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High throughput joint profiling of chromatin accessibility and protein levels in single cells [Tcell KO]

UID: 11057

Author(s): Mimitou, Eleni P.*, Lareau, Caleb A.*, Chen, Kelvin Y., Ludwig, Leif S., Smibert, Peter* * MSK affiliated

Description
Summary from GEO:

"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."

Overall design from GEO:

"Sorted human T-cells from 3 biological donors were activated and target genes were perturbed using CRISPR / Cas9. Gene KOs were generated in a pooled fashion using gRNAs targeting CD4 (HTO2), ZAP70 (HTO4), NFKB2 (HTO5), CD3E (HTO3 + HTO13), CD3E+CD4 (HTO3 + HTO12) and 2 non-targeting controls (NTCs; HTO1). Different gRNA replicates were encoded using HTO12 and HTO13 for CD4, ZAP70, NFKB2, and NTC conditions. Changes in chromatin accessibility and protein abundance were determined concomitantly in single cells."
Subject of Study
Homo sapiens
Subject(s)
Chromatin Immunoprecipitation Sequencing
Gene Expression Profiling
Gene Knockout Techniques
Hematopoiesis
RNA, Guide, CRISPR-Cas Systems
T-Lymphocytes
Access via GEO


Accession #: GSE156476

Access via BioProject


Accession #: PRJNA658083

Access via SRA


Accession #: SRP278087

Access Restrictions
Free to All
Access Instructions
The NCBI Gene Expression Omnibus, BioProject, and SRA databases provides open access to these files.
Associated Publications
Mimitou EP, Lareau CA, Chen KY, Zorzetto-Fernandes AL, Hao Y, Takeshima Y, Luo W, Huang TS, Yeung BZ, Papalexi E, Thakore PI, Kibayashi T, Wing JB, Hata M, Satija R, Nazor KL, Sakaguchi S, Ludwig LS, Sankaran VG, Regev A, Smibert P. Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells. Nat Biotechnol. 2021 Oct;39(10):1246-1258. Epub 2021 Jun 3. PMID: 34083792; PMCID: PMC8763625.
Equipment Used
Illumina NextSeq 550

Sequencing and array capabilities for transcriptome, targeted resequencing and genotype sequencing

Dataset Format(s)
TSV, TAR
Dataset Size
1.9 GB
Data Catalog Record Updated
2023-11-22