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MIER1-FLAG ChIP-seq Analysis in Liver at 0 h and 24 h after 70% Partial Hepatectomy

ABSTRACT: MIER1-FLAG ChIP-seq Analysis in Liver at 0 h and 24 h after 70% Partial Hepatectomy

PROVIDER: PRJNA780074 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16937627.fastq.gz	Fastqsanger.gz
	SRR16937628.fastq.gz	Fastqsanger.gz
	SRR16937629.fastq.gz	Fastqsanger.gz
	SRR16937630.fastq.gz	Fastqsanger.gz

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MIER1-FLAG ChIP-seq Analysis in Liver at 0 h and 24 h after 70% Partial Hepatectomy

Project description:To explore how Mier1 influence liver regeneration, we performed chromatin immunoprecipitation followed by sequencing in liver tissues at 0 h and 24 h after 70% partial hepatectomy (PHx). Due to a lack of available MIER1 antibody for ChIP-seq analysis, exogenous liver expression of MIER1-FLAG under TBG promoter was executed using AAV vectors, and ChIP-seq was conducted using FLAG antibody. Liver tissues from animals receiving empty vectors were also collected for ChIP-seq with FLAG antibody as negative control to remove possible non-specific binding signals from FLAG antibody. We observed in total 9310 sites bound by MIER1 in total, with a majority of these binding sites around the transcription start sites or present in introns or exons. Further analysis combining the results from RNA-seq revealed a significant set of genes involved in cell cycle, DNA replication and chromosome organization, that were bound by MIER1 and upregulated after MIER1 loss in liver tissues 24 hours after surgery, indicating a direct functional regulation of these genes via MIER1.

2022-12-30 | GSE188747 | GEO

Analysis of Control and Liver-specific Mier1 KO Liver Transcriptomes after 70% Partial Hepatectomy

Project description:To explore how Mier1 affiects liver regeneration, we specifically knocked out Mier1 in mouse liver through adeno-associated virus (AAV). The mice we used were knocked in a Cre-induced Cas9 expression cassette. Through tail vein injection, we delivered the AAV expressing Cre-recombinase under TBG promoter, and sgRNA targeting Mier1 (AAV-Mier1 sgRNA), into the adult Cas9 knockin mice to knock out the Mier1 gene in liver. AAV vectors with no sgRNA inserted (AAV-Cre) were used in control animals. To assess the role of MIER1 in liver regeneration, we performed 70% partial hepatectomy, 3 weeks after AAV injection. We then performed RNA sequencing analysis on liver tissues collected from control and Mier1 ko groups at 0 h, 24 h, 36 h, 48 h and 72 h after partial hepatectomy. Interestingly, although MIER1 depletion did not cause a significant difference in expression of cell cycle genes before surgery, the increase of cell cycle gene expression during liver regeneration was significantly enhanced after MIER1 loss. Further analysis showed that after partial hepatectomy, MIER1 loss caused significant upregulation of genes enriched in cell proliferation relevant pathways.

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RNA-seq Analysis of Mier1 Effects in HFD Aging and Adipose Tissue Lipe Knockout Mice after 70% Partial Hepatectomy

Project description:To explore how Mier1 affiects high-fat diet-fed, aging and adipose tissue Lipe knockout mice liver regeneration, we specifically knocked out liver Mier1 in high-fat diet-fed, aging and adipose tissue Lipe knockout mice through adeno-associated virus (AAV). The mice we used were knocked in a Cre-induced Cas9 expression cassette. Through tail vein injection, we delivered the AAV expressing Cre-recombinase under TBG promoter, and sgRNA targeting Mier1 (AAV-Mier1 sgRNA), into the adult Cas9 knockin mice to knock out the Mier1 gene in liver. AAV vectors with no sgRNA inserted (AAV-Cre) were used in control animals. To assess the role of MIER1 in liver regeneration, we performed 70% partial hepatectomy on high-fat diet-fed, aging and adipose tissue Lipe knockout mice. We then performed RNA sequencing analysis on liver tissues collected from control and Mier1 ko groups at 0 h, 48h or 36 h after partial hepatectomy. RNA-seq analysis showed that after partial hepatectomy, MIER1 loss caused significant upregulation of genes enriched in cell proliferation relevant pathways.

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H3K27ac ChIP-seq Analysis in WT and MIER1 Depletion Liver Tissues at 0 h and 24 h after 70% Partial Hepatectomy

Project description:To explore how Mier1 influence the genome H3K27ac levels during liver regeneration, we performed H3K27ac chromatin immunoprecipitation followed by sequencing in control and liver-specific Mier1 ko liver tissues at 0 h and 24 h after 70% partial hepatectomy (PHx). The mice we used were knocked in a Cre-induced Cas9 expression cassette. Through tail vein injection, we delivered the AAV expressing Cre-recombinase under TBG promoter, and sgRNA targeting Mier1 (AAV-Mier1 sgRNA), into the adult Cas9 knockin mice to knock out the Mier1 gene in liver. AAV vectors with no sgRNA inserted (AAV-Cre) were used in control animals.Then we performed 70% partial hepatectomy, 3 weeks after AAV injection. Consistent with the increased expression of cell cycle genes during liver regeneration, we observed increased signals of H3K27ac at 24 h after hepatectomy, especially near some cell cycle genes, after MIER1 depletion in liver tissue.

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ATAC-seq Analysis in Control and Mier1 KO Mice Liver at 0 h and 24 h after 70% Partial Hepatectomy

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Analysis of Control and Liver-specific Mier1 KO Liver Transcriptomes after 70% Partial Hepatectomy

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MicroRNA data in the mouse liver at 48 hrs versus 0 hr post 70% partial hepatectomy

Project description:MicroRNAs have been reported to control liver regeneration though the underlying mechanisms remain largely unclear. We used microarrays to examine microRNA profiles in the mouse liver at 48 hrs versus 0 hr post 70% partial hepatectomy.

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Project description:RNA-seq Analysis of Mier1 Effects in HFD Aging and Adipose Tissue Lipe Knockout Mice after 70% Partial Hepatectomy

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H3K27ac ChIP-seq Analysis in WT and MIER1 Depletion Liver Tissues at 0 h and 24 h after 70% Partial Hepatectomy

Project description:H3K27ac ChIP-seq Analysis in WT and MIER1 Depletion Liver Tissues at 0 h and 24 h after 70% Partial Hepatectomy

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