Results 61 to 70 of about 186,580 (246)

ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretation

Epigenetics & Chromatin, 2020
Background Chromatin dysregulation is associated with developmental disorders and cancer. Numerous methods for measuring genome-wide chromatin accessibility have been developed in the genomic era to interrogate the function of chromatin regulators.
Jake J. Reske, Mike R. Wilson, Ronald L. Chandler   +2 more
doaj   +1 more source

cisTopic: cis-Regulatory topic modelling on single-cell ATAC-seq data

Nature Methods, 2019
We present cisTopic, a probabilistic framework used to simultaneously discover coaccessible enhancers and stable cell states from sparse single-cell epigenomics data (http://github.com/aertslab/cistopic).
C. Bravo González-Blas, Liesbeth Minnoye, Dafni Papasokrati, S. Aibar, Gert J. Hulselmans, Valerie Christiaens, K. Davie, J. Wouters, S. Aerts   +8 more
semanticscholar   +1 more source

Hydrop enables droplet-based single-cell ATAC-seq and single-cell RNA-seq using dissolvable hydrogel beads

eLife, 2022
Single-cell RNA-seq and single-cell assay for transposase-accessible chromatin (ATAC-seq) technologies are used extensively to create cell type atlases for a wide range of organisms, tissues, and disease processes. To increase the scale of these atlases,
Florian V. De Rop, Joy N. Ismail, C. Bravo González-Blas, Gert J. Hulselmans, Christopher C. Flerin, Jasper Janssens, K. Theunis, Valerie Christiaens, J. Wouters, G. Marcassa, Joris de Wit, S. Poovathingal, S. Aerts   +12 more
semanticscholar   +1 more source

Cellcano: supervised cell type identification for single cell ATAC-seq data

Nature Communications, 2023
Accurately annotating cell types is a fundamental step in single-cell omics data analysis. Here, the authors develop a computational method called Cellcano based on a two-round supervised learning algorithm to identify cell types for scATAC-seq data and ...
Wenjing Ma, Jiaying Lu, Hao Wu
semanticscholar   +1 more source

maxATAC ATAC-seq Data

, 2022
ATAC-seq BED files for HepG2, HEK293, and LoVo cell lines used in maxATAC.
openaire   +4 more sources

Cell type-specific chromatin accessibility analysis in the mouse and human brain

Epigenetics, 2022
The Assay for Transposase Accessible Chromatin by sequencing (ATAC-seq) is becoming popular in the neuroscience field where chromatin regulation is thought to be involved in neurodevelopment, activity-dependent gene regulation, hormonal and environmental
Devin Rocks, Ivana Jaric, Lydia Tesfa, John M. Greally, Masako Suzuki, Marija Kundakovic   +5 more
doaj   +1 more source

Benchmarking algorithms for joint integration of unpaired and paired single-cell RNA-seq and ATAC-seq data

Genome Biology, 2023
Background Single-cell RNA-sequencing (scRNA-seq) measures gene expression in single cells, while single-nucleus ATAC-sequencing (snATAC-seq) quantifies chromatin accessibility in single nuclei.
Michelle Y. Y. Lee, Klaus H. Kaestner, Mingyao Li   +2 more
semanticscholar   +1 more source

Subtype‐specific enhancer RNAs define transcriptional regulators and prognosis in breast cancers

Molecular Oncology, EarlyView.
This study employed machine learning methodologies to perform the subtype‐specific classification of RNA‐seq data sets, which are mapped on enhancers from TCGA‐derived breast cancer patients. Their integration with gene expression (referred to as ProxCReAM eRNAs) and chromatin accessibility profiles has the potential to identify lineage‐specific and ...
Aamena Y. Patel, Peyman Zarrineh, Nathnael T. Tuffa, Jigar H. Sheth, Sumitra Mohan, Mudassar Iqbal, Sankari Nagarajan   +6 more
wiley   +1 more source

Transcript-indexed ATAC-seq for precision immune profiling [PDF]

Nature Medicine, 2018
T cells create vast amounts of diversity in the genes that encode their T cell receptors (TCRs), which enables individual clones to recognize specific peptide-major histocompatibility complex (MHC) ligands. Here we combined sequencing of the TCR-encoding genes with assay for transposase-accessible chromatin with sequencing (ATAC-seq) analysis at the ...
Ansuman T. Satpathy, Naresha Saligrama, Jason D. Buenrostro, Yuning Wei, Beijing Wu, Adam J. Rubin, Jeffrey M. Granja, Caleb A. Lareau, Rui Li, Yanyan Qi, Kevin R. Parker, Maxwell R. Mumbach, William S. Serratelli, David G. Gennert, Alicia N. Schep, M. Ryan Corces, Michael S. Khodadoust, Youn H. Kim, Paul A. Khavari, William J. Greenleaf, Mark M. Davis, Howard Y. Chang   +21 more
openaire   +4 more sources

Mapping genetic effects on cell type-specific chromatin accessibility and annotating complex immune trait variants using single nucleus ATAC-seq in peripheral blood

PLoS Genetics, 2023
Gene regulation is highly cell type-specific and understanding the function of non-coding genetic variants associated with complex traits requires molecular phenotyping at cell type resolution.
P. Benaglio, Jacklyn M Newsome, Jee Yun Han, Joshua Chiou, Anthony Aylward, Sierra Corban, Michael Miller, Mei-Lin Okino, Jaspreet Kaur, Sebastian Preissl, David U. Gorkin, K. Gaulton   +11 more
semanticscholar   +1 more source