OSCR

A synaptoid connectome differentiates tanycytic subpopulations and underlies neuroglial communication and neuroendocrine regulation.

Code ↔ Paper

4 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 4 matches · 3 of them tie a paragraph to a whole file, not to given lines: weak matches, whose lines are not tinted
  1. [1] § Methods › scRNAseq data processing ↔ 4.Tanycyte_Mapping _and_CleanUp.r, the whole file · a weak match · score 0.87 · MapMyCells, SCR_024672, AnnData, Tany seq, Seurat, RRID
  2. [2] § Methods › scRNAseq data processing ↔ 5.Integration_of_Tanybase.r, lines 47–106 · score 0.82 · FindClusters, FindNeighbors, dimensionality reduction, joined, UMAP, clustering
  3. [3] § Results › Targeting tanycytic subpopulations ↔ 8.Plots_for_the_Publication.r, the whole file · a weak match · score 0.67 · Col25a1, Sprr1a, Adm, Crym, A2m, transcriptional
  4. [4] § Methods › Fluorescent in situ hybridization ↔ 8.Plots_for_the_Publication.r, the whole file · a weak match · score 0.62 · Avpr1a, Kiss1r, Oxtr, Sstr2, Chrm1, 15 min

Paper

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

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The authors' code

R · 86 lines · 3.5 KB · AGPL-3.0 · 2 matches

  1. ##### Plots for the Publication #####
  3. tany_integrated1 <- subset(x=tany_integrated, subset = Diet == "Chow" & Age == "6+ weeks") #Figures were plotted using Chow diet fed 6+ weeks old adult mice.
  5. #Plot for the Fig 1c.
  7. desired_order <- c("beta 2","beta 1","alpha 2","alpha 1")
  8. tany_integrated1$label <- factor(tany_integrated1$label, levels = desired_order)
  10. features2 <- c("Homer1", "Dlg4", "Shank2", "Nlgn2", "Gphn")
  12. plot <- DotPlot(
  13. tany_integrated1,
  14. features = features2,
  15. assay = "RNA",
  16. cols = c("lightgrey", "blue"),
  17. dot.min = 0,
  18. dot.scale = 6,
  19. group.by = "label",
  20. scale = TRUE,
  21. scale.by = "size"
  22. ) + theme(plot.background = element_rect(fill = "white", colour = NA),
  23. axis.title = element_text(size = 10),
  24. axis.text.x = element_text(angle = 45,face = 'italic', hjust = 1, vjust = 1), # x-axis labels in italics
  25. axis.text.y = element_text(face = 'plain',hjust = 1, vjust = 1) # ,plot.margin = margin(t = 1, r = 5, b = 1, l = 1)
  26. ) +
  27. xlab("Transcripts") +
  28. ylab("Tanycyte Subtypes") # y-axis label
  30. ggsave(filename = "Fig_1c.pdf", height = 4, width = 5, plot = plot)
  32. #Plot for the Supplementary Fig 6a.
  33. tany_integrated1 <- subset(x=tany_integrated, subset = Diet == "Chow" & Age == "6+ weeks") #Figures were plotted using Chow diet fed 6+ weeks old adult mice.
  35. features1 <- c("Gria3", "Gabbr1", "Gabbr2", "Chrm1", "Trhr", "Kiss1r", "Crhr1", "Crhr2", "Oxtr", "Avpr1a", "Sstr2", "Adra1a","Adra2a","Adrb1","Adrb2","Adrb3","Drd1", "Drd2", "Drd5")
  37. plot <- DotPlot(
  38. tany_integrated1,
  39. features = features1,
  40. assay = "RNA",
  41. cols = c("lightgrey", "blue"),
  42. dot.min = 0,
  43. dot.scale = 6,
  44. group.by = "label",
  45. scale = TRUE,
  46. scale.by = "radius",
  47. scale.min = NA,
  48. scale.max = 15
  49. ) + theme(plot.background = element_rect(fill = "white", colour = NA),
  50. axis.title = element_text(size = 14),
  51. axis.text.x = element_text(face = 'plain', hjust = 1, vjust = 1), # x-axis labels in italics
  52. axis.text.y = element_text(face = 'italic',hjust = 1, vjust = 1), # y-axis labels
  53. plot.margin = margin(t = 1, r = 5, b = 1, l = 1), legend.position = "bottom") +
  54. ylab("Tanycyte Subtypes") +
  55. xlab("Transcripts") # y-axis label
  57. # To flip the coordinates
  58. plot <- plot + coord_flip() # Flip the axes
  60. ggsave(filename = "SuppFig6a.pdf", height = 8, width = 4, plot = plot)
  63. #Plot for the Supplementary Fig 8a.
  64. tany_integrated1 <- subset(x=tany_integrated, subset = Diet == "Chow" & Age == "6+ weeks") #Figures were plotted using Chow diet fed 6+ weeks old adult mice.
  66. features <- c("Cd59a", "Lyz2", "Slc17a8", "Pygm", "Ephb1", "Vcan", "Crlf3", "Crym", "Frzb", "Pttg1", "Sprr1a", "A2m", "Scn7a", "Adm", "Col25a1", "Trhr", "Abhd11", "Trhde", "Cers6", "Dio2")
  68. plot <- DotPlot(
  69. tany_integrated1,
  70. features = features,
  71. assay = "RNA",
  72. cols = c("lightgrey", "blue"),
  73. dot.min = 0,
  74. dot.scale = 6,
  75. group.by = "label",
  76. scale = TRUE,
  77. scale.by = "radius"
  78. ) + theme(plot.background = element_rect(fill = "white", colour = NA),
  79. axis.title = element_text(size = 14),
  80. axis.text.x = element_text(angle = 45,face = 'italic', hjust = 1, vjust = 1), # x-axis labels in italics
  81. axis.text.y = element_text(face = 'plain',hjust = 1, vjust = 1), # y-axis labels
  82. plot.margin = margin(t = 1, r = 5, b = 1, l = 1)) +
  83. xlab("Transcripts") +
  84. ylab("Tanycyte Subtypes") # y-axis label
  86. ggsave(filename = "SuppFig8a.pdf", height = 3.5, width =8, plot = plot)

8.Plots_for_the_Publication.r at commit 8b9918a, under AGPL-3.0 · at the source

Overview

Authors: Vanessa Neve1, Daniela Fernandois2, Surya Rai1, Ümit Özorhan1, Sreekala Nampoothiri2, Gaetan Ternier2, Spyridon Sideromenos3, Sarah Gallet2, Cecile Allet2, Marcus Stahr1, Natascha Klaus1, Ines Martinez-Corral2, Caio Fernando Ferreira Coêlho2, Akila Chandrasekar1, Andreea Constantinescu1, Manon Rivagorda1, Simon Dührkop1, Julia Cases Bazarra1, Sonja Binder1, Paolo Giacobini2
and 7 other authorsSowmyalakshmi Rasika2, Ruben Nogueiras4, Tibor Harkany3,5, Martin K. Schwarz6, Helge Müller-Fielitz1, Vincent Prevot2, Markus Schwaninger1
ORCID iDs: Surya Rai, Sreekala Nampoothiri, Gaetan Ternier, Sarah Gallet, Cecile Allet, Ines Martinez-Corral, Akila Chandrasekar, Andreea Constantinescu, Manon Rivagorda, Paolo Giacobini, Sowmyalakshmi Rasika, Ruben Nogueiras, Tibor Harkany, Martin K. Schwarz, Helge Müller-Fielitz, Vincent Prevot, Markus Schwaninger
  1. Institute of Experimental and Clinical Pharmacology and Toxicology, University of Luebeck,Luebeck, Germany
  2. University Lille, Inserm, CHU Lille, Laboratory of Development and Plasticity of the Neuroendocrine Brain, Lille Neuroscience & Cognition, UMR-S 1172, DISTALZ, EGID,Lille, France
  3. Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna,Vienna, Austria
  4. Department of Physiology, CIMUS, University of Santiago de Compostela-Instituto de Investigación Sanitaria,Santiago de Compostela, Spain
  5. Department of Neuroscience, Karolinska Institutet,Solna, Sweden
  6. Institute for Experimental Epileptology and Cognition Research, University of Bonn Medical Center,Bonn, Germany
Institutions: University of Lübeck (Germany); Lille Neurosciences & Cognition (France); Medical University of Vienna (Austria); Universidade de Santiago de Compostela (Spain); Karolinska Institutet (Sweden); University of Bonn (Germany)
Journal: Nature communications, volume 17, issue 1, article 7797
Dates: received 25 September 2025; accepted 5 June 2026; published online 20 June 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1038/s41467-026-74598-5 · PMID 42323316 · PMCID PMC13439102 · OpenAlex W7165395233
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: mouse (organism), cellular / molecular (subfield)
Methods: Spectral & time-frequency, Statistics, Smoothing, state filtering, decompositions, Evoked potentials, Connectivity, fMRI & imaging
Keywords: Synaptic transmission, Reproductive biology, Glial biology
MeSH: Connectome*, Ependymoglial Cells*, Neuroglia*, Neurosecretory Systems*, Synapses*, Animals, Cell Communication, Female, Hypothalamic-Pituitary-Gonadal Axis, Hypothalamus, Kisspeptins, Luteinizing Hormone, Male, Mice, Mice, Inbred C57BL, Neurons (* major topic)
Topic: Hypothalamic control of reproductive hormones (Reproductive Medicine, Medicine), according to OpenAlex
Funding: Deutsche Forschungsgemeinschaft (DFG) (INST 392/135-1, SCHW 416/13-1, SFB TRR 296/1)
Citations: cited by 2 papers (Europe PMC); 109 references in the paper
Research resources: mT/mG RRID:IMSR_JAX:007676, Ai14 RRID:IMSR_JAX:007914, Kiss1-Cre RRID:IMSR_JAX:017701, hM4Di RRID:IMSR_JAX:026219, RRID:SCR_024672

Abstract

Tanycytes are radial-glia-like cells that play important roles in regulating the neuroendocrine system and metabolism. Synapse-like (synaptoid) connections have previously been described between neurons and tanycytes, but their structure and function are unclear. Here, we report that neuron-tanycyte synaptoids are abundant and resemble typical neuronal synapses in shape and composition. Tanycytic subtypes receive specific inputs from a variety of hypothalamic as well as extrahypothalamic neuronal populations and respond to several neurotransmitters and neuromodulators. As proof-of-principle of their functional relevance, we demonstrate in mice, that two distinct populations of kisspeptin neurons, which stimulate the gonadotropic axis, innervate different tanycytic subsets of the mediobasal hypothalamus to control basal levels of the gonadotropin luteinizing hormone (LH) and its pulsatile release pattern, in a sex‑ and region‑specific manner. Neuron-tanycyte synaptoid connections are thus widespread, diverse and functionally specific elements of hypothalamic neural circuits that play a key role in finetuning hormonal axes.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repositories

Its files are read in the Code ↔ Paper reader above, with 4 matches between paragraphs and lines of code.

umitozorhan/Tanybase

License: AGPL-3.0
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 8b9918a18c274b87dc28f86f4f2b01ebaf1031a8, 30 June 2025
Languages: R (9)
Size: 12 files, 9 scripts
Software Heritage: not archived
Found in: “Code availability”
Holds: README, license file
Not found: CITATION.cff, environment file, tests, continuous integration, documentation
Tools: reticulate (2 files), Seurat (2 files), tidyverse (2 files), cowplot (1 file), ggplot2 (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
11 files
At the source: github.com/umitozorhan/Tanybase

Zenodo 19912027

License: apgl-v3
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Size: 1 file
Software Heritage: not checked
Found in: “Code availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: reticulate (2 files), Seurat (2 files), tidyverse (2 files), cowplot (1 file), ggplot2 (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers (HTTP 200)
  • 27 September 2026: the link answers (HTTP 200)
11 files
At the source:

Code availability

The code used for Tanybase is publicly accessible on GitHub, https://github.com/umitozorhan/Tanybase with the 10.5281/zenodo.19912027108.

Reproduced under the paper's license (CC BY), from the paper cited above.

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:

  • 2 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 18 scripts, each with its path and the digest of its content;
  • 4 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

Data availability

The Tanybase data are publicly accessible in the repository Mendeley data, 10.17632/p6jkzkpdd6.1. Other datasets generated during the current study are included in the Source data file. The plasmids used to generate the AAVs and their genetic sequences will be provided by the corresponding author M.Sc. upon request. Source data are provided with this paper.

Reproduced under the paper's license (CC BY), from the paper cited above.

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, 27 authors, 3 keywords, 16 MeSH terms, 1 funder, 108 references, 5 RRIDs.

Cite

This paper

Neve, V., Fernandois, D., Rai, S., Özorhan, Ü., Nampoothiri, S., Ternier, G., Sideromenos, S., Gallet, S., Allet, C., Stahr, M., Klaus, N., Martinez-Corral, I., Coêlho, C. F. F., Chandrasekar, A., Constantinescu, A., Rivagorda, M., Dührkop, S., Cases Bazarra, J., Binder, S., . . . Schwaninger, M. (2026). A synaptoid connectome differentiates tanycytic subpopulations and underlies neuroglial communication and neuroendocrine regulation. Nature communications, 17(1), 7797. https://doi.org/10.1038/s41467-026-74598-5

BibTeX

@article{neve2026synaptoid,
author = {Neve, Vanessa and Fernandois, Daniela and Rai, Surya and Özorhan, Ümit and Nampoothiri, Sreekala and Ternier, Gaetan and Sideromenos, Spyridon and Gallet, Sarah and Allet, Cecile and Stahr, Marcus and Klaus, Natascha and Martinez-Corral, Ines and Coêlho, Caio Fernando Ferreira and Chandrasekar, Akila and Constantinescu, Andreea and Rivagorda, Manon and Dührkop, Simon and Cases Bazarra, Julia and Binder, Sonja and Giacobini, Paolo and Rasika, Sowmyalakshmi and Nogueiras, Ruben and Harkany, Tibor and Schwarz, Martin K. and Müller-Fielitz, Helge and Prevot, Vincent and Schwaninger, Markus},
title = {{A synaptoid connectome differentiates tanycytic subpopulations and underlies neuroglial communication and neuroendocrine regulation}},
journal = {Nature communications},
year = {2026},
month = jun,
volume = {17},
number = {1},
pages = {7797},
publisher = {Nature Publishing Group},
issn = {2041-1723},
doi = {10.1038/s41467-026-74598-5},
url = {https://doi.org/10.1038/s41467-026-74598-5},
pmid = {42323316},
pmcid = {PMC13439102}
}

RIS

TY - JOUR
AU - Neve, Vanessa
AU - Fernandois, Daniela
AU - Rai, Surya
AU - Özorhan, Ümit
AU - Nampoothiri, Sreekala
AU - Ternier, Gaetan
AU - Sideromenos, Spyridon
AU - Gallet, Sarah
AU - Allet, Cecile
AU - Stahr, Marcus
AU - Klaus, Natascha
AU - Martinez-Corral, Ines
AU - Coêlho, Caio Fernando Ferreira
AU - Chandrasekar, Akila
AU - Constantinescu, Andreea
AU - Rivagorda, Manon
AU - Dührkop, Simon
AU - Cases Bazarra, Julia
AU - Binder, Sonja
AU - Giacobini, Paolo
AU - Rasika, Sowmyalakshmi
AU - Nogueiras, Ruben
AU - Harkany, Tibor
AU - Schwarz, Martin K.
AU - Müller-Fielitz, Helge
AU - Prevot, Vincent
AU - Schwaninger, Markus
TI - A synaptoid connectome differentiates tanycytic subpopulations and underlies neuroglial communication and neuroendocrine regulation
T2 - Nature communications
J2 - Nat Commun
PY - 2026
DA - 2026/06/20
VL - 17
IS - 1
SP - 7797
SN - 2041-1723
PB - Nature Publishing Group
DO - 10.1038/s41467-026-74598-5
UR - https://doi.org/10.1038/s41467-026-74598-5
LA - en
ER -

CSL-JSON

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