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Multiple glycoforms of TrkA interact with N-cadherin during trigeminal ganglion neurodevelopment.

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Paper

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The authors' code

R · 70 lines · 2.6 KB · CC-BY-4.0

  1. output <- "/Users/..." # Output Folder
  2. setwd("/Users/...") # Folder with Images
  3. Proteins <- c("TrkA", "Ncad") # Replace TrkA and Ncad throughout code with proteins of interest
  4. Overlap.Threshold <- c(0, 10, 33)
  5. Folder <- "Explant" # "Explant" "InVivo"
  6. Dirs <- list.dirs(path = paste(Folder,sep = ""), full.names = TRUE, recursive = TRUE)
  7. Dirs <- Dirs[-1]
  9. for(d in Overlap.Threshold){
  11. Ncad.Puncta = NULL
  12. Perc.Ncad.Puncta.Overlapping.at.Threshold = NULL
  14. TrkA.Puncta = NULL
  15. Perc.TrkA.Puncta.Overlapping.at.Threshold = NULL
  17. for(i in Dirs){
  19. path1 = paste(i,"/",Proteins[2],"_Puncta_with_Overlap_",Proteins[1],"_Puncta.txt",sep = "")
  21. if (file.exists(path1)) {
  22. print("Files has been read successfully.")
  24. tmp1 <- read.delim(file = paste(i,"/",Proteins[2],"_Puncta_with_Overlap_",Proteins[1],"_Puncta.txt",sep = ""), header = TRUE, sep = '\t')
  25. Ncad.Puncta = c(Ncad.Puncta, nrow(tmp1))
  27. tmp1$pixel.overlap <- apply(tmp1[, c("Area", "Mean")], 1, function(x) {
  28. x[1] * x[2] / 255
  29. })
  30. tmp1$Actual.overlap <- (tmp1$pixel.overlap / tmp1$Area) * 100
  31. index <- which(tmp1$Actual.overlap > d)
  32. Perc.Ncad.Puncta.Overlapping.at.Threshold = c(Perc.Ncad.Puncta.Overlapping.at.Threshold, (length(index)/nrow(tmp1))*100)
  33. rm(index)
  35. tmp2 <- read.delim(file = paste(i,"/",Proteins[1],"_Puncta_with_Overlap_",Proteins[2],"_Puncta.txt",sep = ""), header = TRUE, sep = '\t')
  36. TrkA.Puncta = c(TrkA.Puncta, nrow(tmp2))
  38. tmp2$pixel.overlap <- apply(tmp2[, c("Area", "Mean")], 1, function(x) {
  39. x[1] * x[2] / 255
  40. })
  41. tmp2$Actual.overlap <- (tmp2$pixel.overlap / tmp2$Area) * 100
  42. index <- which(tmp2$Actual.overlap > d)
  43. Perc.TrkA.Puncta.Overlapping.at.Threshold = c(Perc.TrkA.Puncta.Overlapping.at.Threshold, (length(index)/nrow(tmp2))*100)
  44. rm(index)
  45. } else {
  46. # If the file does not exist, display an error message
  47. print("These files do not exist.")
  48. }
  51. } # Directories
  53. master.table <- data.frame("TrkA.Puncta" = TrkA.Puncta,
  54. "Ncad.Puncta" = Ncad.Puncta,
  55. "Perc.Ncad.Puncta.Overlapping.at.Threshold" = Perc.Ncad.Puncta.Overlapping.at.Threshold,
  56. "Perc.TrkA.Puncta.Overlapping.at.Threshold" = Perc.TrkA.Puncta.Overlapping.at.Threshold)
  58. write.table(x = master.table, file = paste(output, Folder,"_Ncad_TrkA_Puncta_Colocalization_at_Threshold_of_",d,"_percentage_of_puncta_pixel_Overlap.txt", sep = ""), sep = '\t', quote = FALSE, row.names = FALSE)
  59. rm(master.table)
  60. } #Overlap Threshold

TrkA_Ncad_FIJI_Output_Analysis.R, under CC-BY-4.0 · at the source

Overview

Authors: Caroline A Halmi1, Lisa A Taneyhill1
ORCID iDs: Lisa A Taneyhill
  1. Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
Institutions: University of Maryland, College Park (United States)
Journal: Journal of cell science, volume 139, issue 9, article jcs264598
Dates: received 14 November 2025; accepted 19 March 2026; published online 11 May 2026; in print May 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1242/jcs.264598 · PMID 42112671 · PMCID PMC13245897 · OpenAlex W4416407883
Open access: hybrid, a free copy (OpenAlex)
Preprint: doi:10.1101/2025.11.14.688512
Status: code verified
Categories: other (organism)
Methods: Statistics
Keywords: Trigeminal ganglion, N-cadherin, TrkA, Glycosylation
MeSH: Cadherins*, Receptor, trkA*, Trigeminal Ganglion*, Animals, Axons, Cell Membrane, Chick Embryo, Glycosylation, Neurodevelopment, Signal Transduction (* major topic)
Topic: Nerve injury and regeneration (Cellular and Molecular Neuroscience, Neuroscience), according to OpenAlex
Funding: NIDCR NIH HHS (1R21 DE033786-01); University of Maryland, College Park
Citations: not cited yet (Europe PMC); 90 references in the paper

Abstract

The trigeminal ganglion is a sensory structure derived from neural crest and placode cells, leading to a heterogeneous neuronal population that transmits somatosensory information to the brain. Proper trigeminal ganglion development relies, in part, on neurotrophic signaling, including interactions between nerve growth factor and its receptor, tropomyosin receptor kinase A (TrkA). Although glycosylation is essential for the trafficking of TrkA to the plasma membrane, the glycan profile and functional relevance of these modifications in sensory neurons remains poorly defined in vivo. Here, we characterized TrkA glycosylation during chick trigeminal ganglion neurodevelopment and identified multiple glycoforms of TrkA corresponding to partially and fully mature protein states reported in vitro. Furthermore, we showed that TrkA interacts with the cell adhesion molecule N-cadherin on neuronal membranes both in cell bodies and axons. The molecular weights of interacting TrkA forms suggest that these associations occur at the plasma membrane as well as on intracellular organelle membranes. Our findings are the first to identify a biochemical association between TrkA and N-cadherin in the trigeminal ganglion, suggesting potential coordination between neurotrophic signaling and cell adhesion during development.

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

Repository

Its files are read in the Code ↔ Paper reader above.

Zenodo 18422165

License: CC-BY-4.0
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Languages: R (1)
Size: 3 files, 1 script
Software Heritage: not checked
Found in: the text, “Footnotes”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 28 September 2026: the link answers (HTTP 200)
  • 28 September 2026: the link answers (HTTP 200)
1 file
At the source: zenodo.org/records/18422165

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;
  • 1 script, 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

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Versions

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Version 2, 28 September 2026

  • Publisher: n/a → The Company of Biologists

Version 1, 28 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 2 authors, 4 keywords, 10 MeSH terms, 2 funders, 90 references.

Cite

This paper

Halmi, C. A., & Taneyhill, L. A. (2026). Multiple glycoforms of TrkA interact with N-cadherin during trigeminal ganglion neurodevelopment. Journal of cell science, 139(9), jcs264598. https://doi.org/10.1242/jcs.264598

BibTeX

@article{halmi2026multiple,
author = {Halmi, Caroline A and Taneyhill, Lisa A},
title = {{Multiple glycoforms of TrkA interact with N-cadherin during trigeminal ganglion neurodevelopment}},
journal = {Journal of cell science},
year = {2026},
month = may,
volume = {139},
number = {9},
pages = {jcs264598},
publisher = {The Company of Biologists},
issn = {0021-9533},
doi = {10.1242/jcs.264598},
url = {https://doi.org/10.1242/jcs.264598},
pmid = {42112671},
pmcid = {PMC13245897}
}

RIS

TY - JOUR
AU - Halmi, Caroline A
AU - Taneyhill, Lisa A
TI - Multiple glycoforms of TrkA interact with N-cadherin during trigeminal ganglion neurodevelopment
T2 - Journal of cell science
J2 - J Cell Sci
PY - 2026
DA - 2026/05/11
VL - 139
IS - 9
SP - jcs264598
SN - 0021-9533
PB - The Company of Biologists
DO - 10.1242/jcs.264598
UR - https://doi.org/10.1242/jcs.264598
LA - en
ER -

CSL-JSON

{
"id": "10.1242/jcs.264598",
"type": "article-journal",
"title": "Multiple glycoforms of TrkA interact with N-cadherin during trigeminal ganglion neurodevelopment",
"container-title": "Journal of cell science",
"author": [
{
"family": "Halmi",
"given": "Caroline A"
},
{
"family": "Taneyhill",
"given": "Lisa A"
}
],
"container-title-short": "J Cell Sci",
"volume": "139",
"issue": "9",
"page": "jcs264598",
"DOI": "10.1242/jcs.264598",
"PMID": "42112671",
"PMCID": "PMC13245897",
"ISSN": "0021-9533",
"publisher": "The Company of Biologists",
"URL": "https://doi.org/10.1242/jcs.264598",
"language": "en",
"issued": {
"date-parts": [
[
2026,
5,
11
]
]
}
}

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