Results 41 to 50 of about 186,580 (246)

Combining signal and sequence to detect RNA polymerase initiation in ATAC-seq data.

PLoS ONE, 2020
The assay for transposase-accessible chromatin followed by sequencing (ATAC-seq) is an inexpensive protocol for measuring open chromatin regions. ATAC-seq is also relatively simple and requires fewer cells than many other high-throughput sequencing ...
Ignacio J Tripodi, Murad Chowdhury, Margaret Gruca, Robin D Dowell   +3 more
doaj   +1 more source

Chromatin structure predicts survival in glioma patients

Scientific Reports, 2022
The pathological changes in epigenetics and gene regulation that accompany the progression of low-grade to high-grade gliomas are under-studied. The authors use a large set of paired atac-seq and RNA-seq data from surgically resected glioma specimens to ...
Matthew C. Garrett, Rebecca Albano, Troy Carnwath, Sanjit Shah, Daniel Woo, Michael Lamba, David R. Plas, Aditi Paranjpe, Krishna Roskin, Chuntao Zhao, Richard Lu   +10 more
doaj   +1 more source

simATAC: a single-cell ATAC-seq simulation framework [PDF]

Genome Biology, 2020
Abstract Single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) identifies regulated chromatin accessibility modules at the single-cell resolution. Robust evaluation is critical to the development of scATAC-seq pipelines, which calls for reproducible datasets for benchmarking.
Navidi, Zeinab, Zhang, Lin, Wang, Bo
openaire   +4 more sources

CoRE-ATAC: A deep learning model for the functional classification of regulatory elements from single cell and bulk ATAC-seq data.

PLoS Computational Biology, 2021
Cis-Regulatory elements (cis-REs) include promoters, enhancers, and insulators that regulate gene expression programs via binding of transcription factors.
Asa Thibodeau, Shubham Khetan, Alper Eroglu, Ryan Tewhey, Michael L Stitzel, Duygu Ucar   +5 more
doaj   +1 more source

AMULET: a novel read count-based method for effective multiplet detection from single nucleus ATAC-seq data

Genome Biology, 2021
Detecting multiplets in single nucleus (sn)ATAC-seq data is challenging due to data sparsity and limited dynamic range. AMULET (ATAC-seq MULtiplet Estimation Tool) enumerates regions with greater than two uniquely aligned reads across the genome to ...
Asa Thibodeau, Alper Eroglu, Christopher S. McGinnis, Nathan Lawlor, Djamel Nehar-Belaid, R. Kursawe, R. Marches, Daniel N. Conrad, G. Kuchel, Zev J. Gartner, J. Banchereau, M. Stitzel, A. E. Cicek, D. Ucar   +13 more
semanticscholar   +1 more source

ATAC2GRN: optimized ATAC-seq and DNase1-seq pipelines for rapid and accurate genome regulatory network inference

BMC Genomics, 2018
Background Chromatin accessibility profiling assays such as ATAC-seq and DNase1-seq offer the opportunity to rapidly characterize the regulatory state of the genome at a single nucleotide resolution.
Thomas J. F. Pranzatelli, Drew G. Michael, John A. Chiorini   +2 more
doaj   +1 more source

Optimization of ATAC-seq in wheat seedling roots using INTACT-isolated nuclei

BMC Plant Biology, 2023
Background The genetic information contained in the genome of an organism is organized in genes and regulatory elements that control gene expression.
Juan M. Debernardi, German Burguener, Kerry Bubb, Qiujie Liu, Christine Queitsch, Jorge Dubcovsky   +5 more
doaj   +1 more source

Integrated analysis of ATAC-seq and RNA-seq unveils the role of ferroptosis in PM2.5-induced asthma exacerbation.

International Immunopharmacology, 2023
BACKGROUND PM2.5 exposure increases asthma exacerbation risk and worsens airway inflammation and mucus secretion, but the underlying mechanisms, especially the epigenetic modification changes, are not fully understood. METHODS ATAC-seq was conducted in
Yi Zhang, M. Jiang, Ying Xiong, Lei Zhang, Anying Xiong, Junyi Wang, Xiang He, Guoping Li   +7 more
semanticscholar   +1 more source

SCALE method for single-cell ATAC-seq analysis via latent feature extraction

Nature Communications, 2019
Single-cell ATAC-seq (scATAC-seq) profiles the chromatin accessibility landscape at single cell level, thus revealing cell-to-cell variability in gene regulation.
Lei Xiong, Kui Xu, Kang Tian, Yanqiu Shao, Lei Tang, Ge Gao, Michael Q. Zhang, Tao Jiang, Q. Zhang   +8 more
semanticscholar   +1 more source

Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility

Nature Protocols, 2023
Natural sequence variation within mitochondrial DNA (mtDNA) contributes to human phenotypes and may serve as natural genetic markers in human cells for clonal and lineage tracing.
C. Lareau, Vincent Liu, C. Muus, Samantha D. Praktiknjo, Lena Nitsch, Pauline Kautz, Katalin D. Sandor, Yajie Yin, Jacob C. Gutierrez, K. Pelka, Ansuman T. Satpathy, A. Regev, V. Sankaran, Leif S. Ludwig   +13 more
semanticscholar   +1 more source