/3 to regulate developmental fates [ChIP-Seq]

Project description:We report the interaction between HEB and PRC2 components in mouse embryonic stem cells (ESCs) ChIP-Seq of HEB and SMAD2/3 in mouse ESC and derived endoderm

2015-06-30 | E-GEOD-53233 | biostudies-arrayexpress

Role of PRC2 complex components in prostate cancer cell lines

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2012-11-30 | E-GEOD-39461 | biostudies-arrayexpress