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| Status |
Public on May 14, 2021 |
| Title |
High throughput joint profiling of chromatin accessibility and protein levels in single cells [Tcell_Intra] |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Other
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| Summary |
Recent technological advances have enabled massively parallel single-cell Assay for Transposase Accessible Chromatin by sequencing (scATAC-seq) to simultaneously profile the epigenomic landscape in thousands of individual cells. scATAC-seq methods sample genomic DNA accessible to transposases, but have not previously been combined with measurement of protein levels. Here, we present ATAC with Select Antigen Profiling by sequencing, ASAP-seq, a tool to simultaneously profile accessible chromatin and protein levels in thousands of single cells, pairing sparse scATAC data with robust detection of hundreds of cell surface and intracellular protein markers, and optionally, enriched mtDNA coverage for lineage tracing (mtscATAC-seq) with minimal impact on ATAC-seq data quality. ASAP-seq makes use of a novel bridging approach to utilize existing commercially available antibody:oligo conjugates developed for CITE-seq and related technologies. We demonstrate the utility of ASAP-seq in the context of hematopoietic differentiation, cell surface marker dynamics following peripheral blood mononuclear cell stimulation, and as a combinatorial decoder of multiplexed perturbations in primary T cells.
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| Overall design |
Sorted human T-cells from one biological donor were activated and target genes were perturbed using CRISPR / Cas9. Gene KOs were generated in a pooled fashion using gRNAs targeting CD69, CTLA4, IFNG, MKI67, CD28, CD45, PD1, CD4, CD3E, ZAP70 with two non-targeting controls. Changes in chromatin accessibility and protein abundance were determined concomitantly in single cells.
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| Contributor(s) |
Mimitou E, Lareau C, Chen K, Ludwig L, Smibert P |
| Citation(s) |
34083792 |
| Submission date |
Feb 04, 2021 |
| Last update date |
Aug 13, 2021 |
| Contact name |
Caleb Lareau |
| E-mail(s) |
lareauc@mskcc.org
|
| Organization name |
Memorial Sloan Kettering
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| Street address |
417 E 68th St, Zuckerman - ZRC 1132
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (6)
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| This SubSeries is part of SuperSeries: |
| GSE156478 |
High throughput joint profiling of chromatin accessibility and protein levels in single cells |
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| Relations |
| BioProject |
PRJNA699565 |
| SRA |
SRP304758 |
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