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Related Experiment Video

Updated: Jun 18, 2026

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

Published on: April 30, 2011

High-plex protein and whole transcriptome co-mapping at cellular resolution with spatial CITE-seq.

Yang Liu^1,2,3,4,5, Marcello DiStasio^3,4,5, Graham Su^1,2

¹Department of Biomedical Engineering, Yale University, New Haven, CT, USA.

Nature Biotechnology

|February 24, 2023

Summary

Spatial CITE sequencing maps proteins and whole transcriptomes simultaneously in tissues. This advanced technique reveals distinct immune responses in human and mouse tissues, including at COVID-19 vaccine sites.

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Last Updated: Jun 18, 2026

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

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Published on: April 30, 2011

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

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Published on: July 6, 2022

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C

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Published on: October 14, 2022

Area of Science:

Single-cell biology
Immunology
Genomics

Background:

Co-indexing of transcriptomes and epitopes (CITE) enables simultaneous measurement of RNA and protein.
Integrating spatial information with molecular profiling is crucial for understanding tissue architecture and function.

Purpose of the Study:

To extend CITE sequencing to the spatial dimension for high-plex protein and whole transcriptome co-mapping.
To apply spatial CITE sequencing to analyze complex biological processes in mouse and human tissues.

Main Methods:

Spatial CITE sequencing was developed and applied to profile multiple mouse tissue types.
The method was further utilized to analyze 273 proteins and transcriptome in human tissues.

Main Results:

High-plex protein and whole transcriptome co-mapping was achieved in spatial dimensions.
Spatially distinct germinal center reactions in tonsil and early immune activation in skin at the COVID-19 vaccine site were identified.

Conclusions:

Spatial CITE sequencing is a powerful tool for high-resolution multi-omic tissue analysis.
The method provides insights into spatially resolved immune responses and cellular heterogeneity in health and disease.