AChIP: efficient, sensitive, robust ChIP-seq for economically important plant organs [ChIP-Seq]
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ABSTRACT:
PROVIDER: PRJNA1020082 | ENA |
REPOSITORIES: ENA
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Project description:aChIP: efficient, sensitive, robust ChIP-seq for economically important plant organs
| PRJNA1020073 | ENA
Project description:aChIP: efficient, sensitive, robust ChIP-seq for economically important plant organs [RNA-Seq]
| PRJNA1020081 | ENA
Project description:Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is crucial for profiling histone modifications and transcription factor binding throughout the genome. However, its application in economically important plant organs (EIPOs) such as seeds, fruits and flowers is challenging due to their sturdy cell walls and complex constituents. Here we present advanced ChIP (aChIP), an optimized method that efficiently isolates chromatin from plant tissues while simultaneously removing cell walls and cellular constituents. aChIP precisely profiles histone modifications in all 14 tested EIPOs and identifies transcription factor and chromatin-modifying enzyme binding sites. In addition, aChIP enhances ChIP efficiency, revealing numerous novel modified sites compared with previous methods in vegetative tissues. aChIP reveals the histone modification landscape for rapeseed dry seeds, highlighting the intricate roles of chromatin dynamics during seed dormancy and germination. Altogether, aChIP is a powerful, efficient and sensitive approach for comprehensive chromatin profiling in virtually all plant tissues, especially in EIPOs.
2024-04-28 | GSE243806 | GEO
Project description:Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a powerful method for profiling histone modifications and transcription factors binding throughout the genome. However, its application in economically important plant organs (EIPOs) such as seeds, fruits, tubers and flowers is challenging due to their sturdy cell walls and complex constituents. Here, we present advanced ChIP (aChIP), an optimized ChIP-seq strategy that efficiently isolates chromatin from plant tissues while simultaneously removing plant cell walls and cellular constituents. aChIP enables precise profiling of histone modifications in all tested EIPOs as well as transcription factors and chromatin-modifying enzymes. Notably, it significantly enhances ChIP efficiency and uncovers numerous novel modified sites compared to previous methods in vegetativetissues. Remarkably, aChIP unveils the first histone modification landscape of dry rapeseed seeds, illuminating the intricate roles of histone marks in EIPOs. Together, aChIP is a potent, efficient, and sensitive approach for comprehensive chromatin protein profiling across virtually all plant tissues, advancing plant epigenomics and functional genomics research, particularly within EIPOs.
2024-04-28 | GSE243804 | GEO
Project description:Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a powerful method for profiling histone modifications and transcription factors binding throughout the genome. However, its application in economically important plant organs (EIPOs) such as seeds, fruits, tubers and flowers is challenging due to their sturdy cell walls and complex constituents. Here, we present advanced ChIP (aChIP), an optimized ChIP-seq strategy that efficiently isolates chromatin from plant tissues while simultaneously removing plant cell walls and cellular constituents. aChIP enables precise profiling of histone modifications in all tested EIPOs as well as transcription factors and chromatin-modifying enzymes. Notably, it significantly enhances ChIP efficiency and uncovers numerous novel modified sites compared to previous methods in vegetativetissues. Remarkably, aChIP unveils the first histone modification landscape of dry rapeseed seeds, illuminating the intricate roles of histone marks in EIPOs. Together, aChIP is a potent, efficient, and sensitive approach for comprehensive chromatin protein profiling across virtually all plant tissues, advancing plant epigenomics and functional genomics research, particularly within EIPOs.
2024-04-28 | GSE243805 | GEO
Project description:Single-tube Linear DNA amplification (LinDA) for robust ChIP-seq
| PRJNA147265 | ENA
Project description:Robust Expansion of Human Pancreatic Progenitors by Small Molecules [ChIP-seq]
| PRJNA658808 | ENA
Project description:The individualized treatment of tumors has always been an urgent problem in clinical practice. Organoids-on-a-chip can reflect the heterogeneity of tumors and is a good model for in vitro anticancer drug screening. In this study, surgical specimens of patients with advanced colorectal cancer will be collected for organoid culture and organoids-on-a- chip. Use organoids-on-a-chip to screen tumor chemotherapy drugs, compare the results of patients’ actual medication regimens, and study the guiding role of organoids in the formulation of precise tumor treatment plans. The investigators will compare the response of organoids to drugs in vitro with the patient’s response to actual chemotherapy and targeted drugs and explore the feasibility and accuracy of organoids-on-a-chip based drug screening for advanced colorectal cancer. The project will establish a screening platform for chemotherapeutic drugs and targeted drugs based on colorectal cancer organoids to quickly and accurately formulate personalized treatment plans for clinical patients.
| 2385953 | ecrin-mdr-crc
Project description:Oncoimmunology represents a biomedical research discipline coined to study the roles of immune system in cancer progression with the aim of discovering novel strategies to arm it against the malignancy. Infiltration of immune cells within the tumor microenvironment is an early event that results in the establishment of a dynamic cross-talk. Here, immune cells sense antigenic cues to mount a specific anti-tumor response while cancer cells emanate inhibitory signals to dampen it. Animals models have led to giant steps in this research context, and several tools to investigate the effect of immune infiltration in the tumor microenvironment are currently available. However, the use of animals represents a challenge due to ethical issues and long duration of experiments. Organs-on-chip are innovative tools not only to study how cells derived from different organs interact with each other, but also to investigate on the crosstalk between immune cells and different types of cancer cells. In this review, we describe the state-of-the-art of microfluidics and the impact of OOC in the field of oncoimmunology underlining the importance of this system in the advancements on the complexity of tumor microenvironment.
| S-EPMC8032996 | biostudies-literature
Project description:Proteotoxicity from insufficient clearance of misfolded/damaged proteins underlies many diseases. Carboxyl terminus of Hsc70-interacting protein (CHIP) is an important regulator of proteostasis in many cells, having E3-ligase and chaperone functions and often directing damaged proteins towards proteasome recycling. While enhancing CHIP functionality has broad therapeutic potential, prior efforts have all relied on genetic upregulation. Here we demonstrate that CHIP-mediated protein turnover is markedly post-translationally enhanced by direct protein kinase G (PKG) phosphorylation at S20 (mouse, S19 human). This increases CHIP binding affinity to Hsc70, CHIP protein halflife, and consequent clearance of stress-induced ubiquitinated-insoluble proteins. PKGmediated CHIP-pS20 or expressing CHIP-S20E (phosphomimetic) reduces ischemic proteo- and cytotoxicity, whereas a phospho-silenced CHIP-S20A amplifies both. In vivo, depressing PKG activity lowers CHIP-S20 phosphorylation and protein, exacerbating proteotoxicity and heart dysfunction after ischemic injury. CHIP-S20E knock-in mice better clear ubiquitinated proteins and are cardio-protected. PKG activation provides post-translational enhancement of protein quality control via CHIP.
2021-09-09 | PXD021531 | Pride