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RIP-seq experiment to evaluate the role of methylation of the spliceosome component LSM4 in the regulation of alternative splicing

ABSTRACT: The RIP-seq experiment was designed to look for the direct targets of LSM4 U6snRNP component. For this plants were grown in Murashige and Skoog (MS) plates in continuous light (LL) for 12 days and were vacuum-infiltrated with 1% formaldehyde for 15 min followed by quenching with 125 mM glycine. A whole-cell extract was prepared in RIP-lysis buffer. The extract was pre-cleared with Sepharose beads and subjected to immunoprecipitation with GFP-Trap beads (Chromotek). After extensive washing with RIP washing buffer, co-precipitated RNAs were extracted with Trizol (Invitrogen) and treated with DNase (Promega). Libraries were prepared and sequenced at the Max Planck-Genome-Centre Cologne (MP-GC).

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Arabidopsis thaliana

SUBMITTER:

PROVIDER: E-MTAB-12369 | biostudies-arrayexpress |

SECONDARY ACCESSION(S): ERP142628

REPOSITORIES: biostudies-arrayexpress

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RNA-seq experiment to evaluate the role of methylation of the spliceosome component LSM4 in the regulation of alternative splicing

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RIP-seq data for CCNT1

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2014-02-20 | E-GEOD-53370 | biostudies-arrayexpress

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2017-07-03 | E-MTAB-5103 | biostudies-arrayexpress

Human Argonaute Immunoaffinity Purification-associated RNA

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2010-06-20 | E-GEOD-18834 | biostudies-arrayexpress

The underlying mechanism by which SFRS8 exerted carcinogenesis and its potential targets in MM

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Explored the underlying mechanism by which ILF3 exerted carcinogenesis and its potential targets in MM

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Human Argonaute Immunoaffinity Purification-associated RNA

2009-11-10 | GSE18834 | GEO

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2016-03-17 | E-GEOD-70094 | biostudies-arrayexpress

circITGB6-pulled down proteins in A549 cells

Project description:A549 cells were transfected with 100 pmol DNA probes complementary to the back-splice site of circITGB6 or PDPN 3’UTR region. 24 h later, cells were washed with PBS and lysed with the lysis buffer (150 mM NaCl, 20 mM Tris-HCl, pH 7.5, 1.5 mM MgCl2, 0.5% NP-40, 0.5% Triton X-100, 10% glycerol, RNase inhibitors (Thermo Scientific), protease and phosphatase inhibitor cocktails). Pre-treated streptavidin magnetic beads were incubated with cell lysates at 4°C for 1 h, followed by washing five times with the washing buffer (20 mM Tri-HCl, pH7.5, 1 mM EDTA and 450 mM NaCl) and elution with Laemmli sample buffer. The circITGB6- or PDPN mRNA- interacting proteins were subjected to SDS-PAGE and visualized by coomassie blue staining or immunoblot analysis. Protein bands were excised and identified by LC-MS/MS mass spectrometry and Proteome Discoverer software (version 1.4; Thermo Scientific).

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