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Shared transcriptomic signatures in perilesional and contralesional cortex after ischemic stroke.

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Paper

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

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The authors' code

MATLAB · 43 lines · 1.8 KB · CC-BY-4.0

  1. addpath(genpath('/work/TIBIR/s175047/aMAP_workflow/workflow/scripts'));
  2. addpath(genpath('/work/TIBIR/s175047/matlab_utilities_1'));
  4. analysis_folder='/project/TIBIR/Ramirez_lab/shared/analysis';
  5. project_dirs={'KPOINS_2021_734_743_MgNp7',...
  6. 'KPOINS_2021_753_764_MgNp8',...
  7. 'KPOINS_2021_780_787_MgNp9','KPOINS_2021_788_793_MgNp10',...
  8. 'KPOINS_2021_794_797_MgNp11','KPOINS_2021_798_807_MgNp12',...
  9. 'KPOINS_2021_808_811_MgNp13'};%,'KPOINS_2022_849_852_MgNp14'
  10. sample_dirs={{'S735','S743'},...%,'S737','S741'
  11. {'S754','S756','S758','S760','S762','S764'},...
  12. {'S781','S787'},...% 'S783','S785'
  13. {'S789','S793'},{'S795'},...
  14. {'S799','S801','S803','S805','S807'},...
  15. {'S809','S811'}};%,{'S852'}
  16. registered_input_file = 'Registered_rh_mirror_v7_0.tif';
  18. avg = uint16(zeros([3284 3934 200 length(project_dirs)]));
  19. avg_img = uint16(zeros([3284 3934 200]));
  20. tmp_img = uint16(zeros([3284 3934 200]));
  22. sc_mask = load_nii('SC_registration_mask_3934x3284x200_1umxy_erode.nii');
  23. sc_mask = sc_mask.img;
  24. sc_mask = uint16(permute(sc_mask,[3 1 2]));
  25. sc_mask = flipud(sc_mask);
  27. for i=1:length(project_dirs)
  28. tic
  29. avg_img_proj = uint16(zeros([3284 3934 200 length(sample_dirs{i})]));
  30. for j=1:length(sample_dirs{i})
  31. filestr = [analysis_folder filesep project_dirs{i} filesep sample_dirs{i}{j} filesep 'fullres' filesep registered_input_file];
  32. a = loadTiffStack(filestr);
  33. a = a.*sc_mask;
  34. avg_img_proj(:,:,:,j) = a;
  35. end
  36. tmp_img = mean(avg_img_proj,4);
  37. tmp_img = medfilt3(tmp_img);
  38. avg(:,:,:,i) = tmp_img;
  39. toc
  40. end
  41. avg_img = mean(avg,4);
  42. avg_img = medfilt3(avg_img);
  43. saveTiffStack(uint16(avg_img),'test.tif');

avg_template_creation_v5.m, under CC-BY-4.0 · at the source

Overview

Authors: Dene Betz1,2, Victoria A Alers1,2, Matthew Kenwood1,2, Kielen R Zuurbier3, Rebeca Coimbra4, Priscilla Rhoton1, Erik J Plautz5,6, Peter M Douglas3, Denise M O Ramirez5,6, Ann M Stowe7,8, Mark P Goldberg1,2
ORCID iDs: Dene Betz, Victoria A Alers, Matthew Kenwood, Denise M O Ramirez, Ann M Stowe, Mark P Goldberg
  1. Department of Neurology, Long School of Medicine, The University of Texas at San Antonio, 7703 Floyd Curl Drive, MSC 7883, San Antonio, TX 78229 USA
  2. Graduate School of Biomedical Science, UT Health San Antonio, San Antonio, TX USA
  3. Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX USA
  4. Texas A&M, College Station, TX USA
  5. Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX USA
  6. Peter O’Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX USA
  7. Department of Neurology, The University of Kentucky, Lexington, KY USA
  8. Department of Neuroscience, The University of Kentucky, Lexington, KY USA
Institutions: The University of Texas at San Antonio Health Science Center (United States); The University of Texas at San Antonio (United States); The University of Texas Southwestern Medical Center (United States); Texas A&M University (United States); University of Kentucky (United States)
Journal: Journal of neuroinflammation, volume 23, issue 1, article 282
Dates: received 27 January 2026; accepted 18 May 2026; published online 15 June 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1186/s12974-026-03885-1 · PMID 42298604 · PMCID PMC13495521 · OpenAlex W7164753564
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: genetics / omics (modality), mouse (organism), stroke (population), cellular / molecular (subfield)
Methods: Statistics, Machine learning, fMRI & imaging, Physiology & signal measures
Keywords: Post-stroke plasticity, Perilesional cortex, Contralesional cortex, Sex-differences in stroke, Axonal sprouting, Stroke, Stroke recovery, Microglia
MeSH: Cerebral Cortex*, Ischemic Stroke*, Transcriptome*, Animals, Female, Male, Mice, Mice, Inbred C57BL (* major topic)
Topic: Neuroscience and Neuropharmacology Research (Cellular and Molecular Neuroscience, Neuroscience), according to OpenAlex
Funding: University of Texas at San Antonio (GSBS Neuroscience Training Fellowship); National Institutes of Health (R01AG076529, R01GM15385, NS088555, OT2OD032581, T32AG082661, T32GM113896, T32NS082145-08, T32GM145432); NIGMS NIH HHS (T32 GM145432, T32 GM113896); Clayton Foundation for Research; NIH HHS (OT2 OD032581, NS088555, R01AG076529, R01GM15385, OT2OD032581, T32AG082661, T32GM113896, T32NS082145-08, T32GM145432); NINDS NIH HHS (R01 NS088555, RF1 NS088555, T32 NS082145); Haggerty Foundation; NIA NIH HHS (R01 AG076529, T32 AG082661); American Heart Association (23PRE1018993); Welch Foundation (I -2061 -20210327); Meier Family Foundation; American Federation of Aging Research (AFAR 2023)
Citations: not cited yet (Europe PMC); 115 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.

Zenodo 14750099

License: CC-BY-4.0
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Size: 7 files
Software Heritage: not checked
Found in: the text, “Materials and methods”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: SimpleITK (40 files), Parallel Computing Toolbox (37 files), Image Processing Toolbox (22 files), circlize (5 files), ComplexHeatmap (5 files), ggplot2 (5 files), tidyverse (5 files), broom (4 files), cowplot (4 files), ggpubr (1 file), Statistics and Machine Learning Toolbox (1 file), Tools for NIfTI and ANALYZE image (MATLAB) (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers (HTTP 200)
  • 27 September 2026: the link answers (HTTP 200)
99 files
At the source:

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;
  • 99 scripts, each with its path and the digest of its content;
  • no match between paragraphs and code yet;
  • 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

No dataset and no data link were found in the paper.

Data availability statement

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

  • no repository, dataset or request procedure was recognized in it

Read it in the paper: doi.org/10.1186/s12974-026-03885-1.

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, 11 authors, 8 keywords, 8 MeSH terms, 12 funders, 115 references.

Cite

This paper

Betz, D., Alers, V. A., Kenwood, M., Zuurbier, K. R., Coimbra, R., Rhoton, P., Plautz, E. J., Douglas, P. M., Ramirez, D. M. O., Stowe, A. M., & Goldberg, M. P. (2026). Shared transcriptomic signatures in perilesional and contralesional cortex after ischemic stroke. Journal of neuroinflammation, 23(1), 282. https://doi.org/10.1186/s12974-026-03885-1

BibTeX

@article{betz2026shared,
author = {Betz, Dene and Alers, Victoria A and Kenwood, Matthew and Zuurbier, Kielen R and Coimbra, Rebeca and Rhoton, Priscilla and Plautz, Erik J and Douglas, Peter M and Ramirez, Denise M O and Stowe, Ann M and Goldberg, Mark P},
title = {{Shared transcriptomic signatures in perilesional and contralesional cortex after ischemic stroke}},
journal = {Journal of neuroinflammation},
year = {2026},
month = jun,
volume = {23},
number = {1},
pages = {282},
publisher = {BMC},
issn = {1742-2094},
doi = {10.1186/s12974-026-03885-1},
url = {https://doi.org/10.1186/s12974-026-03885-1},
pmid = {42298604},
pmcid = {PMC13495521}
}

RIS

TY - JOUR
AU - Betz, Dene
AU - Alers, Victoria A
AU - Kenwood, Matthew
AU - Zuurbier, Kielen R
AU - Coimbra, Rebeca
AU - Rhoton, Priscilla
AU - Plautz, Erik J
AU - Douglas, Peter M
AU - Ramirez, Denise M O
AU - Stowe, Ann M
AU - Goldberg, Mark P
TI - Shared transcriptomic signatures in perilesional and contralesional cortex after ischemic stroke
T2 - Journal of neuroinflammation
J2 - J Neuroinflammation
PY - 2026
DA - 2026/06/15
VL - 23
IS - 1
SP - 282
SN - 1742-2094
PB - BMC
DO - 10.1186/s12974-026-03885-1
UR - https://doi.org/10.1186/s12974-026-03885-1
LA - en
ER -

CSL-JSON

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"id": "10.1186/s12974-026-03885-1",
"type": "article-journal",
"title": "Shared transcriptomic signatures in perilesional and contralesional cortex after ischemic stroke",
"container-title": "Journal of neuroinflammation",
"author": [
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"family": "Betz",
"given": "Dene"
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{
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{
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},
{
"family": "Coimbra",
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{
"family": "Rhoton",
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{
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"DOI": "10.1186/s12974-026-03885-1",
"PMID": "42298604",
"PMCID": "PMC13495521",
"ISSN": "1742-2094",
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"URL": "https://doi.org/10.1186/s12974-026-03885-1",
"language": "en",
"issued": {
"date-parts": [
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2026,
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15
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]
}
}

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