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Genome-wide maps of chromatin state in AML12 cells [SAMMY-Seq]

ABSTRACT: We performed SAMMY (Sequential Analysis of Macro-Molecules accessibilitY) chromatin fraction assay followed by next-generation sequencing in WT and MATR3-depleted AML12 cells to investigate the epigenetic landscape of AML12.

ORGANISM(S): Mus musculus

PROVIDER: GSE228141 | GEO | 2023/06/28

REPOSITORIES: GEO

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Genome-wide maps of chromatin state in AML12 cells [ChIP-Seq]

Project description:We performed chromatin Immunoprecipitation (ChIP) assay followed by next-generation sequencingwith H3K9me3 and H3K27ac antibodies in WT AML12 cells to investigate the epigenetic landscape of AML12. And we performed ChIP-seq using H3K27me3 antibody in WT and MATR3-depleted AML12 cells.

2023-06-28 | GSE200241 | GEO

The nuclear matrix protein MATR3 maintains higher-order chromatin architecture [Hi-C]

Project description:The chromatin structure in eukaryotic nucleus is highly ordered and organized in hierarchical frameworks. We performed Hi-C assay in WT and MATR3-depleted AML12 cells to reveal the MATR3's role in AML12 cells.

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The transcriptome profile before and after knocking-down of nuclear matrix protein MATR3 [ssRNA-Seq]

Project description:We performed RNA-seq assay in WT and MATR3-depleted AML12 cells to reveal the trscriptiome associated with MATR3 protein. The libraries were constructed by poly-A enriched and strand-specific kits.

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The transcriptome profile after antisense L1 ASO treatment [ssRNA-Seq]

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Genome-wide maps of nuclear lamina interactions in AML12 cells.

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Project description:We performed RNA binding protein immunoprecipitation (RIP) assay with anti-IgG/anti-MATR3 antibody. The RNA libraries were constructed using rib-off and strand-specific kits. Next-generation sequencing (NGS) were performed to analyze MATR3-binding RNAs.

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Gene expression analysis of wildtype AML12 versus VWA8-null AML12 cells

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Effect of DUSP6 overexpression or knockdown on gene expression in AML12 cells

Project description:DUSP6 plays important roles in MAPK signaling pathway, but whether and how it is involved in liver funciton remains to be explored. Here, we performed RNA-seq analyses in AML12 cells where DUSP6 is disrupted. We overexpressed GFP-DUSP6 or GFP in AML12 cells, and tested the effects of DUSP6 increase on gene expression in AML12 cells. Meanwhile, we knocked down DUSP6 in AML12 cells and tested the effects of DUSP6 decrease on gene expression in AML12 cells. Taken together, we analyzed the changes of gene expression mediated by DUSP6, which provides new insights for the function of DUSP6 in liver

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Gene expression analysis of wildtype AML12 versus VWA8-null AML12 cells

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