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.

Below are our main protocols for performing CITE-seq and Cell Hashing, specifically on Drop-seq or 10x Genomics single cell 3P chemistry (v2 and v3), followed by supplementary information and supplementary protocols for other technologies or instruments.

CITE-seq antibody-oligos (ADTs): These contain standard small TruSeq RNA read 2 sequences and can be amplified using Illumina’s Truseq Small RNA primer sets (RPIx – primers, see example RPI1 below).

Yes you can make and store CITE-seq panels! Once we know the best titrated concentration for each antibody we typically pool all antibodies at appropriate concentrations into larger panels, given these are directly and irreversibly covalently …

PUBLICATIONS LEAD OR CO-LEAD BY NYGCtech Our ECCITE-seq paper describing the capture of multiple modalities of information from single cells, including direct capture of guide RNAs (Nature Methods, online April 22, 2019). You can also access the pre-print on bioRxiv (online since November 8, 2018).

Rahul Satija’s lab (NYGC & NYU) has developed tools for read level processing of CITE-seq data (listed below) and has recently update their Seurat package to support multimodal data.

Collectively we refer to these capabilities as ECCITE-seq for Expanded CRISPR-compatible CITE-seq. The different modalities can be detected all together, or in desired combinations.

Apr 22, 2019 · 05-02-18: We updated CITE-seq and Cell Hashing to be compatible with the 10x Genomics 5P V (D)J kit. Details can be found here. 02-02-18: CITE-seq and Cell Hashing products, under the brand TotalSeq now available as custom products from BioLegend. Catalog products coming soon

CITE-seq & Cell Hashing Protocol For experiments involving Cell Hashing, use cost per cell calculator to plan experiments, determine number of hashes, number of cells to load, expected doublet rates (detected and undetected) and cost considerations:

Dec 21, 2018 · Cell Hashing is a method that enables sample multiplexing and super-loading on single cell RNA-sequencing platforms, developed in the Technology Innovation lab at the New York Genome Center in collaboration with the Satija lab.