Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Formaldehyde-crosslinking and immunoprecipitation (FA-CLIP) sequencing to identify ECT2 targets in Arabidopsis

ABSTRACT: Developed an efficient method to identify RNA binding sites for RNA-binding proteins in plants.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE108117 | GEO | 2018/06/21

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Formaldehyde-crosslinking and immunoprecipitation (FA-CLIP) sequencing to identify ECT2 targets in Arabidopsis

Project description:Formaldehyde-crosslinking and immunoprecipitation (FA-CLIP) sequencing to identify ECT2 targets in Arabidopsis

| PRJNA422491 | ENA

RNA-seq and FA-CLIP studying ECT2 function in Arabidopsis

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-06-21 | GSE108119 | GEO

Decoding target genes of ESRP1 by crosslinking-immunoprecipitation and high-throughput sequencing (CLIP seq)

Project description:RNA-binding proteins and their mediated alternative splicing play important roles in tumor cell invasion and migration. Here, we report that ESRP1 is a key regulator of gastric cancer cell metastasis. Overexpression of ESRP1 inhibits the invasion and migration of gastric cancer cells, in vivo and in vitro. Through crosslinking-immunoprecipitation and high-throughput sequencing (CLIP seq), we revealed that ESRP1 binding to the CLSTN1 mRNA and mediated its exon skipping, which may be a key mechanism for its inhibition of gastric cancer cell invasion and metastasis. Taken together, our data provide a molecular framework for the role of ESRP1 in gastric cancer development.

2023-12-27 | GSE233931 | GEO

Expression data from mouse T cells after CLIP (Crosslinking immunoprecipitation) procedures

Project description:This SuperSeries is composed of the SubSeries listed below.

2013-01-19 | GSE43636 | GEO

Fast fixing and comprehensive identification to help improve real-time ligands discovery based on formaldehyde crosslinking, immunoprecipitation and SDS-PAGE separation.

Project description:BACKGROUND:Fast Fixation is necessary to study real-time protein-protein interactions under physiological conditions. Fast formaldehyde cross-linking can fix transient and weak protein interactions, thereby reducing the number of false negatives but producing great complexity. To reduce this complexity, immunoaffinity purification can Fish out complexes that include particular target proteins, but affinity-based co-purification has a limited capacity to eliminate nonspecific binding to beads and/or antibodies. To Filter out these complexes, SDS-PAGE is used to disrupt non-covalent bonds, thereby eliminating uncross-linked complexes and simultaneously providing molecular weight information for identification. RESULTS:We described a 4 F strategy to help improve real-time ligands discovery based on formaldehyde crosslinking, immunoprecipitation and SDS-PAGE separation: Fast Fix, Fish, and Filter, using albumin interactome as an example. The use of gel excision without staining makes this strategy comprehensive and sensitive. The target protein must be identified in the same slice as its ligands. The ligands must be identified in slices for the experimental group but not in the corresponding control slices. Only proteins that appear in the range of molecular weights equal to or greater than the sum of the proteins' theoretical molecular weights, together with the target, are considered ligands. In this study, 5 s of cross-linking with 10% formaldehyde was achieved in human blood. The use of this strategy identified 35 ligands for albumin. Comparison with four major previous studies of the albuminome revealed that 68.57% of the 35 ligands identified in our study were identified in these other studies. CONCLUSIONS:Fast cross-linking was achieved. The 4 F strategy can be used to identify real-time in situ interactions without prior intervention and to comprehensively identify ligands of particular target proteins with fewer false positives.

| S-EPMC3922604 | biostudies-literature

RNA-seq and FA-CLIP studying ECT2 function in Arabidopsis

Project description:RNA-seq and FA-CLIP studying ECT2 function in Arabidopsis

| PRJNA422488 | ENA

Expression data from mouse T cells after CLIP (Crosslinking immunoprecipitation) procedures (mRNA)

Project description:Molecular networks based on genome-wide mRNA and miRNA expression in activated T cells are interated by co-regulation with miRNA and protein-coding genes during immune responses, however, accurate prediction of miRs and their targets remains a challenge. Furthermore, the specific changes in the expression of miRNAs and/or mRNAs in allogeneic activated T cells during HCT would be distinct from those responding to non-specific stimulation. Recently, Ago-CLIP has been demonstrated to provide a robust platform for identification of precise miRNA-mRNA interactions by definitively distinguishing direct from indirect miRNA-target interactions. We utilized CLIP procedure followed by screening with standard microarray platforms for miRNA and mRNA transcripts to demonstrate the miR-mRNA landscape and identify novel molecular targets for modulating T cell responses.

2013-01-19 | GSE43635 | GEO

Expression data from mouse T cells after CLIP (Crosslinking immunoprecipitation) procedures (microRNA)

Project description:Molecular networks based on genome-wide mRNA and miRNA expression in activated T cells are integrated by co-regulation with miRNA and protein-coding genes during immune responses, however, accurate prediction of miRs and their targets remains a challenge. Furthermore, the specific changes in the expression of miRNAs and/or mRNAs in allogeneic activated T cells during HCT would be distinct from those responding to non-specific stimulation. Recently, Ago-CLIP has been demonstrated to provide a robust platform for identification of precise miRNA-mRNA interactions by definitively distinguishing direct from indirect miRNA-target interactions. We utilized CLIP procedure followed by screening with standard microarray platforms for miRNA and mRNA transcripts to demonstrate the miR-mRNA landscape and identify novel molecular targets for modulating T cell responses.

2013-01-19 | GSE43634 | GEO

Robust, Cost-Effective Profiling of RNA Binding Protein Targets with Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP).

Project description:Profiling of RNA binding protein targets in vivo provides critical insights into the mechanistic roles they play in regulating RNA processing. The enhanced crosslinking and immunoprecipitation (eCLIP) methodology provides a framework for robust, reproducible identification of transcriptome-wide protein-RNA interactions, with dramatically improved efficiency over previous methods. Here we provide a step-by-step description of the eCLIP method, along with insights into optimal performance of critical steps in the protocol. In particular, we describe improvements to the adaptor strategy that enables single-end enhanced CLIP (seCLIP), which removes the requirement for paired-end sequencing of eCLIP libraries. Further, we describe the observation of contaminating RNA present in standard nitrocellulose membrane suppliers, and present options with significantly reduced contamination for sensitive applications. These notes further refine the eCLIP methodology, simplifying robust RNA binding protein studies for all users.

| S-EPMC5991800 | biostudies-literature

Expression data from mouse T cells after CLIP (Crosslinking immunoprecipitation) procedures

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

2013-01-19 | E-GEOD-43636 | biostudies-arrayexpress