Multi-modal single-cell assays provide high-resolution snapshots of complex cell populations but are mostly limited to transcriptome plus an additional modality. Here, we describe Expanded CRISPR-compatible Cellular Indexing of Transcriptomes and Epitopes by sequencing (ECCITE-seq) for the high-throughput characterization of at least five modalities of information from each single cell. We demonstrate application of ECCITE-seq to multimodal CRISPR screens with robust direct sgRNA capture and to clonotype-aware multimodal phenotyping of cancer samples.
Overall design: All experiments were performed using the 10x genomics V(D)J solution which incorporates scRNA-seq with additional profiling of protein surface markers and sgRNAs (when present). Antibody oligo counts are listed in the ADT and HTO tables and sgRNAs counts in the GDO tables.
>>>The raw data for the samples GSM3596095, GSM3596098, GSM3596099, GSM3596100, GSM3596103, and GSM3596104 are being submitted to dbGaP due to patient privacy concerns<<<
| Accession | PRJNA521522; GEO: GSE126310 |
| Scope | Multispecies |
| Publications | - Herrera A et al., "Low SATB1 Expression Promotes IL-5 and IL-9 Expression in Sézary Syndrome.", J Invest Dermatol, 2020 Mar;140(3):713-716
- Mimitou EP et al., "Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells.", Nat Methods, 2019 May;16(5):409-412
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| Submission | Registration date: 8-Feb-2019
Technology Innovation Lab, New York Genome Center |
| Relevance | Unknown |
Project Data:
| Resource Name | Number
of Links |
|---|
| Sequence data |
| SRA Experiments | 18 |
| Publications |
| PubMed | 2 |
| PMC | 2 |
| Other datasets |
| BioSample | 24 |
| GEO DataSets | 1 |