Evidence map›Paper›PMID 42182181›Full record

ArticlebioRxiv : the preprint server for biology2026

BARseq3: a modular system for integrating spatial multi-omics and cellular barcoding in single cells.

Huihui Qi, Manjari M-G Anant, Dylan Z Faltine-Gonzalez, Ruitao Hu, Lai Wei, Christopher D Workman, Caleb Shi, Ishbel Del Rosario, Justus M Kebschull

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 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

9 authors.

Huihui QiDepartment of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
Manjari M-G AnantKavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, USA.
Dylan Z Faltine-GonzalezDepartment of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
Ruitao HuDepartment of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
Lai WeiDepartment of Neuroscience, Johns Hopkins University, Baltimore, MD, USA.
Christopher D WorkmanDepartment of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
Caleb ShiDepartment of Neuroscience, Johns Hopkins University, Baltimore, MD, USA.
Ishbel Del RosarioLieber Institute of Brain Development, Baltimore, MD, USA.
Justus M KebschullDepartment of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.

Funding

Training Program in Hearing and BalanceT32DC000023 · NIDCD · JOHNS HOPKINS UNIVERSITY · PI CULLEN, KATHLEEN E · 1989 to 2025
$8.7M
BRAIN CONNECTS: Mapping brain-wide connectivity of neuronal types using barcoded connectomicsU01NS132161 · NINDS · ALLEN INSTITUTE · PI CHEN, XIAOYIN, KEBSCHULL, JUSTUS M · 2023 to 2025
$6.7M
Cell type specific vulnerability to agingRF1AG078378 · NIA · JOHNS HOPKINS UNIVERSITY · PI PATRICK O KANOLD, JUSTUS M KEBSCHULL · 2023 to 2026
$4.0M
Circuitry dynamics underlying opioid-dependence: Integrating structural, functional, and transcriptomic mechanismsR01DA056599 · NIDA · UNIVERSITY OF PENNSYLVANIA · PI KEVIN T BEIER, Julie A Blendy · 2022 to 2026
$3.8M
IDENTIFYING EPIGENOMICS AND CONNECTOMICS OF PROTRACTED OPIOID WITHDRAWAL AND RELAPSE USING CELLULAR BARCODINGDP1DA056668 · NIDA · JOHNS HOPKINS UNIVERSITY · PI JUSTUS M KEBSCHULL · 2022 to 2026
$2.5M
Mapping opioid-dependence state transitions across structural, functional, and transcriptomic topologiesR01DA054374 · NIDA · UNIVERSITY OF PENNSYLVANIA · PI BLENDY, JULIE A, CORDER, GREGORY · 2021 to 2025
$2.4M
NIA NIH HHS RF1 AG078378NIDA NIH HHS DP1 DA056668NIDA NIH HHS R01 DA054374NIDA NIH HHS R01 DA056599NIDCD NIH HHS T32 DC000023NINDS NIH HHS U01 NS132161
6 · The paper itself

Abstract

Understanding cellular identity requires multimodal measurements in single cells. Cellular barcoding provides powerful tools for recording the properties or history of individual cells in nucleic acids, while spatial omics techniques enable the measurement of a growing list of molecular features at micron resolution in tissue. However, existing methods that integrate these approaches in single samples are limited in the modalities they support, their flexibility, and efficiency. Here, we present BARseq3, a modular system that combines cellular barcoding with high-efficiency spatial transcriptomics and translatomics at subcellular resolution in tissue. BARseq3 is compatible with fixed samples, immunostaining, diverse species, and can be easily extended to include other spatial assays, enabling a multimodal understanding of cellular identity.

Identifiers

PMID42182181
PMCPMC13192599

What OpenQuestion holds

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LicenceCC BY-NC-ND
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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 OpenQuestion graph.