Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Coupled single-cell epigenome editing and profiling reveals causal gene regulatory networks [Perturb-ATAC (ATAC)]

ABSTRACT: Coupled single-cell epigenome editing and profiling reveals causal gene regulatory networks [Perturb-ATAC (ATAC)]

PROVIDER: PRJNA478045 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Coupled single-cell epigenome editing and profiling reveals causal gene regulatory networks [Perturb-ATAC (ATAC)]

Project description:Here we present Perturb-ATAC, a method which combines multiplexed CRISPR interference or knockout with genome-wide chromatin accessibility profiling in single cells, based on the simultaneous detection of CRISPR guide RNAs and open chromatin sites by Assay of Transposase-accessible Chromatin with sequencing (ATAC-seq). We applied Perturb-ATAC to transcription factors (TFs), chromatin-modifying factors, and noncoding RNAs (ncRNAs) in ~3,700 single cells, encompassing more than 75 unique genotype-phenotype relationships.

2018-12-20 | GSE116249 | GEO

Coupled single-cell epigenome editing and profiling reveals causal gene regulatory networks [Perturb-ATAC (GBC/sgRNA)]

2018-12-20 | GSE116285 | GEO

Coupled single-cell epigenome editing and profiling reveals causal gene regulatory networks [Perturb-ATAC (GBC/sgRNA)]

Project description:Coupled single-cell epigenome editing and profiling reveals causal gene regulatory networks [Perturb-ATAC (GBC/sgRNA)]

| PRJNA478048 | ENA

Coupled single-cell epigenome editing and profiling reveals causal gene regulatory networks [Bulk ATAC-seq]

2018-12-20 | GSE116247 | GEO

Coupled single-cell epigenome editing and profiling reveals causal gene regulatory networks [scATAC-seq]

2018-12-20 | GSE116248 | GEO

Coupled single-cell epigenome editing and profiling reveals causal gene regulatory networks [Bulk ATAC-seq]

Project description:Coupled single-cell epigenome editing and profiling reveals causal gene regulatory networks [Bulk ATAC-seq]

| PRJNA478036 | ENA

Coupled single-cell epigenome editing and profiling reveals causal gene regulatory networks [scATAC-seq]

Project description:Coupled single-cell epigenome editing and profiling reveals causal gene regulatory networks [scATAC-seq]

| PRJNA478037 | ENA

Coupled single-cell CRISPR screening and epigenomic profiling reveals causal gene regulatory networks

Project description:Coupled single-cell CRISPR screening and epigenomic profiling reveals causal gene regulatory networks

| PRJNA478043 | ENA

Perturb-map coupled with spatial transcriptomics identifies mutation associated gene signatures in a mouse model of lung adenocarcinoma

Project description:The cellular architecture of a tumor has a major impact on cancer outcome, and thus there is interest in identifying genes controlling the tumor microenvironment (TME). While CRISPR screens are helping uncover genes regulating many cell-intrinsic processes, existing approaches are suboptimal for identifying gene functions operating extracellularly or within a tissue context. To address this, we developed an approach for spatial functional genomics called Perturb-map, which utilizes protein barcodes (Pro-Code) to enable spatial detection of barcoded cells within tissue. We applied Perturb-map to knockout dozens of genes in parallel in a mouse model of lung cancer and simultaneously assessed how each knockout influenced tumor growth, histopathology, and immune composition. Additionally, we paired Perturb-map and spatial transcriptomics for unbiased molecular analysis of Pro-Code/CRISPR lesions. Our studies found in Tgfbr2 knockout lesions, the TME was converted to a fibro-mucinous state and T-cells excluded, concomitant with upregulated TGFb and TGFb-mediated stroma activation, suggesting Tgfbr2 loss on lung cancer cells increased TGFb bioavailability and enhanced its suppressive effects on the TME. These studies establish Perturb-map for functional genomics within a tissue at single cell-resolution with spatial architecture preserved.

2022-01-15 | GSE193460 | GEO

Perturb-Seq using T2D islets

Project description:Perturb-Seq using T2D islets

| PRJNA568200 | ENA