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| Status |
Public on Dec 20, 2018 |
| Title |
Coupled single-cell epigenome editing and profiling reveals causal gene regulatory networks [Perturb-ATAC (ATAC)] |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
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.
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| |
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| Overall design |
Single-cell epigenome and perturbation identification in lymphoblastoid cells and epidermal keratinocytes.
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| |
|
| Contributor(s) |
Rubin AJ, Parker KR, Satpathy AT, Chang HY, Khavari PA |
| Citation(s) |
30580963 |
| Submission date |
Jun 25, 2018 |
| Last update date |
Mar 26, 2019 |
| Contact name |
Paul Khavari |
| Organization name |
Stanford University
|
| Street address |
269 Campus Drive, CCSR 2150
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL15520 |
Illumina MiSeq (Homo sapiens) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
|
| Samples (4207)
|
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| This SubSeries is part of SuperSeries: |
| GSE116297 |
Coupled single-cell CRISPR screening and epigenomic profiling reveals causal gene regulatory networks |
|
| Relations |
| BioProject |
PRJNA478045 |
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