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

ABSTRACT: The goal of this study is to determine whether hepatic deletion of Ythdc1 affects chromatin accessibility.

ORGANISM(S): Mus musculus

PROVIDER: GSE273788 | GEO | 2025/06/15

REPOSITORIES: GEO

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

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

| PRJNA1143061 | ENA

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.

2022-06-02 | GSE168945 | GEO

Assay for transposase-accessible chromatin-sequencing (ATAC-seq) of heart samples from Wtapflox/flox and Wtap-CKO mice, respectively.

Project description:The goal of this study is to determine whether cardiac deletion of Wtap affects chromatin accessibility.

2024-01-14 | GSE227173 | GEO

The effects of YTHDC1 on liver function [YTHDC1 HKO]

Project description:The goal of this study is to investigate how YTHDC1 regulates liver function.

2025-06-15 | GSE227172 | GEO

The effects of YTHDC1 on liver function [YTHDC1 HKO]

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

| PRJNA943504 | ENA

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).

2025-06-15 | GSE297453 | 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

XIAP promotes metastasis of bladder cancer cells by ubiquitylating YTHDC1

Project description:X-linked inhibitor of apoptosis protein (XIAP), a member of the IAP family, is overexpressed in a variety of tumors and plays an important role in tumor progression. Increasing evidence suggests that XIAP promotes metastasis of bladder cancer but the underlying mechanism is not very clear. The RNA N6-methyladenosine (m6A) reader YTHDC1 regulates RNA splicing, nuclear transport, and mRNA stability and is a potential tumor target; however, its ubiquitin E3 ligase has not been described. In this study, screening of proteins that specifically interact with XIAP identified YTHDC1 to be its degradation substrate. Ectopic overexpression of XIAP promoted degradation of YTHDC1, and knockout of XIAP upregulated YTHDC1, which inhibited metastasis of bladder cancer. Furthermore, YTHDC1 reduced expression of matrix metalloproteinase-2 (MMP-2) by destabilizing its mRNA. These experiments revealed that XIAP promotes ubiquitination of YTHDC1, positively regulating expression of MMP-2 and promoting metastasis of bladder cancer. Collectively, these findings demonstrate that XIAP is a critical regulator of YTHDC1 and pinpoint the XIAP/YTHDC1/MMP-2 axis as a promising target for the treatment of bladder cancer.

2025-05-07 | PXD055868 | Pride

Assay for transposase-accessible chromatin-sequencing (ATAC-seq) of heart samples from Wtapflox/flox and Wtap-CKO mice, respectively.

Project description:Assay for transposase-accessible chromatin-sequencing (ATAC-seq) of heart samples from Wtapflox/flox and Wtap-CKO mice, respectively.

| PRJNA943503 | ENA

Protocol for assay of transposase accessible chromatin sequencing in non-model species.

Project description:The assay for transposase accessible chromatin (ATAC-seq) is a method for mapping genome-wide chromatin accessibility. Coupled with high-throughput sequencing, it enables integrative epigenomics analyses. ATAC-seq requires direct access to cell nuclei, a major challenge in non-model species such as small invertebrates, whose soft tissue is surrounded by a protective exoskeleton. Here, we present modifications of the ATAC-seq protocol for applications in small crustaceans, extending applications to non-model species. For complete information on the use and execution of this protocol, please refer to Buenrostro et al. (2013).

| S-EPMC7896190 | biostudies-literature

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