Evidence map›Paper›PMID 38187533›Full record

ArticlebioRxiv : the preprint server for biology2024

Spatial profiling of the interplay between cell type- and vision-dependent transcriptomic programs in the visual cortex.

Fangming Xie, Saumya Jain, Runzhe Xu, Salwan Butrus, Zhiqun Tan, Xiangmin Xu, Karthik Shekhar, S Lawrence Zipursky

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. 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, 6 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

8 authors at 4 institutions in 1 country.

Fangming XieDepartment of Biological Chemistry, Howard Hughes Medical Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.ORCID 0000-0001-5232-1648
Saumya JainDepartment of Biological Chemistry, Howard Hughes Medical Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Runzhe XuDepartment of Biological Chemistry, Howard Hughes Medical Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Salwan ButrusDepartment of Chemical and Biomolecular Engineering; Helen Wills Neuroscience Institute, California Institute for Quantitative Biosciences (QB3); Center for Computational Biology; Vision Sciences Graduate Program, University of California, Berkeley, Berkeley, CA 94720, USA.
Zhiqun TanCenter for Neural Circuit Mapping (CNCM), Department of Anatomy and Neurobiology, Institute for Memory Impairments and Neurological Disorders (UCIMIND), University of California, Irvine, Irvine, CA 92697, USA.
Xiangmin XuCenter for Neural Circuit Mapping (CNCM), Department of Anatomy and Neurobiology, Institute for Memory Impairments and Neurological Disorders (UCIMIND), University of California, Irvine, Irvine, CA 92697, USA.
Karthik ShekharDepartment of Chemical and Biomolecular Engineering; Helen Wills Neuroscience Institute, California Institute for Quantitative Biosciences (QB3); Center for Computational Biology; Vision Sciences Graduate Program, University of California, Berkeley, Berkeley, CA 94720, USA.ORCID 0000-0003-4349-6600
S Lawrence ZipurskyDepartment of Biological Chemistry, Howard Hughes Medical Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Howard Hughes Medical Institute · USQB3 · USUniversity of California, Irvine · USGeorgia Institute of Technology · US

Funding

Single-cell Transcriptomic Analysis of Cell Type Plasticity in Barrel Cortex of Normal and Autism Model MiceF31NS131016 · NINDS · UNIVERSITY OF CALIFORNIA BERKELEY · PI BUTRUS, SALWAN · 2023 to 2024
$90k
NINDS NIH HHS F31 NS131016
6 · The paper itself

Abstract

How early sensory experience during "critical periods" of postnatal life affects the organization of the mammalian neocortex at the resolution of neuronal cell types is poorly understood. We previously reported that the functional and molecular profiles of layer 2/3 (L2/3) cell types in the primary visual cortex (V1) are vision-dependent (Tan et al., Significance statement: Layer 2/3 (L2/3) glutamatergic neurons are important sites of experience-dependent plasticity and learning in the mammalian cortex. Their properties vary continuously with cortical depth and depend upon experience. Here, by applying spatial transcriptomics and different computational approaches in the mouse primary visual cortex, we show that vision regulates orthogonal gene expression programs underlying cell states and cell types. Visual deprivation not only induces an activity-dependent cell state, but also alters the composition of L2/3 cell types, which are appropriately described as a transcriptomic continuum. Our results provide insights into how experience shapes transcriptomes that may, in turn, sculpt brain wiring, function, and behavior.

Identifiers

PMID38187533
PMCPMC10769288
OpenAlexW4389902215

What OpenQuestion holds

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LicenceCC BY
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 OpenQuestion graph.