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

ABSTRACT: 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.

ORGANISM(S): Mus musculus

PROVIDER: GSE43634 | GEO | 2013/01/19

SECONDARY ACCESSION(S): PRJNA186869

REPOSITORIES: GEO

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

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. Mixed cell culture was performed with T cells in the presence of syngeneic 57BL/6, or allogeneic BALB/c Dendritic cells or cultivated with anti-CD3e and anti-CD28 mAB for 24 h. Purified T cells were processd for CLIP procedures and followed RNA isolation (miReasy Kit and TRIzol LS) and hybridization on Exiqon 6th generation miRCURY LNA microRNA Arrays and Affymetrix microarrays. We sought to obtain that the specific changes in the expression of miRNAs and/or mRNAs from those responding to non-specific stimulation and in allogeneic activated T cells.

2013-01-19 | E-GEOD-43634 | biostudies-arrayexpress

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. Mixed cell culture was performed with T cells in the presence of syngeneic 57BL/6, or allogeneic BALB/c dendritic cells or cultivated with anti-CD3e and anti-CD28 mAB9 for 24 h. Purified T cells were processde for CLIP procedures and followed by RNA isolation (TRIzol LS and miReasy Kit) and hybridization on Affymetrix microarrays and Exiqon 6th generation miRCURY LNA microRNA Arrays . We sought to obtain that the specific changes in the expression of miRNAs and/or mRNAs in allogeneic activated T cells during hematopoietic cells transplantation and that would be distinct from those responding to non-specific stimulation.

2013-01-19 | E-GEOD-43635 | biostudies-arrayexpress

Individual nucleotide resolution Crosslinking Immunoprecipitation (iCLIP)-seq

Project description:Purpose: to identify the AGO1-bound miRNAs and mRNAs in human endothelial cells subject to hypoxic condition (2% oxygen) Methods: human microvascular endothelial cells was cultured under normoxia (20% oxygen) or hypoxia (2%) oxygen for 24 hours. Total RNA was extracted and RNA and small RNA libraries were prepared for Seq. Results: We found substantial changes in AGO1-bound mRNAs due to hypoxia. A portion of CLIP-seq reads also reveal direct binding to miRNA to mRNA. Conclusions: hypoxia induces profound changes in mRNAs associated with AGO1.

2019-09-06 | GSE136907 | 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

High-throughput identification of miRNA targets using CLASH (crosslinking, ligation and sequencing of hybrids)

Project description:Purpose: Identification of miRNA-mRNA interactions in human cells. Method: We used the CLASH technique with PTH-tagged AGO1 protein as a bait. Results: In 6 experiments we identified more than 18,000 miRNA-mRNA interactions in human HEK293 cells, corresponding to targets of 399 miRNAs. Conclusions: The binding of most miRNAs includes the 5' seed region, but around 60% of seed interactions are noncanonical, containing bulged or mismatched nucleotides. Moreover, seed interactions are generally accompanied by specific, non-seed basepairing. 18% of miRNA-mRNA interactions involve the miRNA 3' end, with little evidence for 5' contacts, and some of these were functionally validated. Analyses of miRNA:mRNA basepairing showed that miRNA species systematically differ in their target RNA interactions, and strongly overrepresented motifs were found in the interaction sites of several miRNAs. We speculate that these affect the response of RISC to miRNA-target binding.

2013-08-30 | GSE50452 | GEO

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

High-throughput identification of miRNA targets using CLASH (crosslinking, ligation and sequencing of hybrids)

2013-08-30 | E-GEOD-50452 | biostudies-arrayexpress

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

Implementation of PAR-CLIP to characterize RNA-protein interactions in prokaryotes at nucleotide resolution

Project description:The identification of RNAs that are recognized by RNA-binding proteins (RNA-BPs) using techniques such as Crosslinking and Immunoprecipitation (CLIP) has revolutionized the genome-wide discovery of RNA-BP RNA targets. Among the different versions of CLIP that have been developed, the use of photoactivable nucleoside analogs has resulted in high efficiency photoactivable ribonucleoside-enhanced CLIP (PAR-CLIP) in vivo. Nonetheless, PAR-CLIP has not yet been applied in prokaryotes. To determine if PAR-CLIP can be used in prokaryotes, we determined suitable conditions for the incorporation of 4-thiouridine (4SU), a photoactivable nucleoside, into E. coli RNA and for the isolation of RNA crosslinked to RNA-BPs of interest. Applying this technique to Hfq, a well-characterized regulator of small RNA (sRNA)-messenger RNA (mRNA) interactions, we showed that PAR-CLIP identified most of the known sRNA targets of Hfq, as well as functionally relevant sites of Hfq-mRNA interactions at nucleotide resolution. Based on our findings, PAR-CLIP represents an improved method to identify both the RNAs and the specific regulatory sites that are recognized by RNA-BPs in prokaryotes.

2022-10-18 | MSV000090547 | MassIVE

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