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Temporal orchestration of transcriptional and epigenomic programming underlying maternal embryonic diapause in a cricket model.

Code ↔ Paper

9 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 9 matches · 8 of them tie a paragraph to a whole file, not to given lines: weak matches, whose lines are not tinted
  1. [1] § Methods › De novo genome assembly ↔ blobtools/megablast.sh, the whole file · a weak match · score 0.89 · qseqid staxids bitscore, std sscinames sskingdoms, culling_limit, megablast, BLASTn, outfmt
  2. [2] § Methods › Prediction of repeat regions and annotation of protein-coding genes ↔ structural_gene_annotation/integration_pipeline.sh, lines 1–41 · score 0.87 · StringTie2, Apis mellifera, Tribolium castaneum, GeMoMa, Drosophila melanogaster, GffCompare
  3. [3] § Results › Metabolic regulation and developmental signaling orchestrate diapause preparation ↔ kegg/02_make_plot.R, the whole file · a weak match · score 0.84 · beta alanine metabolism, lysine degradation, tryptophan metabolism, isoleucine degradation, gluconeogenic, valine
  4. [4] § Methods › RNA-seq analysis ↔ rna-seq_analysis/salmon.sh, the whole file · a weak match · score 0.74 · longest isoform, cDNA, RNA seq, Salmon, quant, v1
  5. [5] § Methods › RNA-seq analysis ↔ rna-seq_analysis/longest_isoform.sh, the whole file · a weak match · score 0.72 · longest isoform, cDNA, RNA seq, v1, genome, gene
  6. [6] § Methods › De novo genome assembly ↔ purge_haplotigs/ph.sh, the whole file · a weak match · score 0.72 · Purge_Haplotigs, depth, sr, histogram, coverage, genome
  7. [7] § Results › Metabolic regulation and developmental signaling orchestrate diapause preparation ↔ kegg/02_make_plot.R, the whole file · a weak match · score 0.61 · TGF beta signaling, signaling pathways, metabolic
  8. [8] § Results › Temporal coordination and divergence of gene expression patterns reveal diapause preparation dynamics ↔ mfuzz/07_make_graph.R, the whole file · a weak match · score 0.59 · enriched terms, CC, MF, log10, graphs, Bar
  9. [9] § Methods › Time-series clustering analysis, cluster comparison and classification ↔ mfuzz/02_mfuzz.R, the whole file · a weak match · score 0.50 · ExpressionSet, Mfuzz, mestimate, clusters

Paper

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

The paper is loaded when this pane is shown.

The authors' code

R · 42 lines · 1.5 KB · no license · 2 matches

  1. # Load necessary libraries
  2. library(ggplot2)
  3. library(dplyr)
  5. # Extract rows where the source column is "KEGG"
  6. kegg_data <- combined_data %>% filter(source == "KEGG")
  8. term_order <- c(
  9. "beta-Alanine metabolism",
  10. "Lysine degradation",
  11. "Tryptophan metabolism",
  12. "Valine, leucine and isoleucine degradation",
  13. "Nucleocytoplasmic transport",
  14. "Proteasome",
  15. "Protein processing in endoplasmic reticulum",
  16. "Ribosome",
  17. "Ubiquitin mediated proteolysis",
  18. "Spliceosome",
  19. "Various types of N-glycan biosynthesis",
  20. "Endocytosis",
  21. "SNARE interactions in vesicular transport",
  22. "ATP-dependent chromatin remodeling",
  23. "Glycolysis / Gluconeogenesis",
  24. "TGF-beta signaling pathway"
  25. )
  27. kegg_data$term_name <- factor(kegg_data$term_name, levels = rev(term_order))
  29. kegg_data$Change <- factor(kegg_data$Change, levels = c("up", "down"))
  31. p <- ggplot(kegg_data, aes(x = Time, y = term_name, size = gene_ratio, color = adjusted_p_value)) +
  32. geom_point(alpha = 0.6) +
  33. scale_color_gradient(low = "blue", high = "red") +
  34. theme_minimal() +
  35. labs(title = "GO Enrichment Analysis Results",
  36. x = "Time", y = "Term Name",
  37. color = "Adjusted P-value",
  38. size = "Gene ratio(%)") +
  39. facet_grid(~ Change) +
  40. theme(axis.text.y = element_text(hjust = 1))
  42. print(p)

02_make_plot.R at commit 48da043, no license · at the source

Overview

Authors: Kosuke Kataoka1,2, Yuta Shimizu3, Ryuto Sanno4, Yuichi Koshiishi5, Ken Naito6, Kei Yura7,8, Toru Asahi2,4,8, Shin G. Goto3
ORCID iDs: Kosuke Kataoka, Yuta Shimizu, Yuichi Koshiishi, Kei Yura, Shin G. Goto
  1. Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology,Koganei-shi, Japan
  2. Comprehensive Research Organization, Waseda University,Shinjuku-ku, Japan
  3. Graduate School of Science, Osaka Metropolitan University,Osaka, Japan
  4. Graduate School of Advanced Science and Engineering, Waseda University,Shinjuku-ku, Japan
  5. NODAI Genome Research Center, Tokyo University of Agriculture,Setagaya-ku, Japan
  6. Research Center of Genetic Resources, National Agriculture and Food Research Organization,Tsukuba-shi, Japan
  7. Graduate School of Humanities and Sciences, Ochanomizu University,Bunkyo-ku, Japan
  8. Department of Life Science and Medical Bioscience, Waseda University,Shinjuku-ku, Japan
Institutions: Tokyo University of Agriculture and Technology (Japan); Waseda University (Japan); Osaka Metropolitan University (Japan); Tokyo University of Agriculture (Japan); National Agriculture and Food Research Organization (Japan); Ochanomizu University (Japan)
Journal: Communications biology, volume 9, issue 1, article 825
Dates: received 2 October 2025; accepted 26 May 2026; published online 30 June 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1038/s42003-026-10402-w · PMID 42380220 · PMCID PMC13319455 · OpenAlex W4413019371
Open access: gold, a free copy (OpenAlex)
Preprint: doi:10.1101/2025.08.04.668555
Status: code verified
Categories: genetics / omics (modality), other (organism), developmental (subfield)
Methods: Statistics, Smoothing, state filtering, decompositions
Keywords: Entomology, Developmental biology
MeSH: Diapause*, Diapause, Insect*, Epigenesis, Genetic*, Gene Expression Regulation, Developmental*, Gryllidae*, Transcription, Genetic*, Animals, Chromatin Assembly and Disassembly, Female (* major topic)
Topic: Reproductive Biology and Fertility (Public Health, Environmental and Occupational Health, Medicine), according to OpenAlex
Funding: BRAIN (JPJ009237); Japan Society for the Promotion of Science (21K05614)
Citations: cited by 1 paper (Europe PMC); 105 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 9 matches between paragraphs and lines of code.

Kataoka-K-Lab/Dnigrofasciatus_EggDiapause

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 48da04315ece67e64c966af5a7d2ca176ca6fbbf, 22 January 2026
Languages: Shell (23), R (12)
Size: 66 files, 35 scripts
Software Heritage: not archived
Found in: “Code availability”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: tidyverse (7 files), ggplot2 (4 files), SAMtools (3 files), DESeq2 (1 file), pheatmap (1 file), reshape2 (1 file), Salmon (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
36 files
At the source: github.com/Kataoka-K-Lab/Dnigrofasciatus_EggDiapause.git

Code availability statement

The paper has a code 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/10.1038/s42003-026-10402-w.

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;
  • 35 scripts, each with its path and the digest of its content;
  • 9 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 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:

  • it points to a dataset: figshare 29665742
  • it says that the data are available on request

Read it in the paper: doi.org/10.1038/s42003-026-10402-w.

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, 8 authors, 2 keywords, 9 MeSH terms, 2 funders, 100 references.

Cite

This paper

Kataoka, K., Shimizu, Y., Sanno, R., Koshiishi, Y., Naito, K., Yura, K., Asahi, T., & Goto, S. G. (2026). Temporal orchestration of transcriptional and epigenomic programming underlying maternal embryonic diapause in a cricket model. Communications biology, 9(1), 825. https://doi.org/10.1038/s42003-026-10402-w

BibTeX

@article{kataoka2026temporal,
author = {Kataoka, Kosuke and Shimizu, Yuta and Sanno, Ryuto and Koshiishi, Yuichi and Naito, Ken and Yura, Kei and Asahi, Toru and Goto, Shin G.},
title = {{Temporal orchestration of transcriptional and epigenomic programming underlying maternal embryonic diapause in a cricket model}},
journal = {Communications biology},
year = {2026},
month = jun,
volume = {9},
number = {1},
pages = {825},
publisher = {Nature Publishing Group},
issn = {2399-3642},
doi = {10.1038/s42003-026-10402-w},
url = {https://doi.org/10.1038/s42003-026-10402-w},
pmid = {42380220},
pmcid = {PMC13319455}
}

RIS

TY - JOUR
AU - Kataoka, Kosuke
AU - Shimizu, Yuta
AU - Sanno, Ryuto
AU - Koshiishi, Yuichi
AU - Naito, Ken
AU - Yura, Kei
AU - Asahi, Toru
AU - Goto, Shin G.
TI - Temporal orchestration of transcriptional and epigenomic programming underlying maternal embryonic diapause in a cricket model
T2 - Communications biology
J2 - Commun Biol
PY - 2026
DA - 2026/06/30
VL - 9
IS - 1
SP - 825
SN - 2399-3642
PB - Nature Publishing Group
DO - 10.1038/s42003-026-10402-w
UR - https://doi.org/10.1038/s42003-026-10402-w
LA - en
ER -

CSL-JSON

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"id": "10.1038/s42003-026-10402-w",
"type": "article-journal",
"title": "Temporal orchestration of transcriptional and epigenomic programming underlying maternal embryonic diapause in a cricket model",
"container-title": "Communications biology",
"author": [
{
"family": "Kataoka",
"given": "Kosuke"
},
{
"family": "Shimizu",
"given": "Yuta"
},
{
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{
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{
"family": "Goto",
"given": "Shin G."
}
],
"container-title-short": "Commun Biol",
"volume": "9",
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"page": "825",
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"PMID": "42380220",
"PMCID": "PMC13319455",
"ISSN": "2399-3642",
"publisher": "Nature Publishing Group",
"URL": "https://doi.org/10.1038/s42003-026-10402-w",
"language": "en",
"issued": {
"date-parts": [
[
2026,
6,
30
]
]
}
}

The tracing map gets a citation of its own once an author has validated it and it has a DOI.

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