Cited by 70Stress Responses and CortisolGene expression and cancer classificationSingle-cell and spatial transcriptomics

A gene expression atlas for different kinds of stress in the mouse brain

Open access
Flati, Tiziano, Gioiosa, Silvia, Chillemi, Giovanni, Mele, Andrea, Oliverio, Alberto, Mannironi, Cecilia, Rinaldi, Arianna, Castrignanò, Tiziana·2020·Scientific Data

Abstract

Stressful experiences are part of everyday life and animals have evolved physiological and behavioral responses aimed at coping with stress and maintaining homeostasis. However, repeated or intense stress can induce maladaptive reactions leading to behavioral disorders. Adaptations in the brain, mediated by changes in gene expression, have a crucial role in the stress response. Recent years have seen a tremendous increase in studies on the transcriptional effects of stress. The input raw data are freely available from public repositories and represent a wealth of information for further global and integrative retrospective analyses. We downloaded from the Sequence Read Archive 751 samples (SRA-experiments), from 18 independent BioProjects studying the effects of different stressors on the brain transcriptome in mice. We performed a massive bioinformatics re-analysis applying a single, standardized pipeline for computing differential gene expression. This data mining allowed the identification of novel candidate stress-related genes and specific signatures associated with different stress conditions. The large amount of computational results produced was systematized in the interactive “Stress Mice Portal”.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/s41597-020-00772-z

Cites

77 of 77 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • SCML4 has previously been linked to stress reactions in mice, and modifications to its protein structure might therefore further contribute to related effects in mood phenotypes.

    “SCML4 has previously been linked to stress reactions in mice and modifications to its protein structure might therefore further contribute to related effects in mood phenotypes [52].”

    From Neandertal introgression partitions the genetic landscape of neuropsychiatric disorders and associated behavioral phenotypes (2022) · cites this paper as [52]

    The Results table of stress-related brain transcriptome changes lists Scml4 among differentially expressed genes in the mouse nucleus accumbens, supporting a link to stress-related gene expression. The cited passage does not address changes to SCML4 protein structure or their effects on mood phenotypes; that part is the citing authors’ speculation. (LLM, conf=0.86)

    Experimental — accuracy not yet measured

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

1 of the 78 references couldn’t be matched to a known paper.

Research works printed but not linked: 8

  1. [81]Genome-wide sequencing of hippocampal 5-hydroxymethylcytosine links plasticity genes to acute stress. NCBI BioProject. https://identifiers.org/ncbi/bioproject:PRJNA309704 (2016). PMC4713261 26598390
  2. [82]Ketamine and Imipramine Reverse Transcriptional Signatures of Susceptibility and Induce Resilience-Specific Gene Expression Profiles. NCBI BioProject. https://identifiers.org/ncbi/bioproject:PRJNA322294 (2016). PMC5164982 27569543
  3. [84]Sex Differences in Nucleus Accumbens Transcriptome Profiles Associated with Susceptibility versus Resilience to Subchronic Variable Stress. NCBI BioProject. https://identifiers.org/ncbi/bioproject:PRJNA336339 (2016). PMC4679819 26674863
  4. [87]Sex-specific Transcriptional Signatures in Human Depression. NCBI BioProject. https://identifiers.org/ncbi/bioproject:PRJNA398031 (2017). PMC5734943 28825715
  5. [88]Role of the glial glutamate exchanger xCT in ventral hippocampus in resilience to stress. NCBI BioProject. https://identifiers.org/ncbi/bioproject:PRJNA401858 (2017). 29024663
  6. [89]Ten-eleven translocation proteins modulate the response to environmental stress in mice (house mouse). NCBI BioProject. https://identifiers.org/ncbi/bioproject:PRJNA415948 (2017). PMC6350936 30540950
  7. [91]Dynamic Patterns of Threat-associated Gene Expression in the Amygdala and Blood (house mouse). NCBI BioProject. https://identifiers.org/ncbi/bioproject:PRJNA479752 (2018). PMC6344436 30705647
  8. [94]REM sleep’s unique associations with corticosterone regulation, apoptotic pathways and behavior in chronic stress in mice (house mouse). NCBI BioProject. https://identifiers.org/ncbi/bioproject:PRJNA516641 (2019). PMC6377491 30683720

Cited by

Sorted by citations

Authors
Flati, T., Gioiosa, S., Chillemi, G., Mele, A., Oliverio, A., Mannironi, C., Rinaldi, A., & Castrignanò, T.
Affiliations
  • Cineca (IT)
  • Università degli Studi della Tuscia (IT)
  • Sapienza University of Rome (IT)
  • Institute of Molecular Biology and Pathology (IT)
Corresponding author
  • Rinaldi, Arianna
  • Castrignanò, Tiziana
Venue
Scientific Data
Published
2020-12-16
Volume
7
Issue
1
Pages
437-437
ISSN
2052-4463 (ISSN-L)
OpenAlex
W3111074515
Cited by
65
References
78
Citations by year
2026: 10 · 2025: 13 · 2024: 12 · 2023: 17 · 2022: 11 · 2021: 2
Type
data paper
Language
en
Open access
Locations
  • Scientific Data (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • IRIS Research product catalog (Sapienza University of Rome) (submittedVersion, cc-by)
  • Cineca Institutional Research Information System (Tor Vergata University) (submittedVersion, other-oa)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • UnitusOpen (Tuscia University) (submittedVersion)
  • UnitusOpen (Tuscia University) (submittedVersion, cc-by-nc-nd)
Funders
  • Dipartimenti di Eccellenza
  • Ministero dell’Istruzione, dell’Università e della Ricerca (“Landscape 4.0, 2018-2019)
  • Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali, Università degli Studi della Tuscia
Topics
  • Life Sciences › Neuroscience › Behavioral Neuroscience › Stress Responses and Cortisol
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
Keywords
stress response, brain transcriptome, gene expression atlas, mouse brain, differential gene expression, stress-related genes
MeSH terms
Animals, Brain, Female, Male, Stress, Physiological, Stress, Psychological, Gene Expression, Computational Biology, Mice, Data Mining, Transcriptome, Datasets as Topic

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review