We present Omni-ATAC, an improved ATAC-seq protocol for chromatin accessibility profiling that works across multiple applications with substantial improvement of signal-to-background ratio and information content. The Omni-ATAC protocol generates chromatin accessibility profiles from archival frozen tissue samples and 50-μm sections, revealing the activities of disease-associated DNA elements in distinct human brain structures. The Omni-ATAC protocol enables the interrogation of personal regulomes in tissue context and translational studies.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5623106 | PMC |
| http://dx.doi.org/10.1038/nmeth.4396 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Integrating scRNA-seq and scATAC-seq with inter-type attention heterogeneous graph neural networks.
Brief Bioinform
November 2024
Department of Electronic Engineering, Tsinghua University, 100084 Beijing, China.
Single-cell multi-omics techniques, which enable the simultaneous measurement of multiple modalities such as RNA gene expression and Assay for Transposase-Accessible Chromatin (ATAC) within individual cells, have become a powerful tool for deciphering the intricate complexity of cellular systems. Most current methods rely on motif databases to establish cross-modality relationships between genes from RNA-seq data and peaks from ATAC-seq data. However, these approaches are constrained by incomplete database coverage, particularly for novel or poorly characterized relationships.
View Article and Find Full Text PDFDecreased expression of LEF1 caused defective decidualization by inhibiting IL-11 expression in patients with adenomyosis.
Mol Med
January 2025
Department of Obstetrics and Gynecology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
Reduced lymphoid enhancer-binding factor 1 (LEF1) expression in patients with adenomyosis during the mid-secretory phase leads to impaired endometrial receptivity, affecting embryo implantation. This study investigated the molecular mechanisms underlying reduced endometrial receptivity in 25 adenomyosis patients and 25 controls. Functional experiments were conducted using human endometrial stromal cells (HESCs) and TERT-immortalized HESCs(T-HESCs), with final validation performed using a mouse model.
View Article and Find Full Text PDFPAXIP1 is regulated by NRF1 and is a prognosis‑related biomarker in hepatocellular carcinoma.
Biomed Rep
March 2025
Department of Central Laboratory, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu 223300, P.R. China.
Hepatocellular carcinoma (HCC) is characterized by a poor prognosis globally. PAX-interacting protein 1 (PAXIP1) serves a key role in the development of numerous human cancer types. Nevertheless, its specific involvement in HCC remains poorly understood.
View Article and Find Full Text PDFDisruption of tumor-intrinsic PGAM5 increases anti-PD-1 efficacy through the CCL2 signaling pathway.
J Immunother Cancer
January 2025
Department of Radiation Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
Background: Immunosuppressive phenotype compromised immunotherapy efficacy of hepatocellular carcinoma. Tumor cells intrinsic mitochondria dynamics could pass effects on the extracellular microenvironment through mtDNA stress. PGAM5 anchors at mitochondria and regulates mitochondria functions.
View Article and Find Full Text PDFBinding of transcription factors (TFs) at gene regulatory elements controls cellular epigenetic state and gene expression. Current genome-wide chromatin profiling approaches have inherently limited resolution, complicating assessment of TF occupancy and co-occupancy, especially at individual alleles. In this work, we introduce Accessible Chromatin by Cytosine Editing Site Sequencing with ATAC-seq (ACCESS-ATAC), which harnesses a double-stranded DNA cytosine deaminase (Ddd) enzyme to stencil TF binding locations within accessible chromatin regions.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!