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Assay for transposase-accessible chromatin-sequencing (ATAC-seq) of liver samples from Ythdc1flox/flox and Ythdc1-HKO mice, respectively.

ABSTRACT: Assay for transposase-accessible chromatin-sequencing (ATAC-seq) of liver samples from Ythdc1flox/flox and Ythdc1-HKO mice, respectively.

PROVIDER: PRJNA1143061 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	SRR30104600_1.fastq.gz	Fastqsanger.gz
	SRR30104600_2.fastq.gz	Fastqsanger.gz

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The effects of FOXA1 and FOXA2 on gene expression in Ythdc1-HKO livers

Project description:The goal of this study is to investigate how FOXA1 and FOXA2 regulates gene expression in Ythdc1-HKO livers. Four-week-old male Ythdc1flox/flox mice were injected with AAV8-TBG-βGal via tail vein. Four-week-old male Ythdc1-HKO mice were injected with equal amounts of AAV8-TBG-βGal, AAV8-TBG-FOXA1, or AAV8-TBG-FOXA2 via tail vein. Mice were sacrificed three weeks later.Total RNA was extracted from liver tissues using Tripure Isolation Reagent (Roche, Mannheim, Germany). RNA-seq was performed using Illumina novaseq x plus (n=3 for each group).

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Assay for transposase-accessible chromatin-sequencing (ATAC-seq) of liver samples from Ythdc1flox/flox and Ythdc1-HKO mice, respectively.

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Assay for transposase-accessible chromatin-sequencing (ATAC-seq) of liver samples in Wtapflox/flox and hepatocyte-specific Wtap knockout (Wtap-HKO) mice

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.

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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.

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Project description:The effects of YTHDC1 on liver function [YTHDC1 HKO]

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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.

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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

m6ARIP-Seq of liver in Wtapflox/flox and hepatocyte-specific Wtap knockout (HKO) mice

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.

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Title: RNA-seq analysis of mRNA profiles in the livers of HuR flox/flox and hepatocyte-specific HuR knockout (HKO) mice fed with an MCD for 3 weeks.

Project description:ionPurpose: The goal of this study is to investigate how HuR regulates NASH progression. Methods: The hepatic mRNA profiles of HuR flox/flox and hepatocyte-specific HuR knockout (HKO) mice (n=3 for each group) fed with an MCD for 3 weeks 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 HuR flox/flox and hepatocyte-specific HuR knockout (HKO) mice fed with an MCD for 3 weeks, generated by RNA-seq technology. Our results show that 353 genes were upregulated and 422 genes were downregulated. Gene Ontology (GO) analysis showed that genes related to leukocyte migration, leukocyte chemotaxis, cell chemotaxis, neutrophil migration and Fc receptor signaling pathway were significantly decreased, which contributes to the protective effects of NASH progression in HKO mice.

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

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.

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