Genomics

Dataset Information

0

Multiplex indexing approach for the detection of DNase I hypersensitive sites in single cells


ABSTRACT: Single cell chromatin accessibility assays reveal epigenomic variability at cis-regulatory elements among individual cells. We previously developed a single-cell DNase-seq assay (scDNase-seq) to profile accessible chromatin in a limited number of single cells. Here, we report a novel indexing strategy to resolve single-cell DNase hypersensitivity profiles based on bulk cell analysis. This new technique, termed indexing single-cell DNase sequencing (iscDNase-seq), employs the activities of terminal DNA transferase (TdT) and T4 DNA ligase to add unique cell barcodes to DNase-digested chromatin ends. By a three-layer indexing strategy, it allows profiling genome-wide DHSs for more than 15,000 single-cells in a single experiment. Application of iscDNase-seq to human white blood cells accurately revealed specific cell types and inferred regulatory transcription factors (TF) specific to each cell type. We found that iscDNase-seq detected DHSs with specific properties related to gene expression and conservation missed by scATAC-seq for the same cell type. Also, we found that the cell-to-cell variation in accessibility computed using iscDNase-seq data is significantly correlated with the cell-to-cell variation in gene expression. Importantly, this correlation is significantly higher than that between scATAC-seq and scRNA-seq, suggesting that iscDNase-seq data can better predict the cellular heterogeneity in gene expression compared to scATAC-seq. Thus, iscDNase-seq is an attractive alternative method for single-cell epigenomics studies.

ORGANISM(S): Homo sapiens

PROVIDER: GSE156017 | GEO | 2020/12/14

REPOSITORIES: GEO

Dataset's files

Source:
Action DRS
Other
Items per page:
1 - 1 of 1

Similar Datasets

2022-08-26 | GSE136987 | GEO
2015-11-25 | E-GEOD-61844 | biostudies-arrayexpress
2015-11-25 | GSE61844 | GEO
2018-07-23 | GSE96688 | GEO
2021-03-11 | GSE168620 | GEO
| PRJNA728882 | ENA
2015-05-07 | E-GEOD-68102 | biostudies-arrayexpress
2017-08-17 | GSE98561 | GEO
2016-06-03 | GSE76642 | GEO
| PRJNA587152 | ENA