Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide RBR1 (Retinoblastoma related 1) binding sites in Arabidopsis thaliana dividing cells.

ABSTRACT: Genome-wide RBR1 (Retinoblastoma related 1) binding sites in Arabidopsis thaliana dividing cells.

PROVIDER: PRJNA428472 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR6439903.fastq.gz	Fastqsanger.gz
	SRR6439904.fastq.gz	Fastqsanger.gz

Items per page:

1 - 2 of 2

Similar Datasets

Genome-wide RBR1 (Retinoblastoma related 1) binding sites in Arabidopsis thaliana dividing cells.

Project description:ChIP-seq experiments using an anti-RBR1 antibody were performed on MM2d cell culture material from Arabidopsis thaliana (3d after sub-culture).

2018-11-10 | GSE108741 | GEO

PA-seq of retinoblastoma and retina

Project description:To obtain a global view of APA during the development of retinoblastoma, we subjected total RNAs from five retina sample and five retinoblastoma samples to PA-seq, which precisely identify poly(A) sites at the genome scale.

2023-02-03 | GSE224022 | GEO

Divergence of Transcription Factor Binding Sites in Related Yeast Species

Project description:Divergence of Transcription Factor Binding Sites in Related Yeast Species

| PRJNA96077 | ENA

Genome-wide mapping of retinoblastoma (Rb) binding sites in prostate cancer cell lines VCaP and LNCaP

Project description:Although well characterized as a transcriptional activator, androgen receptor (AR) can also function as a direct transcriptional repressor in prostate cancer cells. The major targets of the AR repressive function are genes mediating DNA synthesis. In this study, we found that AR was recruited to the majority of these DNA synthesis genes and rapidly repressed their transcription. This direct AR mediated repression was enhanced in prostate cancer cells expressing higher levels of AR, and was mediated by recruitment of hypophosphorylated retinoblastoma protein (Rb).

2015-12-19 | GSE76141 | GEO

Expression data from retinoblastoma

Project description:Genomic losses on chromosome 16q are among the most frequent alterations found in retinoblastoma. In this study, Affymetrix GeneChip analyses along with LOH analysis of microsatellie markers was used to identify candidate tumor suppressor loci in a set of retinoblastoma. We used microarrays to identify genes differentially expressed in retinoblastoma with LOH on 16q (M19484, M22590, M22641, M22860) compared to retinoblastoma without alterations in this region (M20517, M22067, M22233, M23209, M23449, M23818, M23896, M23978) Keywords: Disease progression

2007-01-29 | GSE5222 | GEO

QUANTITATIVE PHOSPHOPROTEOMIC PROFILING OF PRIMARY RETINOBLASTOMA TUMORS

Project description:Retinoblastoma is a malignant tumor of the retina which most often occurs in children below 5 years of age with an incident rate of about 1 in 15,000 to 18,000 live births. Retinoblastoma is the first ever cancer that was reported to have a genetic basis. It occurs widely due to inactivating mutations in RB1 gene. Gene expression studies, copy number variation analysis, epigenetic profiling including miRNA and methylation of retinoblastoma has been carried to understand the disease mechanism and key players in the disease. Our group has earlier performed differential proteomics of retinoblastoma to identify proteins of therapeutic importance. However, there are no studies to understand the signalling mechanisms associated with retinoblastoma. Hence, global phosphoproteomics of retinoblastoma was carried out to identify signalling events associated with this cancer. Our study identified stress response proteins to be hyper phosphorylated which included H2AFX and sirtuin 1. In particular, Ser140 of H2AFX also known as gamma-H2AX was found to be hyperphosphorylated in retinoblastoma that indicated activation of DNA damage response pathways. We also observed activation of anti-apoptotic proteins in retinoblastoma compared to control. These observations showed activation of survival pathways and signalling networks activated in tumors.

2019-11-11 | PXD007228 | Pride

Genome-wide mapping of retinoblastoma (Rb) binding sites in prostate cancer cell lines VCaP and LNCaP

2015-12-19 | E-GEOD-76141 | biostudies-arrayexpress

Gene expression profiles of retinoblastoma cell lines

Project description:In order to identify the gene targets of frequently altered chromosomal regions in retinoblastoma, a meta-analysis of genome-wide copy number alterations studies on primary retinoblastoma tissue and retinoblastoma cell lines was performed. Published studies were complemented by copy number and gene expression analysis on primary and cell line samples of retinoblastoma. This dataset includes the gene expression data of the retinoblastoma cell lines

2016-03-31 | GSE77094 | GEO

Gene Expression profiles in Retinoblastoma

Project description:Gene expression profiles in retinoblastoma by whole Human Genome DNA microarrays in comparison to the normal retina gave an insight into several genes and pathways that were regulated in the tumor. The upregulated and the downregulated genes were further validated by quantitative real time PCR and tissue microarray (TMA) on retinoblastoma tumors. Theoverall goal is to determine the global gene expression profile in retinoblastoma tumors which is first of its kind on a whole genome microarray. Two coloured microarray:retinoblastoma tumor (4 samples) vs. normal retina (4 samples).

2012-03-30 | E-GEOD-33048 | biostudies-arrayexpress

Genome-wide identification of RETINOBLASTOMA RELATED 1 binding sites in Arabidopsis reveals novel DNA damage regulators.

Project description:Retinoblastoma (pRb) is a multifunctional regulator, which was likely present in the last common ancestor of all eukaryotes. The Arabidopsis pRb homolog RETINOBLASTOMA RELATED 1 (RBR1), similar to its animal counterparts, controls not only cell proliferation but is also implicated in developmental decisions, stress responses and maintenance of genome integrity. Although most functions of pRb-type proteins involve chromatin association, a genome-wide understanding of RBR1 binding sites in Arabidopsis is still missing. Here, we present a plant chromatin immunoprecipitation protocol optimized for genome-wide studies of indirectly DNA-bound proteins like RBR1. Our analysis revealed binding of Arabidopsis RBR1 to approximately 1000 genes and roughly 500 transposable elements, preferentially MITES. The RBR1-decorated genes broadly overlap with previously identified targets of two major transcription factors controlling the cell cycle, i.e. E2F and MYB3R3 and represent a robust inventory of RBR1-targets in dividing cells. Consistently, enriched motifs in the RBR1-marked domains include sequences related to the E2F consensus site and the MSA-core element bound by MYB3R transcription factors. Following up a key role of RBR1 in DNA damage response, we performed a meta-analysis combining the information about the RBR1-binding sites with genome-wide expression studies under DNA stress. As a result, we present the identification and mutant characterization of three novel genes required for growth upon genotoxic stress.

| S-EPMC6268010 | biostudies-literature