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| Status |
Public on Mar 01, 2019 |
| Title |
Expanding the CITE-seq tool-kit: Detection of proteins, transcriptomes, clonotypes and CRISPR perturbations with multiplexing, in a single assay |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
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.
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| 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<<<
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| Contributor(s) |
Mimitou E, Smibert P |
| Citation(s) |
31011186, 31465740 |
| Submission date |
Feb 08, 2019 |
| Last update date |
Oct 05, 2020 |
| Contact name |
Eleni Mimitou |
| E-mail(s) |
emimitou@gmail.com
|
| Organization name |
New York Genome Center
|
| Lab |
Technology Innovation Lab
|
| Street address |
101 Avenue of the Americas
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10013 |
| Country |
USA |
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| Platforms (3) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL22245 |
Illumina HiSeq 2500 (Homo sapiens; Mus musculus) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (24)
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| Relations |
| BioProject |
PRJNA521522 |
| SRA |
SRP184710 |
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