henhaobio
Sign in

bioRxivMolecular BiologyPreprint

Integrated Spatial Transcriptomic and Proteomic Analysis of Fresh Frozen Tissue Based on Stereo-seq

Sha LiaoiD, Yang HengiD, Weiqing LiuiD, Jinqiong Xiang, Yong MaiD, Ligen CheniD, Xiuwen FengiD, Dongmei JiaiD, Diyan Liang, Caili Huang, Jiajun ZhangiD, Min JianiD, Kui SuiD, Mei LiiD, Yuin‐Han LohiD, Ao CheniD, Xun XuiD

PDFDOI
Structured summary available · Jump to summary ↓

Abstract

To simultaneously detect whole transcriptomes and protein markers on the same tissue section, we combined Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) and Stereo-seq to develop the Stereo-CITE-seq workflow. Here, we demonstrated that Stereo-CITE-seq can co-detect mRNAs and proteins in immune organs with high spatial resolution, reproducibility and accuracy.

Abstract summary

Claude Opus 5.5 · xhigh effort · 2 Nov 2026 · from the abstract

Stereo-CITE-seq combines CITE-seq with Stereo-seq to simultaneously profile whole transcriptomes and protein markers on the same fresh-frozen tissue section.

Profiling both whole transcriptomes and protein markers within the same tissue section requires integrating spatial transcriptomics with multiplexed protein detection. Stereo-CITE-seq pairs Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) with Stereo-seq to co-detect mRNAs and proteins spatially.

Key results

  1. ClaimedStereo-CITE-seq co-detects mRNAs and proteins on the same fresh-frozen immune organ tissue sections.

    Demonstrated on immune organ tissues and described in the abstract as achieving high spatial resolution, reproducibility, and accuracy, though no numerical metrics or protein marker counts are reported in the abstract. · Abstract

Methods, data and reproducibility

The Stereo-CITE-seq workflow integrates Stereo-seq with Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) on fresh-frozen tissue sections to co-detect whole transcriptomes and protein markers.

  • Fresh-frozen immune organ tissue sections assayed by Stereo-CITE-seq
Methods & tools
Stereo-CITE-seq, CITE-seq, Stereo-seq
Reproducibility gaps
Abstract only; organism species, number of protein markers, resolution metrics, and data accessions are not stated in the abstract.
Limitations (1)
  • The two-sentence abstract reports no quantitative metrics, sample sizes, protein marker counts, or species information for the profiled immune organs. · noted in this summary

Read this if you perform spatial multi-omics and want an experimental workflow for joint whole-transcriptome and protein profiling on fresh-frozen tissue sections.

Citations
68

Reproducibility ledger

Nobody has reported trying to reproduce this paper yet. Did you replicate an experiment or run the code? Your report saves the next lab a week.

Sign in to file a reproducibility report.

Related papers

Similarity Map
SelectedSame fieldCross-field
THISLiu '22Zhang '25Duchini '26Allen '26Kim '24Neil '23
71% semantic matchGenomics
Yang Liu, Marcello DiStasio, Graham Su+12 more·bioRxiv·Apr 1, 2022· 21 citations