OSCR

Müller Glia-Exclusive CLRN1 Expression Drives Non-Cell-Autonomous Photoreceptor Degeneration in Usher Syndrome Type 3A.

Code ↔ Paper

11 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 11 matches
  1. [1] § Results › CLRN1 Expression Exclusively in Müller Glia ↔ scripts/02_clustering/02_cluster_markers.R, lines 1–43 · score 0.86 · SLC6A9, clustering identified, bipolar cells, amacrine cells, horizontal cells, ARR3
  2. [2] § Results › CLRN1 Expression Exclusively in Müller Glia ↔ scripts/02_clustering/01_cell_type_identification.R, lines 1–39 · score 0.85 · retinal ganglion cells, SLC6A9, bipolar cells, amacrine cells, horizontal cells, ARR3
  3. [3] § Results › Convergent HSP90-Mediated Stress Responses in Inner Retinal Neurons ↔ scripts/05_visualization/01_generate_figures.R, lines 1–57 · score 0.84 · HSP90 family, HSP90AA1, HSP90B1, HSP90AB1, log2FC, CANX
  4. [4] § Results › Convergent HSP90-Mediated Stress Responses in Inner Retinal Neurons ↔ scripts/05_visualization/Fig6B_CHAPERONE_HEATMAP.R, lines 1–29 · score 0.79 · HSP90AA1, HSP90B1, HSP90AB1, log2FC, CANX, HSPA5
  5. [5] § Results › Müller Glia: Primary Site of CLRN1 Dysfunction ↔ scripts/05_visualization/Figure6A GO_enrichment.R, lines 1–62 · score 0.79 · glutamate receptor signaling, GABAergic, receptor localization, transmission, regulation, synapses
  6. [6] § Results › Müller Glia: Primary Site of CLRN1 Dysfunction ↔ scripts/05_visualization/Figure6A GO_enrichment.R, lines 64–112 · score 0.73 · log10 Padj, glial support, GO enrichment, stress response, fibrosis, ECM
  7. [7] § Results › Photoreceptor Dysfunction Through Non–Cell-Autonomous Mechanisms ↔ scripts/05_visualization/Figure6A GO_enrichment.R, lines 1–62 · score 0.64 · connective tissue, cartilage development, regulatory, enrichment, GO, stress
  8. [8] § Methods › Bioinformatic Analysis › Differential Expression Analysis ↔ scripts/03_differential_expression/01_pseudobulk_DESeq2.R, lines 7–50 · score 0.60 · AggregateExpression, DESeq2, sum, Seurat, Pseudobulk, RNA
  9. [9] § Results › Cell-Type-Specific Transcriptional Responses ↔ scripts/03_differential_expression/01_pseudobulk_DESeq2.R, lines 52–95 · score 0.60 · Pseudobulk DESeq2, CWF19L2, amacrine cells, TENM2, CTNNA2, ller glia
  10. [10] § Results › Convergent HSP90-Mediated Stress Responses in Inner Retinal Neurons ↔ scripts/05_visualization/01_generate_figures.R, lines 1–57 · score 0.57 · HSP90 family, HSP90AB1, log2FC, Bipolar, rods, cones
  11. [11] § Methods › Bioinformatic Analysis › Gene Ontology Enrichment Analysis ↔ scripts/04_pathway_analysis/01_GO_enrichment.R, lines 118–199 · score 0.57 · downregulated genes, Ontology, hs, cutoff, db, GO

Paper

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The authors' code

R · 112 lines · 4.4 KB · MIT · 3 matches

  1. # ============================================
  2. # COMPREHENSIVE GO ENRICHMENT HEATMAP
  3. # All cell types in one figure
  4. # ============================================
  6. library(ggplot2)
  7. library(dplyr)
  9. # Build a combined pathway summary for all cell types
  10. # Select key representative pathways
  11. pathway_summary <- data.frame(
  12. Cell_Type = c(
  13. # Rods Up
  14. rep("Rods ↑", 3),
  15. # Cones Down
  16. rep("Cones ↓", 3),
  17. # Amacrine Up
  18. rep("Amacrine ↑", 3),
  19. # RGC Up
  20. rep("RGC ↑", 3),
  21. # Horizontal Up
  22. rep("Horizontal ↑", 3),
  23. # Müller Down
  24. rep("Müller ↓", 3)
  25. ),
  26. Pathway = c(
  27. # Rods Up
  28. "ECM organization", "Connective tissue dev.", "Cartilage development",
  29. # Cones Down
  30. "Synapse organization", "Visual perception", "cAMP/PKA signaling",
  31. # Amacrine Up
  32. "Protein folding / ER stress", "Glycolytic process", "Synaptic vesicle cycle",
  33. # RGC Up
  34. "Aerobic respiration", "Presynaptic endocytosis", "Chaperone assembly",
  35. # Horizontal Up
  36. "Response to heat", "Ca²⁺ channel regulation", "Lactate metabolism",
  37. # Müller Down
  38. "Glutamate receptor signaling", "Receptor localization to synapse", "GABAergic transmission"
  39. ),
  40. neg_log10_padj = c(
  41. # Rods Up
  42. -log10(2.44e-06), -log10(3.67e-05), -log10(7.64e-06),
  43. # Cones Down
  44. -log10(0.006), -log10(0.026), -log10(0.008),
  45. # Amacrine Up
  46. -log10(5.17e-05), -log10(1.43e-04), -log10(3.07e-04),
  47. # RGC Up
  48. -log10(7.13e-05), -log10(7.13e-05), -log10(6.15e-04),
  49. # Horizontal Up
  50. -log10(0.023), -log10(0.023), -log10(0.023),
  51. # Müller Down
  52. -log10(0.031), -log10(0.031), -log10(0.034)
  53. ),
  54. Category = c(
  55. rep("ECM / Fibrosis", 3),
  56. rep("Synaptic / Visual", 3),
  57. rep("Stress / Metabolic", 3),
  58. rep("Stress / Metabolic", 3),
  59. rep("Stress / Metabolic", 3),
  60. rep("Glial Support", 3)
  61. )
  62. )
  64. # Order cell types
  65. pathway_summary$Cell_Type <- factor(pathway_summary$Cell_Type,
  66. levels = c("Müller ↓", "Rods ↑", "Cones ↓",
  67. "Amacrine ↑", "RGC ↑", "Horizontal ↑"))
  69. # Create bubble plot
  70. fig_go_summary <- ggplot(pathway_summary, aes(x = Cell_Type, y = Pathway,
  71. size = neg_log10_padj, color = Category)) +
  72. geom_point() +
  73. scale_size_continuous(range = c(4, 12), name = "-Log10(padj)") +
  74. scale_color_manual(values = c("ECM / Fibrosis" = "#d62728",
  75. "Synaptic / Visual" = "#1f77b4",
  76. "Stress / Metabolic" = "#ff7f0e",
  77. "Glial Support" = "#2ca02c")) +
  78. labs(title = "GO Enrichment Summary Across All Retinal Cell Types",
  79. subtitle = "CLRN1 KO vs WT", x = "", y = "") +
  80. theme_minimal() +
  81. theme(plot.title = element_text(face = "bold", size = 13),
  82. axis.text.x = element_text(angle = 45, hjust = 1, size = 11),
  83. axis.text.y = element_text(size = 10),
  84. legend.position = "right",
  85. panel.grid.major = element_line(color = "grey90"))
  87. fig_go_summary
  88. ggsave("Figures/Fig_GO_Summary_AllCellTypes.pdf", fig_go_summary, width = 10, height = 8)
  89. ggsave("Figures/Fig_GO_Summary_AllCellTypes.png", fig_go_summary, width = 10, height = 8, dpi = 300)
  91. # ============================================
  92. # UPDATED COMPLETE SUPPLEMENTARY TABLE
  93. # ============================================
  95. complete_go_table <- data.frame(
  96. Cell_Type = c("Rods", "Rods", "Cones", "Amacrine", "RGC", "Horizontal", "Horizontal", "Müller Glia"),
  97. Direction = c("Up in KO", "Down in KO", "Down in KO", "Up in KO", "Up in KO", "Up in KO", "Down in KO", "Down in KO"),
  98. n_DEGs = c(119, 113, 50, 131, 27, 23, 14, 59),
  99. Top_GO_Term = c("ECM organization", "No significant terms", "Synapse organization",
  100. "Protein folding", "Presynaptic endocytosis", "Response to heat",
  101. "Smooth muscle relaxation", "Glutamate receptor signaling"),
  102. GO_padj = c("2.4e-06", "NA", "0.006", "5.2e-05", "7.1e-05", "0.023", "0.014", "0.031"),
  103. Biological_Theme = c("Fibrotic remodeling", "–", "Synaptic/visual dysfunction",
  104. "ER stress & metabolic shift", "Metabolic stress & synaptic",
  105. "Stress response", "–", "Impaired glial support")
  106. )
  108. print(complete_go_table)
  109. write.csv(complete_go_table, "Complete_GO_Summary_AllCellTypes.csv", row.names = FALSE)
  111. cat("\n✅ All GO summary figures and tables saved!\n")
  112. list.files("Figures")

Figure6A GO_enrichment.R at commit 2c9e9dd, under MIT · at the source

Overview

Authors: Yeachan Lee1,2, Yuanyuan Gao1, Van Phuc Nguyen2, Bo Liang1, Diane M. Prieskorn3, Lisa Beyer3, Zhuying Wei1, Naheed Khan4, James Weiland4, Michael Iannuzzi5, Charles Bisgaier5, Yehoash Raphael3, Y. Eugene Chen1, Yannis M. Paulus2, Dongshan Yang1
ORCID iDs: Dongshan Yang
  1. Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical School, Ann Arbor, Michigan, United States
  2. Department of Ophthalmology and Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States
  3. Kresge Hearing Research Institute, Department of Otolaryngology-Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan, United States
  4. Department of Biomedical Engineering and Ophthalmology and Visual Sciences, University of Michigan Medical Center, Ann Arbor, Michigan, United States
  5. GeneToBe Inc., Ann Arbor, Michigan, United States
Institutions: Johns Hopkins University (United States); University of Michigan (United States); Michigan Medicine (United States)
Journal: Investigative ophthalmology & visual science, volume 67, issue 8, article 9
Dates: received 19 March 2026; accepted 4 June 2026; published online 2 July 2026; in print July 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1167/iovs.67.8.9 · PMID 42390169 · PMCID PMC13332521 · OpenAlex W7167028397
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: genetics / omics (modality), other (modality), histology / microscopy (modality), other (organism), cellular / molecular (subfield)
Methods: Statistics, Smoothing, state filtering, decompositions, Connectivity
Keywords: Usher syndrome type 3A, CLRN1, rabbit model, single-nucleus RNA sequencing, non–cell-autonomous degeneration
MeSH: Ependymoglial Cells*, Gene Expression Regulation*, Membrane Proteins*, Photoreceptor Cells, Vertebrate*, Retinal Degeneration*, Usher Syndromes*, Animals, Disease Models, Animal, Electroretinography, Rabbits, Tomography, Optical Coherence (* major topic)
Journal subjects: Retina
Topic: Hearing, Cochlea, Tinnitus, Genetics (Sensory Systems, Neuroscience), according to OpenAlex
Citations: not cited yet (Europe PMC); 32 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 11 matches between paragraphs and lines of code.

doyang-um/CLRN1_snRNAseq_10M

License: MIT
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 2c9e9dd3ca6a58641c367b6b3f62bf6e3a654dc9, 18 May 2026
Languages: R (14)
Size: 41 files, 14 scripts
Software Heritage: not archived
Found in: the acknowledgements
Holds: README, license file
Not found: CITATION.cff, environment file, tests, continuous integration, documentation
Tools: tidyverse (13 files), ggplot2 (11 files), patchwork (10 files), Seurat (8 files), pheatmap (2 files), clusterProfiler (1 file), DESeq2 (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
16 files
At the source: github.com/doyang-um/CLRN1_snRNAseq_10M

Tracing map

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  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
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  • 11 matches between paragraphs of the paper and lines of the code (method lexical-v1);
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Data

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Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 15 authors, 5 keywords, 11 MeSH terms, 32 references.

Cite

This paper

Lee, Y., Gao, Y., Nguyen, V. P., Liang, B., Prieskorn, D. M., Beyer, L., Wei, Z., Khan, N., Weiland, J., Iannuzzi, M., Bisgaier, C., Raphael, Y., Chen, Y. E., Paulus, Y. M., & Yang, D. (2026). Müller Glia-Exclusive CLRN1 Expression Drives Non-Cell-Autonomous Photoreceptor Degeneration in Usher Syndrome Type 3A. Investigative ophthalmology & visual science, 67(8), 9. https://doi.org/10.1167/iovs.67.8.9

BibTeX

@article{lee2026muller,
author = {Lee, Yeachan and Gao, Yuanyuan and Nguyen, Van Phuc and Liang, Bo and Prieskorn, Diane M. and Beyer, Lisa and Wei, Zhuying and Khan, Naheed and Weiland, James and Iannuzzi, Michael and Bisgaier, Charles and Raphael, Yehoash and Chen, Y. Eugene and Paulus, Yannis M. and Yang, Dongshan},
title = {{Müller Glia-Exclusive CLRN1 Expression Drives Non-Cell-Autonomous Photoreceptor Degeneration in Usher Syndrome Type 3A}},
journal = {Investigative ophthalmology \& visual science},
year = {2026},
month = jul,
volume = {67},
number = {8},
pages = {9},
publisher = {Association for Research in Vision and Ophthalmology},
issn = {0146-0404},
doi = {10.1167/iovs.67.8.9},
url = {https://doi.org/10.1167/iovs.67.8.9},
pmid = {42390169},
pmcid = {PMC13332521}
}

RIS

TY - JOUR
AU - Lee, Yeachan
AU - Gao, Yuanyuan
AU - Nguyen, Van Phuc
AU - Liang, Bo
AU - Prieskorn, Diane M.
AU - Beyer, Lisa
AU - Wei, Zhuying
AU - Khan, Naheed
AU - Weiland, James
AU - Iannuzzi, Michael
AU - Bisgaier, Charles
AU - Raphael, Yehoash
AU - Chen, Y. Eugene
AU - Paulus, Yannis M.
AU - Yang, Dongshan
TI - Müller Glia-Exclusive CLRN1 Expression Drives Non-Cell-Autonomous Photoreceptor Degeneration in Usher Syndrome Type 3A
T2 - Investigative ophthalmology & visual science
J2 - Invest Ophthalmol Vis Sci
PY - 2026
DA - 2026/07/01
VL - 67
IS - 8
SP - 9
SN - 0146-0404
PB - Association for Research in Vision and Ophthalmology
DO - 10.1167/iovs.67.8.9
UR - https://doi.org/10.1167/iovs.67.8.9
LA - en
ER -

CSL-JSON

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"id": "10.1167/iovs.67.8.9",
"type": "article-journal",
"title": "Müller Glia-Exclusive CLRN1 Expression Drives Non-Cell-Autonomous Photoreceptor Degeneration in Usher Syndrome Type 3A",
"container-title": "Investigative ophthalmology & visual science",
"author": [
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"family": "Lee",
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"PMCID": "PMC13332521",
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"issued": {
"date-parts": [
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}

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