The effects of WTAP on m6A mRNA modification pancreatic islets
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE215360 | GEO | 2023/01/31
REPOSITORIES: GEO
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Project description:The goal of this study is to investigate how WTAP regulates islet β-cell function. Islets were isolated from pancreatic islets of Wtapflox/flox and Wtap-βKO mice at 7 weeks old. One islet sample was combined from three mice. Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany). 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/mm10) with Hisat2 v2.0.5, and the aligned reads were used to quantify mRNA expression by using featureCounts v1.5.0-p3. Our study represents the first detailed analysis of islet transcriptomes from Wtapflox/flox and Wtap-βKO mice, generated by RNA-seq technology. The RNA-seq analysis showed that 3015 genes were downregulated and 2900 genes were upregulated in the pancreatic islets of Wtap-βKO mice.
2023-01-31 | GSE215156 | GEO
Project description:Through m6A mRNA-profiling, we aim to characterize the m6A mRNA changes in the hearts of Wtapflox/flox and Wtap-CKO mice.
2024-01-14 | GSE227174 | GEO
Project description:Purpose: Through mRNA m6A-profiling, we aim to characterize the mRNA m6A changes in the liver obtained from Wtapflox/flox and Wtap-HKO mice. Methods: Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany) from liver of Wtap flox/flox and Wtap-HKO mice at 8 weeks old. Each sample (300 μg total RNA) was pooled from 5 mice for each group. Two independent biological replicates for each group were used for m6ARIP-seq. Poly(A)+ RNA was purified using Dynabeads™ mRNA Purification Kit (Invitrogen) following the manufacturer’s instructions. Fragmented mRNA was incubated with m6A antibody (Synaptic System, 202003) for immunoprecipitation. Then, immunoprecipitated mRNAs or Input was used for library construction with NEBNext ultra RNA library prepare kit for Illumina (New England Biolabs).The library preparations were sequenced on an Illumina Novaseq 6000 platform with a paired-end read length of 150 bp according to the standard protocols. The m6A peaks were detected by exomePeak R package (version 2.16.0). The motif search was detected by HOMER(version 4.9.1). Conclusion: The mRNA m6A profiles in the liver of Wtapflox/flox and Wtap-HKO mice were characterized.
2022-06-02 | GSE192884 | GEO
Project description:Purpose: Through mRNA m6A-profiling, we aim to characterize the mRNA m6A changes in iBAT obtained from Wtapflox/flox and Wtap-BKO mice. Methods: Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany) from iBAT of Wtap flox/flox and Wtap-BKO mice at 8 weeks old. Each sample (300 μg total RNA) was pooled from 8 mice for each group. Poly(A)+ RNA was purified using Dynabeads™ mRNA Purification Kit (Invitrogen) following the manufacturer’s instructions. Fragmented mRNA was incubated with m6A antibody (Synaptic System, 202003) for immunoprecipitation. Then, immunoprecipitated mRNAs or Input was used for library construction with NEBNext ultra RNA library prepare kit for Illumina (New England Biolabs).The library preparations were sequenced on an Illumina Novaseq 6000 platform with a paired-end read length of 150 bp according to the standard protocols. The m6A peaks were detected by exomePeak R package (version 2.16.0). The motif search was detected by HOMER(version 4.9.1). Conclusion: The iBAT mRNA m6A profiles in Wtapflox/flox and BKO mice were characterized.
2022-10-19 | GSE202668 | GEO
Project description:Purpose: Through Single-nucleus transcriptome analysis, we aim to characterize the changes of cell heterogeneity in iBAT obtained from Wtap-BKO mice compared with that in Wtapflox/flox mice. Methods: Nuclei were isolated from iBAT of Wtap flox/flox and Wtap-BKO mice at 8 weeks old. Each sample was pooled from 4 mice for each group. Conclusion: The Single-nucleus transcriptomes of iBAT in Wtapflox/flox and BKO mice were characterized.
2022-10-20 | GSE202630 | GEO
Project description:Purpose: The goal of this study is to compare transcriptome profilings of liver from Wtapflox/flox and hepatocyte-specific Wtap knockout (HKO) mice. Methods: Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany) from livers of Wtap flox/flox and Wtap-HKO mice at 8 weeks old. mRNA profiles were generated by deep sequencing using an Illumina Novaseq platform. Paired-end clean reads were aligned to the mouse reference genome(Ensemble_GRCm38.p6) with TopHat (version 2.0.12), and the aligned reads were used to quantify mRNA expression by using HTSeq-count (version 0.6.1). Conclusion: Our study represents the first detailed analysis of hepatic mRNA profiles in Wtapflox/flox and Wtap-HKO mice at 8 weeks old, generated by RNA-seq technology. Our results showed that 3486 genes were downregulated, and 3706 genes were upregulated. Gene ontology (GO) analysis showed that downregulated genes were associated with small molecule catabolic process, fatty acid metabolic process, amino acid metabolic process, steroid metabolic process, cholesterol metabolic process, xenobiotic metabolic process, fatty acid beta-oxidation, alcohol metabolic process, and glucose metabolic process, whereas the upregulated genes were associated with wound healing, leukocyte migration, chemotaxis, and positive regulation of cytokine production.
2022-06-02 | GSE168850 | GEO
Project description:Purpose: The goal of this study is to determine whether hepatic deletion of Wtapaffects chromatin accessibility. Methods: Each liver sample was pooled from three Wtap-HKO and Wtapflox/flox mice, respectively. Three independent biological replicates of each group were used for ATAC-seq. 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 Wtapflox/flox and Wtap-HKO mice were characterized.
2022-06-02 | GSE168945 | GEO
Project description:N(6)-methyladenosine (m6A) plays an important role in the tumorigenesis and progression of cancers. However, the clinical significance of m6A and their regulatory mechanisms in nasopharyngeal carcinogenesis (NPC) remain largely unknown. In this study, we used the microarray analysis to study WTAP-mediated m6A modification profiles in human nasopharyngeal carcinoma cell line, HONE-1, by comparing 3 pairs of samples with or without WTAP knockdown.
2022-06-15 | GSE160644 | GEO
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
Project description:m6ARIP-Seq of liver in Wtapflox/flox and hepatocyte-specific Wtap knockout (HKO) mice
| PRJNA793678 | ENA