Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of mRNA clients of SYNJ2BP by RIP-seq

ABSTRACT: We discovered SYNJ2BP is an OMM-localized RNA binding protein. We identified the potential mRNA clients of SYNJ2BP by RIP-seq and validated by CLIP-qPCR.

ORGANISM(S): Homo sapiens

PROVIDER: GSE169264 | GEO | 2021/07/16

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Identification of mRNA clients of SYNJ2BP by RIP-seq

Project description:Identification of mRNA clients of SYNJ2BP by RIP-seq

| PRJNA715920 | ENA

Long noncoding RNA CCTT recruits CENP-C to centromeres by directly binding to centromeric DNA [RIP-Seq]

Project description:To identify potential lncRNAs that associate with CENP-C, RNA immunoprecipitation (RIP) using the CENP-C and control IgG antibody was performed in the whole-cell lysates of HeLa cells, followed by Illumina short-read sequencing (RIP-seq). We found three CENP-C-binding lncRNAs that meet the enrichment criteria (fold change > 2, p < 0.01), including AGAP2-AS1, GS1-124K5.4, and AC124789.1 (lnc-CCTT) . Consistent with the results of RIP-seq, RIP-qPCR assay in whole-cell lysates showed that all three lncRNAs could bind to CENP-C, while lnc-CCTT showing the most robust association of CENP-C. ). It is well-established that the localization of lncRNAs within the cell is the primary determinant of their molecular functions. RT-qPCR (quantitative PCR with reverse transcription) assay of subcellular fractionation and RNA fluorescence in situ hybridization (RNA-FISH) revealed that AGAP2-AS1 and GS1-124K5.4 dominantly distributed in the cytoplasm, whereas lnc-CCTT, specifically and almost exclusively, localized to the nucleus. Thus, lnc-CCTT appears to be a prime interacting RNA of CENP-C at centromere.

2022-04-20 | GSE149528 | GEO

STAT6 in mitochondrial outer membrane impairs mitochondrial fusion by inhibiting MFN2 dimerization

Project description:Although it is reported that mitochondria-localized nuclear transcription factors (TFs) regulate mitochondrial processes such as apoptosis and mitochondrial transcription/respiration, their functions and mechanisms of mitochondrial dynamics regulated by mitochondria-localized nuclear TFs are yet to be fully characterized. Here, we identify STAT6 as a mitochondrial protein that is localized in the outer membrane of mitochondria (OMM). In addition to regulating mitochondrial gene expression as a nuclear TF, STAT6 in OMM inhibits mitochondrial fusion by blocking MFN2 dimerization. This implies that STAT6 has dual role in overall mitochondrial process. Moreover, mitochondrial accumulation of STAT6 in response to these findings reveal that STAT6 is a new regulator of mitochondrial processes including mitochondrial biogenesis and fusion/fission mechanisms.

2024-04-01 | GSE255693 | GEO

Transcriptome-wide identification of IGF2BP binding RNAs by RIP-seq.

Project description:We identified the mRNA targets of the insulin-like growth factor-2 (IGF2) mRNA-binding proteins 1, 2, and 3 (IGF2BP1/2/3) by RNA immunoprecipitation and sequencing (RIP-seq). HEK293T cells transfected with Flag-tagged IGF2BP1/2/3 plasmids were expanded and UV-crosslinked before harvest. We performed RIP of individual IGF2BP using anti-Flag antibody from nuclear extractions, and identified the associated mRNAs by next generation sequencing. More than 5000 transcripts, including protein coding and non-coding transcripts, were identified from each RIP-seq sample.

2018-03-15 | GSE90639 | GEO

Identification of miR-203a target genes [RIP-seq]

Project description:To identify targets of miR-203a we coupled RNA-seq and AGO2-RNA immunoprecipitation (RIP-seq) in MCF10A cells expressing a control pre-miR-203a or control, empty vector

2023-10-30 | GSE244854 | GEO

Identification of CaMKIIβ binding lncRNAs in mouse hippocampus via RIP-seq

Project description:In order to screen for CaMKIIβ binding lncRNAs, we performed a RIP-seq analysis on mouse hippocampus. Potential CaMKIIβ binding RNAs are identified through differential expression analysis between CaMKIIβ RIP-seq results and the control groups, IgG and input. Differentially expressed genes are subsequently filtered by biotype and expression level.

2020-12-27 | GSE163873 | GEO

RNA immunoprecipitation sequencing (RIP-seq) of PQBP1 in ovarian cancer cells

Project description:Dysregulated expression of splicing factors has important roles in cancer development and progression. However, it remains a major challenge to identify the cancer-specific splicing variants. Here we demonstrated that splicing factor PQBP1 is commonly overexpressed in high-grade serous ovarian carcinoma (HGSOC) and high level of PQBP1 is associated with poor prognosis. To gain global insights into PQBP1-RNA binding property, RNA immunoprecipitation sequencing (RIP-seq) and SpyTag-based CLIP (SpyCLIP) were performed to analysis the interaction between PQBP1 and the target RNA.

2024-05-01 | GSE223090 | GEO

RIP-seq data for CCNT1

Project description:To demonstrate RIPSeeker program that is developed for RIP-seq analyses, we generated RIP-seq data corresponding to the protein CCNT1 in HEK293 cell line using standard RIP-seq protocols described in Zhao et al., (2010).

2012-12-28 | GSE43170 | GEO

Identification of AtGRP7 targets by RIP-seq

Project description:A key function for RNA-binding proteins in orchestrating plant development and environmental responses is well established. However, the lack of a genome-wide view on their in vivo binding targets and binding landscapes represents a gap in understanding the mode of action of plant RNA-binding proteins. Here, we conducted RNA Immunoprecipitation (RIP-seq) for genome-wide determining the binding repertoire of the circadian clock-regulated Arabidopsis thaliana glycine-rich RNA-binding protein AtGRP7.

2017-09-28 | GSE99464 | GEO

SELEX and RIP-Seq identification of nucleic acid sequences bound by CIRBP

Project description:SELEX (systematic evolution of ligands by exponential enrichment) and RNA Immunoprecipitation (RIP)-seq revealed that CIRBP directly binds the 3’UTR of Atp5g3.

2021-01-11 | GSE164523 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data