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Brain injury reactivates a developmental program driving genesis and integration of transient LGE-class interneurons.

Code ↔ Paper

5 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 5 matches
  1. [1] § Results › Astrocyte-generated striatal and cortical neuroblasts belong to the LGE interneurons class ↔ mouse/MouseWbGeKDCbAdult4_cellrank.py, lines 123–202 · score 0.63 · CGE_NR2F2, OB_MEIS2, LGE_MEIS2, PROX1, mapped, adult
  2. [2] § Results › Astrocyte-generated striatal and cortical neuroblasts belong to the LGE interneurons class ↔ mouse/MouseWbGeKDCbAdult.py, lines 200–257 · score 0.60 · CGE_NR2F2, OB_MEIS2, LGE_MEIS2, PROX1, adult, PAX6
  3. [3] § Results › Astrocyte-generated striatal and cortical neuroblasts belong to the LGE interneurons class ↔ mouse/MouseWbGeKDCbAdult2.py, lines 124–212 · score 0.57 · NR2F2, LGE_MEIS2, nkx2, ERBB4, LHX6, Prox1
  4. [4] § STAR★Methods › Method details › scRNA-seq quality control and clustering ↔ merge/QvMWbGeKDCb.py, lines 120–186 · score 0.57 · Cell Cycle scores, log, subsetting, batches, PCA, PCs
  5. [5] § STAR★Methods › Method details › scRNA-seq quality control and clustering ↔ mouse/MouseWbGeKDCb1Subset.py, lines 204–249 · score 0.51 · Cell Cycle scores, subsetting, Rank, log, batches, genes

Paper

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The authors' code

Python · 703 lines · 32 KB · no license · 1 match

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It can be read at the source: mouse/MouseWbGeKDCbAdult4_cellrank.py.

Overview

Authors: G Nato1,2, M Fogli1,3, N Marichal4,5, V Cerrato1,2, G Turrini1,2, V Proserpio3,6, I Ghia1,3, G Zanotto1,3, I Molineris3, M Bergami7,8,9,10, S Oliviero3,6,11, P Peretto1,3, B Berninger4,5,12,13, A Buffo1,2, F Luzzati1,3
ORCID iDs: B Berninger, A Buffo, F Luzzati
13 affiliations
  1. Neuroscience Institute Cavalieri Ottolenghi, Orbassano, Turin, Italy
  2. Department of Neurosciences “Rita Levi Montalcini”, University of Turin, Turin, Italy
  3. Department of Life Sciences and System Biology, University of Turin, Turin, Italy
  4. Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, UK
  5. Institute of Physiological Chemistry, University Medical Center Johannes Gutenberg University, Mainz, Germany
  6. Molecular Biotechnology Center “Guido Tarone”, University of Turin, Turin, Italy
  7. Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
  8. Center for Molecular Medicine, 50931 Cologne, Germany
  9. Institute of Genetics, University of Cologne, Cologne, Germany
  10. University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
  11. Italian Institute for Genomic Medicine, Candiolo, Turin, Italy
  12. MRC Centre for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, UK
  13. Focus Program Translational Neurosciences, Johannes Gutenberg University, Mainz, Germany
Institutions: Neuroscience Institute Cavalieri Ottolenghi (Italy); University of Turin (Italy); King's College London (United Kingdom); Johannes Gutenberg University Mainz (Germany); University Medical Center of the Johannes Gutenberg University Mainz (Germany); University of Cologne (Germany); Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (Germany); University Hospital Cologne (Germany); Italian institute for Genomic Medicine (Italy); MRC Centre for Neurodevelopmental Disorders (United Kingdom)
Journal: Stem cell reports, volume 21, issue 8, article 103015
Dates: received 19 September 2025; accepted 17 June 2026; published online 16 July 2026; in print August 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1016/j.stemcr.2026.103015 · PMID 42462713 · PMCID PMC13476880 · OpenAlex W4414705307
Open access: gold, a free copy (OpenAlex)
Preprint: doi:10.1101/2025.09.30.679475
Status: code verified
Categories: mouse (organism)
Methods: Statistics, Smoothing, state filtering, decompositions, Machine learning, Connectivity, Evoked potentials
Keywords: reactive neurogenesis, circuit integration, dormant stem cells, cell fate specification, lateral ganglionic eminence interneurons, cortico-striatal-thalamic circuits, neuronal identity, neurorepair, astrocyte neural stem cell potential, postnatal development
MeSH: Interneurons*, Neurogenesis*, Animals, Astrocytes, Cell Differentiation, Gene Expression Regulation, Developmental, Mice, Neural Stem Cells, Neurodevelopment, PAX6 Transcription Factor, Telencephalon (* major topic)
Topic: Neonatal Respiratory Health Research (Pulmonary and Respiratory Medicine, Medicine), according to OpenAlex
Funding: Compagnia di San Paolo (S1618); Dipartimenti di Eccellenza (2023-2027, 2018–2022); European Commission (2018-2022, HORIZON2020, 874758); Deutsche Forschungsgemeinschaft (2018-2022, 357058359); Ministero dell’Istruzione, dell’Università e della Ricerca (2023/2027, 20182022); University of Turin; HORIZON EUROPE Framework Programme; Ministero dell'Istruzione e del Merito
Citations: not cited yet (Europe PMC); 107 references in the paper
Research resources: Chicken polyclonal anti-GFP (1:1000) RRID:AB_10000240, RRID:AB_10000321, Guinea Pig polyclonal anti-DCX (1:1500) RRID:AB_1586992, RRID:AB_1964214, RRID:AB_2064130, Goat polyclonal anti-DCX (1:2000) RRID:AB_2088494, Rabbit polyclonal anti-FOXP2 (1:1000) RRID:AB_2107107, Mouse monoclonal anti-MEIS1/2/3 (1:250) RRID:AB_2143143, Goat polyclonal anti-SOX9 (1:1200) RRID:AB_2194160, RRID:AB_2195374, Rabbit polyclonal anti-RFP (1:1000) RRID:AB_2209751, RRID:AB_2247211, Mouse monoclonal anti-NeuN (1:1000) RRID:AB_2298772, RRID:AB_2307351, RRID:AB_2307443, RRID:AB_2315777, RRID:AB_2340375, RRID:AB_2340432, RRID:AB_2340437, RRID:AB_2340470, RRID:AB_2340681, RRID:AB_2340684, RRID:AB_2341099, Rabbit anti-cleaved caspase 3 (Asp175) RRID:AB_2341188, RRID:AB_2492288, Goat polyclonal anti-human ErbB4 (1:250) RRID:AB_354620, Monoclonal mouse anti-DARPP-32 (1:1000) RRID:AB_398980, RRID:AB_531793, RRID:AB_609566, Rabbit anti-IBA1 (1:1000) RRID:AB_839504, Rabbit anti-Sp8 (1:8000) RRID:AB_877304, Fiji RRID:SCR_002285, Imaris RRID:SCR_007370

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.

Repositories

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bunbunet

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: the link answers
Software Heritage: not checked
Found in: “Data and code availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 27 September 2026: the link answers (HTTP 200)
  • 27 September 2026: the link answers (HTTP 200)
At the source: github.com/bunbunet

mtvector/dev-and-evo-of-primate-inhibitory-neurons

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 616c7381a136fceec3da4e2d9f2710a0b664abf0, 8 November 2022
Languages: Python (35), Jupyter (2), Shell (1), JavaScript (1)
Size: 79 files, 39 scripts
Software Heritage: archived
Found in: the text, “Public datasets”
Holds: README, 1 notebook
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: NumPy (36 files), Matplotlib (34 files), pandas (34 files), scikit-learn (34 files), seaborn (32 files), SciPy (31 files), Scanpy (29 files), anndata (27 files), scVelo (27 files), Numba (10 files), NetworkX (6 files), statsmodels (6 files), h5py (2 files), ImageJ / Fiji (2 files), Plotly (2 files), OpenCV (1 file), tifffile (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
40 files, not copied: shown from their source

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At the source: github.com/mtvector/dev-and-evo-of-primate-inhibitory-neurons/tree/main/mouse

The paper's code and data availability statement is in the Data section.

Tracing map

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What the map holds:

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  • 39 scripts, each with its path and the digest of its content;
  • 5 matches between paragraphs of the paper and lines of the code (method lexical-v1);
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Data

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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/10.1016/j.stemcr.2026.103015.

Versions

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Version 2, 28 September 2026

  • Authors: added F Luzzati (0000-0003-0648-9989); removed F Luzzati
  • Funding: added Compagnia di San Paolo: S1618; Dipartimenti di Eccellenza: 2023-2027, 2018–2022; European Commission: 2018-2022, HORIZON2020, 874758; Deutsche Forschungsgemeinschaft: 2018-2022, 357058359; Ministero dell’Istruzione, dell’Università e della Ricerca: 2023/2027, 20182022; Università degli Studi di Torino; HORIZON EUROPE Framework Programme; Ministero dell'Istruzione e del Merito

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 15 authors, 10 keywords, 11 MeSH terms, 102 references, 33 RRIDs.

Cite

This paper

Nato, G., Fogli, M., Marichal, N., Cerrato, V., Turrini, G., Proserpio, V., Ghia, I., Zanotto, G., Molineris, I., Bergami, M., Oliviero, S., Peretto, P., Berninger, B., Buffo, A., & Luzzati, F. (2026). Brain injury reactivates a developmental program driving genesis and integration of transient LGE-class interneurons. Stem cell reports, 21(8), 103015. https://doi.org/10.1016/j.stemcr.2026.103015

BibTeX

@article{nato2026brain,
author = {Nato, G and Fogli, M and Marichal, N and Cerrato, V and Turrini, G and Proserpio, V and Ghia, I and Zanotto, G and Molineris, I and Bergami, M and Oliviero, S and Peretto, P and Berninger, B and Buffo, A and Luzzati, F},
title = {{Brain injury reactivates a developmental program driving genesis and integration of transient LGE-class interneurons}},
journal = {Stem cell reports},
year = {2026},
month = jul,
volume = {21},
number = {8},
pages = {103015},
publisher = {Elsevier},
issn = {2213-6711},
doi = {10.1016/j.stemcr.2026.103015},
url = {https://doi.org/10.1016/j.stemcr.2026.103015},
pmid = {42462713},
pmcid = {PMC13476880}
}

RIS

TY - JOUR
AU - Nato, G
AU - Fogli, M
AU - Marichal, N
AU - Cerrato, V
AU - Turrini, G
AU - Proserpio, V
AU - Ghia, I
AU - Zanotto, G
AU - Molineris, I
AU - Bergami, M
AU - Oliviero, S
AU - Peretto, P
AU - Berninger, B
AU - Buffo, A
AU - Luzzati, F
TI - Brain injury reactivates a developmental program driving genesis and integration of transient LGE-class interneurons
T2 - Stem cell reports
J2 - Stem Cell Reports
PY - 2026
DA - 2026/07/16
VL - 21
IS - 8
SP - 103015
SN - 2213-6711
PB - Elsevier
DO - 10.1016/j.stemcr.2026.103015
UR - https://doi.org/10.1016/j.stemcr.2026.103015
LA - en
ER -

CSL-JSON

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