OSCR

Th17 effector cytokines induce shared and distinct microglial and endothelial cell responses in a mouse model for post-streptococcal encephalitis.

Code ↔ Paper

14 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 14 matches
  1. [1] § Methods › Multiplexed error-robust in situ hybridization (MERFISH) ↔ 04_WayneEtAl_MERFISH-2.R, lines 283–338 · score 1.00 · Ap2m1, Baiap2l1, C1qa, C1qbp, C1qc, C3ar1
  2. [2] § Methods › Multiplexed error-robust in situ hybridization (MERFISH) ↔ 01_WayneEtAl_scRNAseq.R, lines 1116–1181 · score 1.00 · Csf1r, Il1a, Il1rn, Il2rg, Tnfsf13b, Csf2ra
  3. [3] § Methods › Quantification and statistical analysis › Analysis of scRNA-seq data ↔ 01_WayneEtAl_scRNAseq.R, lines 1116–1181 · score 0.99 · Oas1a, H2 Ab1, H2 Eb1, H2 K1, H2 D1, Cx3cr1
  4. [4] § Methods › Quantification and statistical analysis › Analysis of scRNA-seq data ↔ 01_WayneEtAl_scRNAseq.R, lines 323–399 · score 0.99 · Atp13a5, Cd209a, Col1a1, Klrb1c, dendritic cells, Ly6g
  5. [5] § Methods › Quantification and statistical analysis › Analysis of MERFISH data ↔ 04_WayneEtAl_MERFISH-2.R, lines 223–281 · score 0.92 · Cd3e, olfactory ensheathing cells, Cd8a, P2ry12, Cemip, Mmp9
  6. [6] § Methods › Quantification and statistical analysis › Analysis of scRNA-seq data ↔ 03_WayneEtAl_MERFISH-1.R, lines 166–216 · score 0.76 · linear dimensional reduction, batch correction, variable features, endothelial cells, PCA, resolution
  7. [7] § Results › Microglia upregulate inflammatory and antigen-presentation programs after GAS infections ↔ 01_WayneEtAl_scRNAseq.R, lines 978–1029 · score 0.71 · srMG2, hMG1, srMG1, srMG4, Ccl3, Ccl4
  8. [8] § Results › GAS infection alters predicted cell–cell communication networks in the OB ↔ 05_WayneEtAl_CellChat.R, lines 52–100 · score 0.69 · ligand receptor interactions, CellChat, Inferred, networks, signaling, pathways
  9. [9] § Results › BECs upregulate inflammatory programs and downregulate BBB-related transcripts after GAS infections ↔ 01_WayneEtAl_scRNAseq.R, lines 732–793 · score 0.68 · Mfsd2a, Itm2a, ECM, Cav1, Cavin1, junctions
  10. [10] § Methods › Quantification and statistical analysis › Analysis of MERFISH data ↔ 03_WayneEtAl_MERFISH-1.R, lines 218–256 · score 0.61 · python script, Nearest neighbor, Endothelial cell, distance, OB, MERFISH
  11. [11] § Results › Streptococcus-responsive microglia are enriched in the glomerular OB layer in close proximity to T cells ↔ 04_WayneEtAl_MERFISH-2.R, lines 421–486 · score 0.60 · granular layer, P2ry12, gene expression, Axl, Gpr34, Ifi30
  12. [12] § Methods › Quantification and statistical analysis › Analysis of scRNA-seq data ↔ 01_WayneEtAl_scRNAseq.R, lines 795–860 · score 0.60 · batch correction, variable features, Elbow, Harmony, UMAP, PCA
  13. [13] § Results › Microglia and BECs show major transcriptional shifts after multiple GAS infections ↔ 02_WayneEtAl_CrossEntropy.R, lines 1–43 · score 0.55 · scRNAseq, cross entropy, olfactory bulb, GAS infection, UMAP, mice
  14. [14] § Results › Microglia and BECs show major transcriptional shifts after multiple GAS infections ↔ 02_WayneEtAl_CrossEntropy.R, lines 244–274 · score 0.55 · cross entropy, olfactory ensheathing cells, OECs, filtering, astrocytes, UMAP

Paper

Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC

The paper is loaded when this pane is shown.

The authors' code

R · 1,477 lines · 73 KB · no license · 6 matches

The registry keeps no copy of this file: its repository has no license, so its authors keep all their rights to it. Your browser shows it from its source, with JavaScript.

It can be read at the source: 01_WayneEtAl_scRNAseq.R.

Overview

Authors: Charlotte R. Wayne1, Uğur Akcan1, Travis E. Faust2, Violeta Durán-Laforet2, Danny Jamoul1, Luca Bremner1, Nicole Ampatey1, Büşra T. Akcan1, Sarah J. Ho1, Bogoljub Ciric3, Shannon L. Delaney4, Wendy S. Vargas1, Susan Swedo5, Vilas Menon1, Dorothy P. Schafer2, Tyler Cutforth1, Dritan Agalliu1,6
ORCID iDs: Charlotte R. Wayne, Travis E. Faust, Vilas Menon, Dorothy P. Schafer, Dritan Agalliu
  1. Department of Neurology, Columbia University Irving Medical Center,New York, NY USA
  2. Department of Neurobiology, Brudnick Neuropsychiatric Research Institute, University of Massachusetts Chan Medical School,Worcester, MA USA
  3. Department of Neurology, Thomas Jefferson University,Philadelphia, PA USA
  4. Lyme and Tick-Borne Diseases Research Center, Department of Psychiatry, Columbia University Irving Medical Center,New York, NY USA
  5. Section of Behavioral Pediatrics, National Institute of Mental Health,Bethesda, MD USA
  6. Department of Pathology and Cell Biology, Columbia University Irving Medical Center,New York, NY USA
Institutions: Columbia University Irving Medical Center (United States); University of Massachusetts Chan Medical School (United States); Thomas Jefferson University (United States); National Institute of Mental Health (United States)
Journal: Nature communications, volume 17, issue 1, article 9658
Dates: received 13 April 2023; accepted 13 July 2026; published online 11 August 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1038/s41467-026-76232-w · PMID 42717209 · PMCID PMC13558752 · OpenAlex W7202203061
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: genetics / omics (modality), human (organism), mouse (organism), other condition (population), cellular / molecular (subfield)
Methods: Statistics, Smoothing, state filtering, decompositions, Evoked potentials, Machine learning, fMRI & imaging
Keywords: Neuroimmunology, Infection, Paediatric neurological disorders
MeSH: Cytokines*, Encephalitis*, Endothelial Cells*, Microglia*, Streptococcal Infections*, Th17 Cells*, Animals, Blood-Brain Barrier, Brain, Chemokines, Disease Models, Animal, Female, Granulocyte-Macrophage Colony-Stimulating Factor, Humans, Interleukin-17, Mice, Mice, Inbred C57BL, Mice, Knockout, Receptors, Interleukin-17, Signal Transduction (* major topic)
Topic: Neuroinflammation and Neurodegeneration Mechanisms (Neurology, Neuroscience), according to OpenAlex
Funding: National Institute of Mental Health (R01MH112849, 56MH109987, R01MH113743); National Heart, Lung, and Blood Institute (R61HL159949, R33HL159949); National Eye Institute (R01EY033994); National Institute on Aging (RF1AG078352, RF1AG068281, R01AG068281); International OCD Foundation (International Obsessive-Compulsive Disorder Foundation); National Institute of Neurological Disorders and Stroke (2T32NS064928, R01NS117533); BrightFocus Foundation (BFF) (A2022006F); Alzheimer's Association (AARF-22-923219); Massachusetts Life Sciences Center (MLSC)
Citations: not cited yet (Europe PMC); 103 references in the paper

Abstract

The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.

Repository

Its files are read in the Code ↔ Paper reader above, with 14 matches between paragraphs and lines of code.

AgalliuLab/s-pyogenes-scRNAseq

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 28b8a8e8ac4fdf7fb9e078ef138eb37f4cb856c6, 27 October 2025
Languages: R (5)
Size: 5 files, 5 scripts
Software Heritage: not archived
Found in: “Code availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: Seurat (5 files), tidyverse (5 files), ggplot2 (4 files), patchwork (2 files), circlize (1 file), clusterProfiler (1 file), ComplexHeatmap (1 file), cowplot (1 file), ggpubr (1 file), Harmony (1 file), reshape2 (1 file), reticulate (1 file), rstatix (1 file), SingleCellExperiment (1 file), UMAP (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
5 files, not copied: shown from their source

OSCR keeps no copy of these files: this repository has no license that allows it. The reader above shows each one from its source, fetched by your browser at commit 28b8a8e, when its fingerprint is the one OSCR verified. How this works.

At the source: github.com/AgalliuLab/s-pyogenes-scRNAseq

Code availability statement

The paper has a code availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:

Read it in the paper: doi.org/10.1038/s41467-026-76232-w.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 5 scripts, each with its path and the digest of its content;
  • 14 matches between paragraphs of the paper and lines of the code (method lexical-v1);
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

Datasets cited

Code and data availability statement

The paper has a code and data availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:

Read it in the paper: doi.org/10.1038/s41467-026-76232-w.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 17 authors, 3 keywords, 20 MeSH terms, 9 funders, 103 references.

Cite

This paper

Wayne, C. R., Akcan, U., Faust, T. E., Durán-Laforet, V., Jamoul, D., Bremner, L., Ampatey, N., Akcan, B. T., Ho, S. J., Ciric, B., Delaney, S. L., Vargas, W. S., Swedo, S., Menon, V., Schafer, D. P., Cutforth, T., & Agalliu, D. (2026). Th17 effector cytokines induce shared and distinct microglial and endothelial cell responses in a mouse model for post-streptococcal encephalitis. Nature communications, 17(1), 9658. https://doi.org/10.1038/s41467-026-76232-w

BibTeX

@article{wayne2026th17,
author = {Wayne, Charlotte R. and Akcan, Uğur and Faust, Travis E. and Durán-Laforet, Violeta and Jamoul, Danny and Bremner, Luca and Ampatey, Nicole and Akcan, Büşra T. and Ho, Sarah J. and Ciric, Bogoljub and Delaney, Shannon L. and Vargas, Wendy S. and Swedo, Susan and Menon, Vilas and Schafer, Dorothy P. and Cutforth, Tyler and Agalliu, Dritan},
title = {{Th17 effector cytokines induce shared and distinct microglial and endothelial cell responses in a mouse model for post-streptococcal encephalitis}},
journal = {Nature communications},
year = {2026},
month = aug,
volume = {17},
number = {1},
pages = {9658},
publisher = {Nature Publishing Group},
issn = {2041-1723},
doi = {10.1038/s41467-026-76232-w},
url = {https://doi.org/10.1038/s41467-026-76232-w},
pmid = {42717209},
pmcid = {PMC13558752}
}

RIS

TY - JOUR
AU - Wayne, Charlotte R.
AU - Akcan, Uğur
AU - Faust, Travis E.
AU - Durán-Laforet, Violeta
AU - Jamoul, Danny
AU - Bremner, Luca
AU - Ampatey, Nicole
AU - Akcan, Büşra T.
AU - Ho, Sarah J.
AU - Ciric, Bogoljub
AU - Delaney, Shannon L.
AU - Vargas, Wendy S.
AU - Swedo, Susan
AU - Menon, Vilas
AU - Schafer, Dorothy P.
AU - Cutforth, Tyler
AU - Agalliu, Dritan
TI - Th17 effector cytokines induce shared and distinct microglial and endothelial cell responses in a mouse model for post-streptococcal encephalitis
T2 - Nature communications
J2 - Nat Commun
PY - 2026
DA - 2026/08/11
VL - 17
IS - 1
SP - 9658
SN - 2041-1723
PB - Nature Publishing Group
DO - 10.1038/s41467-026-76232-w
UR - https://doi.org/10.1038/s41467-026-76232-w
LA - en
ER -

CSL-JSON

{
"id": "10.1038/s41467-026-76232-w",
"type": "article-journal",
"title": "Th17 effector cytokines induce shared and distinct microglial and endothelial cell responses in a mouse model for post-streptococcal encephalitis",
"container-title": "Nature communications",
"author": [
{
"family": "Wayne",
"given": "Charlotte R."
},
{
"family": "Akcan",
"given": "Uğur"
},
{
"family": "Faust",
"given": "Travis E."
},
{
"family": "Durán-Laforet",
"given": "Violeta"
},
{
"family": "Jamoul",
"given": "Danny"
},
{
"family": "Bremner",
"given": "Luca"
},
{
"family": "Ampatey",
"given": "Nicole"
},
{
"family": "Akcan",
"given": "Büşra T."
},
{
"family": "Ho",
"given": "Sarah J."
},
{
"family": "Ciric",
"given": "Bogoljub"
},
{
"family": "Delaney",
"given": "Shannon L."
},
{
"family": "Vargas",
"given": "Wendy S."
},
{
"family": "Swedo",
"given": "Susan"
},
{
"family": "Menon",
"given": "Vilas"
},
{
"family": "Schafer",
"given": "Dorothy P."
},
{
"family": "Cutforth",
"given": "Tyler"
},
{
"family": "Agalliu",
"given": "Dritan"
}
],
"container-title-short": "Nat Commun",
"volume": "17",
"issue": "1",
"page": "9658",
"DOI": "10.1038/s41467-026-76232-w",
"PMID": "42717209",
"PMCID": "PMC13558752",
"ISSN": "2041-1723",
"publisher": "Nature Publishing Group",
"URL": "https://doi.org/10.1038/s41467-026-76232-w",
"language": "en",
"issued": {
"date-parts": [
[
2026,
8,
11
]
]
}
}

The tracing map gets a citation of its own once an author has validated it and it has a DOI.

Similar papers

The papers with a page that share the most with this one: the tools found in their code, their categories, datasets, cited references and authors, the rarest counting most.

[1] doi:10.1038/s41593-026-02367-0 [code]
A reproducible three-dimensional model of human brain tissue to investigate physiological and disease-associated microglia phenotypes.
Journal: Nature neuroscience
In common: Harmony, SingleCellExperiment, reticulate, 10 other tools, cellular / molecular, 4 references
[2] doi:10.1038/s41586-026-10629-x [code]
Whole-genome duplication shaped cell-type evolution in the vertebrate brain.
Journal: Nature
In common: Harmony, reticulate, rstatix, 10 other tools, genetics / omics, mouse, cellular / molecular, 1 reference
[3] doi:10.1002/imt2.70163 [code]
Spatial multi-omics unveils sphingolipid metabolic reprogramming within the retinal pathological niche.
Journal: iMeta
In common: Harmony, SingleCellExperiment, rstatix, 10 other tools, genetics / omics, mouse, cellular / molecular, 1 reference
[4] doi:10.1038/s41398-026-04200-5 [code]
Postmortem brain single-nucleus and bulk gene expression analyses identify shared and distinct abnormalities in bipolar disorder and major depressive disorder.
Journal: Translational psychiatry
In common: Harmony, SingleCellExperiment, rstatix, 9 other tools, genetics / omics, cellular / molecular, 2 references
[5] doi:10.1016/j.celrep.2026.117500 [code]
Spatio-molecular gene expression reflects dorsal anterior cingulate cortex structure and function in the human brain.
Journal: Cell reports
In common: Harmony, SingleCellExperiment, reticulate, 9 other tools, genetics / omics, cellular / molecular, 2 references
[6] doi:10.1126/sciadv.aeb4265 [code]
Single-nucleus profiling reveals a core disease signature and cell type-specific vulnerabilities in early Rett syndrome.
Journal: Science advances
In common: Harmony, SingleCellExperiment, rstatix, 8 other tools, genetics / omics, other condition, mouse, 1 other category, 2 references
[7] doi:10.1038/s41467-026-71595-6 [code]
A single-cell and spatial atlas of early human olfactory development.
Journal: Nature communications
In common: Harmony, SingleCellExperiment, circlize, 8 other tools, genetics / omics, 3 references
[8] doi:10.1016/j.stemcr.2026.102922 [code]
Spatially resolved transcriptomics identifies intercellular signaling post-ischemic stroke that controls neural stem cell proliferation.
Journal: Stem cell reports
In common: SingleCellExperiment, reticulate, UMAP, 8 other tools, genetics / omics, mouse, 3 references
[9] doi:10.1073/pnas.2523130123 [code]
FABP7 controls radial glial scaffold stability during human cortical development.
Journal: Proceedings of the National Academy of Sciences of the United States of America
In common: Harmony, reticulate, UMAP, 10 other tools, mouse
[10] doi:10.1038/s41467-026-76341-6 [code]
Neonatal inflammation disrupts a temporally restricted postnatal Numb-enriched microglial state in mice.
Journal: Nature communications
In common: Harmony, SingleCellExperiment, circlize, 8 other tools, mouse, 2 references

Contribute

The authors of this paper can claim it, correct its record and validate its tracing map, and the maintainers of its code (its owner, or a public member of its organization) correct what it says of their repository; anyone signed in can ask for its removal. Every request goes to OSCR's own machine, which answers it; your account page follows them.

Sign in with ORCID to claim this paper as one of its authors, correct its record or validate its tracing map: when the paper's metadata lists your ORCID iD, you are recognized at once. Maintainers of its code: sign in with GitHub, then claim the repository on your account page.

Request its removal

To ask OSCR to remove this record, the copies of its authors' scripts or its tracing map, use the removal request page: signed in, you say who you are, what to remove and why, then review and confirm the request. Published rules decide every request (how).

Discussion, reproductions, activity

Discussion: questions and error reports about this paper and its code, from signed-in readers and its authors. It opens with sign-in.

Reproductions: reports from readers who ran the authors' code: what they reproduced, with which environment, commit and data. It opens with sign-in.

Activity: what happens around this paper: new versions of its record, its map's validation, discussions and reproductions. It opens with sign-in.