Single-cell ATAC-seq data are sparse and noisy, and analyzing such data is challenging. Existing computational methods cannot accurately reconstruct activities of individual cis-regulatory elements (CREs) in individual cells or rare cell subpopulations. We present a new statistical framework, SCATE, ...
and then sequenced on a single flow cell. Assuming the FASTQs have been generated withcellranger-atac mkfastq, you just need to runcellranger-atac countas described
Fig. 1: Chromatin reprogramming in enzalutamide resistance. aOverview of the cell-line models, assays, and treatments included in the study. Boxes with sample names are colored according to the data types generated from the sample (single-cell (sc) assay for transposase-accessible chromatin (ATAC...
Single-cell ATAC sequencing analysis: from data preprocessing to hypothesis generation. Comput. Struct. Biotechnol. J. 18, 1429–1439 (2020). Article CAS PubMed PubMed Central Google Scholar Chen, H. et al. Assessment of computational methods for the analysis of single-cell ATAC-seq data. ...
Cellatac functionality Running cellatac Cellatac needs Useful options Example invocations Downstream analysis Outputs Introduction Sanger Cellular Genetics ATAC-seq pipeline by Luz Garcia Alonso, Simon Murray, Ni Huang and Stijn van Dongen. cellatactakes scATAC-seq aligned data (such as the fragments fi...
到了2011年Nicholas等人开发了单细胞基因组测序技术。2013年又开发出了单细胞全基因组DNA甲基化检测技术。随后,科学家在细胞分选技术、核酸扩增技术、信噪比提高方面等进行不断优化和改进,也进一步开创了单细胞Hi-C、单细胞ChIP-seq、单细胞ATAC-seq技术等。
Lei Xiong, Kui Xu, Kang Tian, Yanqiu Shao, Lei Tang, Ge Gao, Michael Zhang, Tao Jiang & Qiangfeng Cliff Zhang. SCALE method for single-cell ATAC-seq analysis via latent feature extraction. Nature Communications, (2019). Releases5
To comprehensively delineate chromatin accessibility during root development of an important crop, we applied single-cell ATAC-seq (scATAC-seq) to 46,758 cells from rice root tips under normal and heat stress conditions. Our data revealed cell type-specific accessibility variance across most of the...
Motivation: The assay for transposase-accessible chromatin using sequencing (ATAC-seq) reveals the landscape and principles of DNA regulatory mechanisms by identifying the accessible genome of mammalian cells. When done at single-cell resolution, it provides an insight into the cell-to-cell variability...
dysfunction and type 2 diabetes instigators such asHHEX, HMGA2, GLIS3, MTNR1B,PARK2and some previously associated single-nucleotide polymorphisms (SNPs) (Bysani et al.2019). Furthermore, a large proportion of ATAC-seq peaks were mapped near to transcription start sites for easy manipulation ...