Evidence map›Paper›PMID 42498883›Full record

ArticleNature methods2026

Full-length single-cell spatial transcriptomics reveals spatial and cell-type-specific transcript isoforms in the primate brain.

Hengxin Liu, Yanhong Hong, Yao Santo Zhang, Liyuan Xi, Huiying Yan, Yuxuan Liu, Qianqian Yang, Xing Sun, Shouliang Guan, Zan Chen and 16 more

Abstract read
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In one paragraph

Article in Nature methods, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

26 authors.

Hengxin Liu *Lingang Laboratory, Shanghai, China.ORCID http://orcid.org/0000-0002-8994-5494
Yanhong Hong *Lingang Laboratory, Shanghai, China.
Yao Santo Zhang *Lingang Laboratory, Shanghai, China.ORCID http://orcid.org/0009-0006-8683-9369
Liyuan XiShanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
Huiying YanLingang Laboratory, Shanghai, China.
Yuxuan LiuLingang Laboratory, Shanghai, China.
Qianqian YangLingang Laboratory, Shanghai, China.
Xing SunLingang Laboratory, Shanghai, China.
Shouliang GuanLingang Laboratory, Shanghai, China.
Zan ChenLingang Laboratory, Shanghai, China.ORCID http://orcid.org/0009-0008-0879-9765
Yu FengState Key Laboratory of Genome and Multi-omics Technologies, BGI Research, Shenzhen, China.ORCID http://orcid.org/0000-0001-8358-8740
Tao ZengState Key Laboratory of Genome and Multi-omics Technologies, BGI Research, Shenzhen, China.
Juan MengInstitute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.ORCID http://orcid.org/0000-0001-8495-1388
Sha LiaoState Key Laboratory of Genome and Multi-omics Technologies, BGI Research, Shenzhen, China.
Nini YuanInstitute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
Zhen LiuLingang Laboratory, Shanghai, China.ORCID http://orcid.org/0000-0001-5671-2320
Chao LiInstitute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
Zhiyong LiuInstitute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
Lei HanState Key Laboratory of Genome and Multi-omics Technologies, BGI Research, Shenzhen, China.ORCID http://orcid.org/0000-0002-7535-7915
Zhiming ShenInstitute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.ORCID http://orcid.org/0000-0003-4560-7650
Ao ChenState Key Laboratory of Genome and Multi-omics Technologies, BGI Research, Shenzhen, China.
Yidi SunInstitute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
Yuliang DongState Key Laboratory of Genome and Multi-omics Technologies, BGI Research, Shenzhen, China.
Longqi LiuState Key Laboratory of Genome and Multi-omics Technologies, BGI Research, Shenzhen, China.
Chengyu LiLingang Laboratory, Shanghai, China.
Wu WeiLingang Laboratory, Shanghai, China. wuwei@lglab.ac.cn.ORCID http://orcid.org/0000-0001-5643-8739

Funding

National Natural Science Foundation of China (National Science Foundation of China) 81870187National Natural Science Foundation of China (National Science Foundation of China) 81911530167
6 · The paper itself

Abstract

The primate brain exhibits complex RNA alternative splicing heterogeneity crucial for functional complexity, yet systematic spatial isoform characterization has been lacking. We developed Fullscope-seq, a full-length single-molecule large field-of-view spatial transcriptomics sequencing method at single-cell resolution, based on programmed concatenation cDNA for multiple long-read sequencing platforms. Applying Fullscope-seq to the macaque brain, we uncovered thousands of genes exhibiting differential transcript usage (DTU) across cortical layers, cell types and brain regions. Fullscope-seq resolved hundreds of major isoform switches across distinct brain regions and identified DTUs between superficial and deep cortical layers. Cortical layer-specific DTUs showed cell-composition dependence, whereas regional DTUs were regulated according to both cellular composition and spatial contexts. These isoform variations showed substantial enrichment for neuropsychiatric disorder-associated genes and were conserved across platforms and species. Our study establishes a scalable framework for spatial isoform analysis and provides a resource for understanding transcriptomic diversity in complex tissues.

Indexed as

BrainSingle-Cell AnalysisTranscriptomeAlternative SplicingAnimalsGene Expression ProfilingProtein IsoformsSingle-Cell Gene Expression AnalysisSpatial TranscriptomicsProtein Isoforms

Identifiers

PMID42498883

What Socratic holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.