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Identification of miRNA target genes in C. elegans by RIP-chip-SRM

ABSTRACT: RIP-chip-SRM : a New Combinatorial Large Scale Approach Identifies a Set of Translationally Regulated bantam/miR 58 Targets in C. elegans RNA binding protein immunopurification + microarray + targeted protein quantification via Selected Reaction Monitoring This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE32944 | GEO | 2012/03/01

SECONDARY ACCESSION(S): PRJNA146457

REPOSITORIES: GEO

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Identification of miRNA target genes in C. elegans by RIP-chip-SRM

Project description:RIP-chip-SRM : a New Combinatorial Large Scale Approach Identifies a Set of Translationally Regulated bantam/miR 58 Targets in C. elegans RNA binding protein immunopurification + microarray + targeted protein quantification via Selected Reaction Monitoring This SuperSeries is composed of the following subset Series: GSE32941: Purification of TAP::ALG-1 complexes and associated RNA from mixed-stage TAP::ALG-1 transgenic (WS4303) and wild-type (N2) animals GSE32942: Microarray analysis of TAP::ALG-1 associated RNAs isolated from synchronized 'wild-type' animals and 'mir-58' mutants GSE32943: Expression analysis of WS4303 (wild type) vs WS5041 (mir-58 mutants) total mRNA Refer to individual Series

2012-03-01 | E-GEOD-32944 | biostudies-arrayexpress

trf4, trf5, and trf4-DADA mutant cells gene expression; Trf4p X-RIP-Chip

Project description:This SuperSeries is composed of the following subset Series: GSE16103: Wild-type versus trf4, trf5, and trf4-DADA mutant cells GSE16105: Trf4p in vivo crosslinking and ribonucleoprotein-immunopurification-chip analysis (X-RIP-Chip) Refer to individual Series

2010-06-24 | E-GEOD-16107 | biostudies-arrayexpress

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Project description:In vivo cross-linking and ribonucleoprotein-immunopurification experiments followed by microarray analysis of bound RNAs (X-RIP-chip). Cells expressing recombinant tandem-affinity purification (TAP)-tagged Trf4 protein were cross-linked with formaldehyde, and Trf4-containing ribonucleoprotein complexes were recovered by affinity selection on IgG-coupled beads (see linked protocol). As a control for non-specifically enriched RNAs, the same experiment was done with untagged WT cells and with cells expressing Fpr1-TAP, a peptidyl-prolyl-cis-trans-isomerase not expected to bind RNA. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Antigenic peptide used in IP: Protein A derivative Computed

2010-06-24 | E-GEOD-16105 | biostudies-arrayexpress

Trf4p in vivo crosslinking and ribonucleoprotein-immunopurification-chip analysis (X-RIP-Chip)

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Quantifying RNA binding sites transcriptome-wide using DO-RIP-seq

Project description:RNA-binding proteins (RBPs) and non-coding RNAs orchestrate post-transcriptional processes through the recognition of specific sites on targeted transcripts. Thus, understanding the connection between binding to specific sites and active regulation of the whole transcript is essential. Many immunoprecipitation techniques have been developed that identify either whole transcripts or binding sites of RBPs on each transcript using cell lysates. However, none of these methods simultaneously measures the strength of each binding site, and quantifies binding to whole transcripts. In this study, we compare current procedures and present Digestion Optimized (DO)-RIP-seq, a simple method that locates and quantifies RBP binding sites using a continuous metric. We have used the RBP HuR/ELAVL1 to demonstrate that DO-RIP-seq can quantify HuR binding sites with high coverage across the entire human transcriptome, thereby generating metrics of relative RNA binding strength. We demonstrate that this quantitative enrichment of binding sites is proportional to the relative in vitro binding strength for these sites. Also, we used DO-RIP-seq to quantify and compare HuR's binding to whole transcripts, thus allowing for seamless integration of binding site data with whole transcript measurements. Finally, we demonstrate that DO-RIP-seq is useful for identifying functional mRNA target sets, and binding sites where combinatorial interactions between HuR and AGO-microRNAs regulate the fate of the transcripts. Our data indicate that DO-RIP-seq will be useful for quantifying RBP binding events that regulate dynamic biological processes.

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MLL RIP-seq

Project description:MLL RIP-seq

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RIP-seq data for CCNT1

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2012-12-28 | E-GEOD-43170 | biostudies-arrayexpress

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Project description:We analyzed orbitofrontal cortex post-mortem brain tissue from patients. We generated an organellar proteome map from different subcellular fractions such as mitochondria (MIT), crude nuclear fraction (NUC) and cytoplasm (CYT) with the aim to monitor the subproteome changes using iTRAQ labelling for relative quantification and Selected Reaction Monitoring (SRM) for targeted quantification.

2019-10-10 | PXD014284 | Pride

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