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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

Project description:The RNA-seq experiment looks for the role of methylation in the control of alternatives. Wild-type, lsm4-1, LSM4R and LSM4RxK in lsm4-1 background seedlings were grown on Murashige and Skoog (MS) medium containing 0.8% (w/v) agar for 12 days under continuous light at 22°C. Three biological replicates were collected. Whole seedlings were harvested and total RNA was extracted with RNeasy Plant Mini Kit (QIAGEN) following the manufacturer’s protocols. To estimate RNA concentration NanoDrop 2000c (Thermo Scientific) was used. Libraries were prepared and sequenced at the Max Planck-Genome-Centre Cologne (MP-GC).

2023-05-31 | E-MTAB-12370 | biostudies-arrayexpress

RIP-seq data for CCNT1

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

RNA m5C Methylation in breast cancer using MeRIP-Seq

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

Gene expression between dry and imbibed seeds in vitamin C defective (vtc) mutants and wild-type Arabidopsis thaliana

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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

Project description:An RIP experiment was performed in ARP1 cell following the instructions of the article.~5-20 × 10e6 cells were harvested and lysed. Protein A/G MagBeads pre-coated with 5μg of the antibody of interest (SFRS8, abcam) and incubated with cell lysate supernatant overnight at 4°C.The beads containing immunoprecipitated RNA-protein complex were treated with 150μL of Proteinase K buffer to digest the proteins. Specific binding RNAs were isolated by using TRIzol

2022-12-31 | GSE174823 | GEO

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

RNA-seq time-course analysis of the transcriptional dynamics of the two root-infecting fungi Colletotrichum tofieldiae (mutualistic) and Colletotrichum incanum (pathogenic) and their plant host Arabidopsis thaliana during root colonization

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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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