May 29, 2018
CITE-seq Protocols
- Marlon Stoeckius1,
- Peter Smibert1
- 1New York Genome Center
- Human Cell Atlas Method Development Community
External link: https://cite-seq.com/protocol/
Collection Citation: Marlon Stoeckius, Peter Smibert 2018. CITE-seq Protocols. protocols.io https://dx.doi.org/10.17504/protocols.io.ngzdbx6
License: This is an open access collection distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: February 26, 2018
Last Modified: May 29, 2018
Collection Integer ID: 10489
Keywords: cellular transcriptome, tags alongside the cellular transcriptome, cellular indexing of transcriptome, single cell rna, cell hashing, oligos act as synthetic transcript, epitopes by sequencing, transcriptome, 10x genomic, seq library preparation protocol, unbiased transcriptome analysis, new york genome center in collaboration, new york genome center, synthetic transcript, sequencing approach, barcoded antibody, surface proteins with different barcode, sequencing platform, sequencing, rna, performing cite, seq protocol, single cell, multimodal single cell phenotyping method, tagged antibody, seq run, cellular indexing, seq, expressed surface protein, antibody, cite, based scrna, detection of protein, seq protocols this collection
Abstract
This collection contains our main protocols for performing CITE-seq and Cell Hashing, specifically on Drop-seq or 10x Genomics single cell 3′ v2 chemistry.
CITE-seq:
Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) is a multimodal single cell phenotyping method developed in the Technology Innovation lab at the New York Genome Center in collaboration with the Satija lab.
CITE-seq uses DNA-barcoded antibodies to convert detection of proteins into a quantitative, sequenceable readout. Antibody-bound oligos act as synthetic transcripts that are captured during most large-scale oligodT-based scRNA-seq library preparation protocols (e.g. 10x Genomics, Drop-seq, ddSeq).
This allows for immunophenotyping of cells with a potentially limitless number of markers and unbiased transcriptome analysis using existing single-cell sequencing approaches.
Cell Hashing:
Sample multiplexing and super-loading on single cell RNA-sequencing platforms.
Cell Hashing uses a series of oligo-tagged antibodies against ubiquitously expressed surface proteins with different barcodes to uniquely label cells from distinct samples, which can be subsequently pooled in one scRNA-seq run. By sequencing these tags alongside the cellular transcriptome, we can assign each cell to its sample of origin, and robustly identify doublets originating from multiple samples.
Troubleshooting
