Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Global analysis of enhancer targets: Mosaic-seq

ABSTRACT: Single-cell perturbation assays such as Mosaic-seq enable highly multiplexed functional assessment of enhancers in their endogenous genomic context. By introducing a few computational and experimental improvements, we expanded the Mosaic-seq analysis to capture the secondary gene targets of enhancers. Our analysis of >500 putative enhancers in K562 cells demonstrates that many secondary hits are shared among enhancers targeting different transcriptional factors, which reveals an interwoven enhancer-driven gene regulatory network. Together, our data underscore the flexibility of manipulating gene transcription by modifying enhancer activity.

ORGANISM(S): Homo sapiens

PROVIDER: GSE129826 | GEO | 2019/10/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Global analysis of enhancer targets: Bulk RNA-Seq validation

Project description:Single-cell perturbation assays such as Mosaic-seq enable highly multiplexed functional assessment of enhancers in their endogenous genomic context. By introducing a few computational and experimental improvements, we expanded the Mosaic-seq analysis to capture the secondary gene targets of enhancers. Our analysis of >500 putative enhancers in K562 cells demonstrates that many secondary hits are shared among enhancers targeting different transcriptional factors, which reveals an interwoven enhancer-driven gene regulatory network. Together, our data underscore the flexibility of manipulating gene transcription by modifying enhancer activity.

2019-10-31 | GSE129825 | GEO

Multiplexed engineering and analysis of endogenous enhancer activity in single cells: Mosaic-Seq of 10 enhancers in combination

Project description:Transcriptional enhancers orchestrate cell-type specific gene expression programs critical to eukaryotic development, physiology, and disease. However, despite the large number of enhancers now identified, only a small number have been functionally assessed. Here, we develop MOsaic Single-cell Analysis by Indexed CRISPR Sequencing (Mosaic-seq), a method that measures one direct phenotype of enhancer repression: change of the transcriptome, at the single cell level. Using dCas9-KRAB to suppress enhancer function, we first implement a multiplexed system to allow the simultaneous measurement of the transcriptome and detection of sgRNAs by single cell RNA sequencing. We validate this approach by targeting the HS2 enhancer in the well-studied beta-globin locus. Next, through computational simulation, we demonstrate strategies to robustly detect changes in gene expression in these single cell measurements. Finally, we use Mosaic-seq to target 71 hypersensitive regions belonging to 15 super-enhancers in K562 cells by utilizing a lentiviral library containing 241 unique-barcoded sgRNAs. Our results demonstrate that Mosaic-seq is a reliable approach to study enhancer function in single cells in a high-throughput manner.

2017-04-13 | GSE96827 | GEO

Multiplexed engineering and analysis of endogenous enhancer activity in single cells: Mosaic-Seq TNF-alpha treatment versus mock

2017-04-13 | GSE81749 | GEO

Multiplexed engineering and analysis of endogenous enhancer activity in single cells: Mosaic-Seq of beta-globin locus (separate infection)

2017-04-13 | GSE81748 | GEO

Multiplexed engineering and analysis of endogenous enhancer activity in single cells: Mosaic-Seq of beta-globin locus (pooled infection)

2017-04-13 | GSE81747 | GEO

Multiplexed engineering and analysis of endogenous enhancer activity in single cells: Mosaic-Seq of 15 SEs, 71 HSs, 241 sgRNAs

2017-04-13 | GSE81750 | GEO