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Assay for Transposase-Accessible Chromatin in E4BP4 overexpressed RAW264.7 cells

ABSTRACT: ATACseq was performed by overexpressing E4BP4 in RAW264.7 cells using lentivirus.

ORGANISM(S): Mus musculus

PROVIDER: GSE233928 | GEO | 2024/03/31

REPOSITORIES: GEO

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Expression profiles of E4BP4 overexpression RAW264.7 cells

Project description:E4BP4 was overexpressed in RAW264.7 cells using lentivirus and RNAseq was performed.

2024-03-31 | GSE233929 | GEO

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Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to evaluate the gene expression of E4BP4 knockout (KO) RAW264.7 cells. Methods: We generated E4BP4-KO RAW264.7 Cell Line using CRISPR-CAS9 system. Control plasmid was encoding the Cas9 nuclease without gRNA sequence. Total RNA of E4BP4-KO and Control (CTRL) RAW264.7 cells was extracted. RAW264.7 cells RNA profiles were generated by deep sequencing for two groups (E4BP4-KO versus CTRL RAW264.7 cells) with three samples each. Results: There were significant differences between E4BP4-KO and CTRL RAW264.7 cells. Conclusions: Deletion of E4BP4 in RAW264.7 cells induced various changes at the transcription level.

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ChIP_seq for E4BP4 in RAW264.7 cells [RAW_ChIP-seq]

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ChIP-seq for E4BP4 in CD4+ T cell

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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type (WT) and E4BP4 Overexpressed Liver Transcriptomes

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to evaluate the effects of liver-specific E4BP4 overexpression under mouse albumin promoter on the liver glucose and lipid metabolism. Methods: We generated transgenic mice (TG) with liver-specific E4BP4 overexpression. Livers were isolated at Zeitgeber Time (ZT) 2 or 14 from transgenic mice and WT littermates and total RNA was extracted. Liver RNA profiles were generated by deep sequencing for four groups with three mouse samples each. Results: Compared with the livers from the WT mice, those from Transgenic mice featured 290 differentially expressed genes (DEGs) (106 at ZT2, 134 at ZT14, and 14 at both times). Conclusions: Lipid metabolism might be altered in the transgenic liver.

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Identification of candidate genes regulated by E4bp4 in murine bone marrow

Project description:E4bp4 is essential for the development of natural killer (NK) cells. We sought to identify downstream targets of E4bp4 by comparing mRNA expression in wild type vs. E4bp4 knockout Lineage-depleted bone marrow, which is enriched for haematopoietic progenitor cells. We then went on to validate these targets using real time PCR, genetic complementation assays and ChIP Total RNA was extracted from linege-depleted bone marrow from six wild type and six E4bp4 knockout mice. Labelled cDNA was hybridised to a GeneChip Mouse Gene 1.0 ST Array. The data generated was imported into GeneSpring GXv11 (Agilent) and normalised using the Robust Multi-Array (RMA16) algorithm. Genes were filtered on expression value between 20th and 100th percentile to remove those with very low or no expression across all the samples. A moderated t-test was applied to the data and p values were adjusted for multiple testing using a Benjamini-Hochberg False Discovery Rate correction.

2014-03-21 | E-GEOD-55014 | biostudies-arrayexpress

ChIP-seq for E4BP4 in the liver from transgenic mouse with liver specific E4BP4 overexpression

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Identification of candidate genes regulated by E4bp4 in murine bone marrow

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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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