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MeRIP-seq to explore the targets of METTL3 in pancreatic cancer

ABSTRACT: MeRIP-seq to explore the targets of METTL3 in pancreatic cancer

PROVIDER: PRJNA785790 | ENA |

REPOSITORIES: ENA

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MeRIP-seq to explore the targets of METTL3 in pancreatic cancer

Project description:We performed MeRIP-seq of METTL3-knockdown (KD) MIAPaCa-2 and control cells to detect METTL3-methylated genes and extracted genes whose methylation was lost in METTL3-KD cells compared with control cells. Next, we performed mRNA expression analysis using dates of input samples at MeRIP-seq. Genes whose methylation peaks were abolished by METTL3-KD and whose expression changes were observed were analyzed as candidates for METTL3-regulated genes.

2021-12-13 | GSE190078 | GEO

MeRIP-Seq of pancreatic islets in Mettl3flox/flox and islet β cell-specific Mettl3 knockout (β-Mettl3-KO) mice

Project description:Purpose: Through mRNA m6A-profiling, we aim to characterize the mRNA m6A changes in pancreatic islets obtained from Mettl3flox/flox and β-Mettl3-KO mice. Methods: Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany) from pancreatic islets of Mettl3flox/flox and β-Mettl3-KO mice at 8 weeks old. A total of 2-3 μg RNAs were pooled from nine Mettl3flox/flox mice and twelve β-Mettl3-KO mice, respectively. Three independent biological replicates of each group were used for MeRIP-seq. Fragmented RNA (~100 nt) was incubated for 2 hr at 4oC with anti-m6A polyclonal antibody (Merk Millipore) in the immunoprecipitation experiment. Then, immunoprecipitated RNAs or Input was used for library construction with Ovation SoLo RNA-Seq System Core Kit (NuGEN). The library preparations were sequenced on an Illumina Novaseq platform with a paired-end read length of 150 bp according to the standard protocols. After mapping reads to the reference genome, exomePeak R package (version 2.16.0) was used for the m6A peak identification in each anti-m6A immunoprecipitation group with the corresponding input samples serving as a control, and q-value threshold of enrichment of 0.05 was used for all data sets. The m6A-enriched motifs of each group were identified by HOMER (version 4.9.1). Conclusion: The islet mRNA m6A profiles in Mettl3flox/flox and β-Mettl3-KO mice were characterized.

2020-11-13 | GSE155614 | GEO

MeRIP-sequencing data from H1975 cells with NC or METTL3-sh

Project description:We use MeRIP-sequencing to evaluate the effect of METTL3 knockdown on the gene changes in H1975 cells.

2020-12-07 | GSE147171 | GEO

MeRIP-Seq (m6A-Seq) identifies the mRNA m6A modification target in negative control and METTL3 knockdwon HULEC-5a

Project description:To identify the molecular mechanism by which METTL3 regulates endothelial barrier function, we performed RNA-seq and MeRIP-seq in HULEC-5a cells with stable METTL3 knockdown and control cells. The RNA-seq results revealed that 437 transcripts were significantly downregulated (fold change <0.5) after METTL3 knockdown. The MeRIP-seq results revealed that the m6A peaks in 1011 transcripts were decreased in abundance (fold change >1.2). Intriguingly, 55 transcripts overlapped in the RNA-seq and MeRIP-seq data

2022-05-20 | GSE200648 | GEO

MeRIP-Seq of pancreatic islets in Mettl3flox/flox and islet β cell-specific Mettl3 knockout (β-Mettl3-KO) mice

Project description:MeRIP-Seq of pancreatic islets in Mettl3flox/flox and islet β cell-specific Mettl3 knockout (β-Mettl3-KO) mice

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METTL3 mediated m6A mRNA methylation regulates neutrophil activation through targeting TLR4 signaling (meRIP-Seq)

Project description:To investigate the effect of METTL3 function in the regulation of neutrophil activation, we established neutrophil METTL3 knock out mice by crossing METTL3flox/flox mice with Lyzm-cre mice. We then performed gene expression profiling analysis using data obtained from MeRIP-seq of isolated neutrophil from METTL3f/f and METTL3f/f Lyzm-Cre mice .

2023-03-31 | GSE225139 | GEO

Mettl3-mediated m6A Methylation Determines the Size of Endocrine Progenitor Pool and Postnatal Islet Mass

Project description:To investigate the role of RNA methyltransferase-like 3 (Mettl3)-mediated m6A modification in pancreatic endocrine differentiation in early embryonic period. We then performed m6A MeRIP-seq (GenSeq®️ m6A MeRIP Kit) at E15.5 Mettl3pKO pancreas group and E15.5 WT pancreas group

2023-04-16 | GSE229502 | GEO

TBK1-METTL3 axis facilitates antiviral immunity [MeRIP-seq]

Project description:TBK1-METTL3 axis facilitates antiviral immunity [MeRIP-seq]

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Determine the methyltransferase activities of METTL3, METTL14, and METTL16 via MeRIP-seq (m6A-seq)

Project description:All the three enzymes, METTL3, METTL14, and METTL16, belong to methyltransferase like (METTL) family and possess the ability to deposit N6-methyladenosine (m6A) in mRNA. Via immunofluorescence staining and wertern blotting, we discovered either METTL3 or METTL14 mainly localize in nuclear, but METTL16 localizes in both cytosol and nuclei. To compare the m6A methyltransferase activities of the three m6A 'writers' and better understand their differences, MeRIP-seq (m6A-seq) was conducted with poly(A) RNAs isolaed from HEK293T cells with METTL3, 14 and 16 knockout.

2021-10-28 | GSE182607 | GEO

METTL3-dependent m6A modification programs human neural progenitor cell proliferation [MeRIP-seq]

Project description:To investigate whether the role of METTL3 in hNPCs is dependent on its m6A activity,samples form neural progenitor cell (NPC) differentiation in the small molecule-assisted shut-off (SMASh) tagged hESC groups were collected. Gene expression levels were quantitated by RNA-seq analysis, and the potential target genes were identified by MeRIP-seq analysis and RIP-seq.

2023-11-22 | GSE242519 | GEO

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