Simultaneous profiling of gene expression and chromatin accessibility in single cells

M Reyes, K Billman, N Hacohen… - Advanced …, 2019 - Wiley Online Library
Profiling multiple omic layers in a single cell enables the discovery and analysis of biological
phenomena that are not apparent from analysis of mono‐omic data. While methods for …

Profiling chromatin accessibility at single-cell resolution

S Sinha, AT Satpathy, W Zhou, H Ji… - Genomics …, 2021 - academic.oup.com
How distinct transcriptional programs are enacted to generate cellular heterogeneity and
plasticity, and enable complex fate decisions are important open questions. One key …

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

DA Cusanovich, R Daza, A Adey, HA Pliner… - Science, 2015 - science.org
Technical advances have enabled the collection of genome and transcriptome data sets
with single-cell resolution. However, single-cell characterization of the epigenome has …

[HTML][HTML] Cobolt: integrative analysis of multimodal single-cell sequencing data

B Gong, Y Zhou, E Purdom - Genome biology, 2021 - Springer
A growing number of single-cell sequencing platforms enable joint profiling of multiple omics
from the same cells. We present Cobolt, a novel method that not only allows for analyzing …

[HTML][HTML] Single-cell sequencing techniques from individual to multiomics analyses

Y Kashima, Y Sakamoto, K Kaneko, M Seki… - … & Molecular Medicine, 2020 - nature.com
Here, we review single-cell sequencing techniques for individual and multiomics profiling in
single cells. We mainly describe single-cell genomic, epigenomic, and transcriptomic …

Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells

EP Mimitou, CA Lareau, KY Chen… - Nature …, 2021 - nature.com
Recent technological advances have enabled massively parallel chromatin profiling with
scATAC-seq (single-cell assay for transposase accessible chromatin by sequencing). Here …

[HTML][HTML] Best practices for single-cell analysis across modalities

L Heumos, AC Schaar, C Lance, A Litinetskaya… - Nature Reviews …, 2023 - nature.com
Recent advances in single-cell technologies have enabled high-throughput molecular
profiling of cells across modalities and locations. Single-cell transcriptomics data can now …

[HTML][HTML] ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis

JM Granja, MR Corces, SE Pierce, ST Bagdatli… - Nature …, 2021 - nature.com
The advent of single-cell chromatin accessibility profiling has accelerated the ability to map
gene regulatory landscapes but has outpaced the development of scalable software to …

[HTML][HTML] Statistical single cell multi-omics integration

M Colomé-Tatché, FJ Theis - Current Opinion in Systems Biology, 2018 - Elsevier
Single cell high throughput genomic measurements are revolutionizing the fields of biology
and medicine, providing a means to tackle biological problems that have thus far been …

Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility

QR Xing, CA El Farran, YY Zeng, Y Yi… - Genome …, 2020 - genome.cshlp.org
Joint profiling of transcriptome and chromatin accessibility within single cells allows for the
deconstruction of the complex relationship between transcriptional states and upstream …