Unknown

Dataset Information

0

Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation.


ABSTRACT: Analysis of chromatin accessibility can reveal transcriptional regulatory sequences, but heterogeneity of primary tissues poses a significant challenge in mapping the precise chromatin landscape in specific cell types. Here we report single-nucleus ATAC-seq, a combinatorial barcoding-assisted single-cell assay for transposase-accessible chromatin that is optimized for use on flash-frozen primary tissue samples. We apply this technique to the mouse forebrain through eight developmental stages. Through analysis of more than 15,000 nuclei, we identify 20 distinct cell populations corresponding to major neuronal and non-neuronal cell types. We further define cell-type-specific transcriptional regulatory sequences, infer potential master transcriptional regulators and delineate developmental changes in forebrain cellular composition. Our results provide insight into the molecular and cellular dynamics that underlie forebrain development in the mouse and establish technical and analytical frameworks that are broadly applicable to other heterogeneous tissues.

SUBMITTER: Preissl S 

PROVIDER: S-EPMC5862073 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature

altmetric image

Publications

Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation.

Preissl Sebastian S   Fang Rongxin R   Huang Hui H   Zhao Yuan Y   Raviram Ramya R   Gorkin David U DU   Zhang Yanxiao Y   Sos Brandon C BC   Afzal Veena V   Dickel Diane E DE   Kuan Samantha S   Visel Axel A   Pennacchio Len A LA   Zhang Kun K   Ren Bing B  

Nature neuroscience 20180212 3


Analysis of chromatin accessibility can reveal transcriptional regulatory sequences, but heterogeneity of primary tissues poses a significant challenge in mapping the precise chromatin landscape in specific cell types. Here we report single-nucleus ATAC-seq, a combinatorial barcoding-assisted single-cell assay for transposase-accessible chromatin that is optimized for use on flash-frozen primary tissue samples. We apply this technique to the mouse forebrain through eight developmental stages. Th  ...[more]

Similar Datasets

2018-01-27 | GSE100033 | GEO
| PRJNA390526 | ENA
| S-EPMC4329551 | biostudies-literature
| S-EPMC7804394 | biostudies-literature
| S-EPMC3772044 | biostudies-literature
| S-EPMC6896263 | biostudies-literature
| S-EPMC4536593 | biostudies-literature
| S-EPMC2581427 | biostudies-literature
| S-EPMC373381 | biostudies-literature
| S-EPMC5639698 | biostudies-literature