Epigenetics of atherosclerosis: emerging mechanisms and methods

N Khyzha, A Alizada, MD Wilson, JE Fish - Trends in molecular medicine, 2017 - cell.com
Atherosclerosis is a vascular pathology characterized by inflammation and plaque build-up
within arterial vessel walls. Vessel occlusion, often occurring after plaque rupture, can result …

Spatial-CUT&Tag: spatially resolved chromatin modification profiling at the cellular level

Y Deng, M Bartosovic, P Kukanja, D Zhang, Y Liu, G Su… - Science, 2022 - science.org
Spatial omics emerged as a new frontier of biological and biomedical research. Here, we
present spatial-CUT&Tag for spatially resolved genome-wide profiling of histone …

Detect accessible chromatin using ATAC-sequencing, from principle to applications

Y Sun, N Miao, T Sun - Hereditas, 2019 - Springer
Background Chromatin accessibility is crucial for gene expression regulation in specific cells
and in multiple biological processes. Assay for Transposase Accessible Chromatin with high …

ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data

J Ou, H Liu, J Yu, MA Kelliher, LH Castilla, ND Lawson… - BMC genomics, 2018 - Springer
Background ATAC-seq (Assays for Transposase-Accessible Chromatin using sequencing)
is a recently developed technique for genome-wide analysis of chromatin accessibility …

Single-cell transcriptome conservation in cryopreserved cells and tissues

A Guillaumet-Adkins, G Rodríguez-Esteban, E Mereu… - Genome biology, 2017 - Springer
A variety of single-cell RNA preparation procedures have been described. So far, protocols
require fresh material, which hinders complex study designs. We describe a sample …

Profiling chromatin regulatory landscape: insights into the development of ChIP-seq and ATAC-seq

S Ma, Y Zhang - Molecular biomedicine, 2020 - Springer
Chromatin regulatory landscape plays a critical role in many disease processes and embryo
development. Epigenome sequencing technologies such as chromatin immunoprecipitation …

Answer ALS, a large-scale resource for sporadic and familial ALS combining clinical and multi-omics data from induced pluripotent cell lines

EG Baxi, T Thompson, J Li, JA Kaye, RG Lim… - Nature …, 2022 - nature.com
Answer ALS is a biological and clinical resource of patient-derived, induced pluripotent stem
(iPS) cell lines, multi-omic data derived from iPS neurons and longitudinal clinical and …

Genome-wide epigenomic profiling for biomarker discovery

RAM Dirks, HG Stunnenberg, H Marks - Clinical epigenetics, 2016 - Springer
A myriad of diseases is caused or characterized by alteration of epigenetic patterns,
including changes in DNA methylation, post-translational histone modifications, or chromatin …

An integrated multi-omic analysis of iPSC-derived motor neurons from C9ORF72 ALS patients

H Phatnani, J Kwan, D Sareen, JR Broach, Z Simmons… - Iscience, 2021 - cell.com
Neurodegenerative diseases are challenging for systems biology because of the lack of
reliable animal models or patient samples at early disease stages. Induced pluripotent stem …

An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice

JPL Castro, MN Yancoskie, M Marchini, S Belohlavy… - elife, 2019 - elifesciences.org
Evolutionary studies are often limited by missing data that are critical to understanding the
history of selection. Selection experiments, which reproduce rapid evolution under …