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

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

PROVIDER: PRJNA650499 | ENA |

REPOSITORIES: ENA

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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

The effects of METTL3 on islet β-cell function

Project description:Purpose: The goal of this study is to investigate how METTL3 regulates islet β-cell function. 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. Each RNA sample was pooled from four Mettl3flox/flox and β-Mettl3-KO mice, respectively. Three independent biological replicates for each group were used for RNA-seq. RNA-seq was performed by deep sequencing using an Illumina Novaseq 6000 platform. Paired-end clean reads were aligned to the mouse reference genome(GRCm38.p6) with Hisat2 v2.0.5, and the aligned reads were used to quantify mRNA expression by using featureCounts v1.5.0-p3. Conclusion: Our study represents the first detailed analysis of islet transcriptomes from Mettl3flox/flox and β-Mettl3-KO mice, generated by RNA-seq technology. The RNA-seq analysis showed that 2560 genes were downregulated and 3408 genes were upregulated in the pancreatic islets of β-Mettl3-KO mice. GO analysis showed that the downregulated genes were primarily related to insulin secretion, SNARE binding, and mitochondrial respiratory chain, whereas the upregulated genes were associated with the immune response, B cell activation, and antigen binding.

2020-11-13 | GSE155612 | GEO

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

RNA-seq analysis of mRNA profiles in the livers of Mettl3 flox/flox and hepatocyte-specific Mettl3 knockout (HKO) mice

Project description:Purpose: The goal of this study is to compare transcriptome profilings of liver from Mettl3 flox/flox and hepatocyte-specific Mettl3 knockout (HKO) mice. Methods: Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany) from livers of Mettl3 flox/flox and HKO mice at 8 weeks old. mRNA profiles were generated by deep sequencing using an Illumina HiSeq X Ten platform. Paired-end clean reads were aligned to the mouse reference genome(Ensemble_GRCm38.90) with Hisat2 (version 2.0.4), and the aligned reads were used to quantify mRNA expression by using HTSeq (version 0.9.1). Conclusion: The hepatic mRNA profiles in Mettl3 flox/flox and HKO mice were characterized.

2021-10-29 | GSE141216 | GEO

ATAC-seq of liver samples in Mettl3 flox/flox and hepatocyte-specific Mettl3 knockout (HKO) mice

Project description:Purpose: The goal of this study is to determine whether hepatic deletion of Mettl3 affects chromatin accessibility. Methods: Liver samples were pooled from livers of Mettl3 HKO and Mettl3 flox/flox mice (n=4 for each group). Nuclei was extracted from liver samples, and the nuclei pellet was resuspended in the Tn5 transposase reaction mix. The transposition reaction was incubated at 37°C for 30 min. Equimolar Adapter1 and Adatper 2 were added after transposition, PCR was then performed to amplify the library. After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed with Qubit. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufactuer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina NovaSeq 6000 platform and 150 bp paired-end reads were generated. ATAC-seq analysis was performed using a standard protocol. Results: The hepatic chromatin accessibility in Mettl3 flox/flox and HKO mice were characterized.

2021-10-29 | GSE141245 | GEO

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

m6A MeRIP-Seq of liver in Mettl3flox/flox and hepatocyte-specific Mettl3 knockout (HKO) mice

Project description:Purpose: Through mRNA m6A-profiling, we aim to characterize the mRNA m6A changes in the liver obtained from Mettl3flox/flox and HKO mice. Methods: Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany) from liver of Mettl3 flox/flox and HKO mice at 8 weeks old. Each sample (300 μg total RNA) was pooled from 3 mice for each group. Poly(A)+ RNA was purified using Dynabeads™ mRNA Purification Kit (Invitrogen) following the manufacturer’s instructions. Chemically fragmented poly(A)+ RNA was incubated with m6A antibody (Synaptic System, 202003) for immunoprecipitation following the standard protocol of Magna MeRIPTM m6A Kit (MERCK, 17-10499). Enrichment of m6A mRNA was then analyzed by high-throughput sequencing using Illumina Hiseq X platform. The m6A peaks were detected by MACS2. The motif search was detected by MEME and DREME. Conclusion: The mRNA m6A profiles in the liver of Mettl3flox/flox and HKO mice were characterized.

2021-10-29 | GSE142835 | GEO

m6A MeRIP-Seq of liver in Mettl3flox/flox and hepatocyte-specific Mettl3 knockout (HKO) mice

Project description:m6A MeRIP-Seq of liver in Mettl3flox/flox and hepatocyte-specific Mettl3 knockout (HKO) mice

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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

ATAC-seq of liver samples in Mettl3 flox/flox and hepatocyte-specific Mettl3 knockout (HKO) mice

Project description:ATAC-seq of liver samples in Mettl3 flox/flox and hepatocyte-specific Mettl3 knockout (HKO) mice

| PRJNA592920 | ENA