Evidence map›Paper›PMID 40777313›Full record

ArticlebioRxiv : the preprint server for biology2025

An image-based transcriptomics atlas reveals the regional and microbiota-dependent molecular, cellular, and spatial structure of the murine gut.

Rosalind J Xu, Paolo Cadinu, Phillip B Nicol, Uli S Herrmann, Tyrone Lee, Ludwig Geistlinger, Rafael A Irizarry, Jeffrey R Moffitt

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. 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

5 · Who and what money

Authors and funding

8 authors.

Rosalind J XuProgram in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
Paolo CadinuProgram in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
Phillip B NicolDepartment of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA.
Uli S HerrmannProgram in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
Tyrone LeeCore for Computational Biomedicine, Department of Biomedical Informatics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
Ludwig GeistlingerCore for Computational Biomedicine, Department of Biomedical Informatics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
Rafael A IrizarryDepartment of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA.
Jeffrey R MoffittProgram in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA.ORCID 0000-0002-3836-3101

Funding

STRUCTURE-FUNCTION RELATIONSHIPS IN THE ALIMENTARY TRACTP30DK034854 · NIDDK · HARVARD UNIVERSITY (MEDICAL SCHOOL) · PI JONATHAN C KAGAN · 1986 to 2026
$32.4M
Rapid, Robust, and Routine: Multiplexed Microscopy for Spatially Resolved Whole-Transcriptomic Single-Cell Profiling and the Construction of Cell Atlases of all Tissues and in all OrganismsR01GM143277 · NIGMS · BOSTON CHILDREN'S HOSPITAL · PI MOFFITT, JEFFREY · 2021 to 2024
$1.6M
NIDDK NIH HHS P30 DK034854NIGMS NIH HHS R01 GM143277
6 · The paper itself

Abstract

The gastrointestinal environment is home to a massive diversity of diet-, host-, and microbiota-derived small molecules, collectively sensed by a remarkable variety of cells. To explore the cellular and spatial organization of sensation, we used MERFISH to profile receptor expression across 2.1 million cells in multiple regions of the murine gut under specific-pathogen-free (SPF) and germ-free (GF) conditions. This atlas revealed expected and novel cell types-including a candidate murine homolog of human BEST4

Indexed as

Gastrointestinal tractgut microbiotaMERFISHsingle-cell transcriptomicsspatial transcriptomics

Identifiers

PMID40777313
PMCPMC12330561

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Registered trials

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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.