OSCR

Long non-coding RNA transcripts in crucian carp brain - annotation and expression patterns in anoxia and reoxygenation.

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 · 6 of them tie a paragraph to a whole file without given lines: weak matches, whose lines are not tinted
  1. [1] § Materials and methods › Annotation of LncRNAs ↔ 5_4_cpat/cpat.sh, lines 1 to 16 · score 0.83 · Zebrafish_logitModel.RData, zebrafish_Hexamer.tsv, cc transcriptome, genomic, fa, orf · Report a mismatch
  2. [2] § Materials and methods › Annotation of LncRNAs ↔ 5_2_cnci/5_2_1_cnci.sh, the whole file · a weak match · score 0.79 · reference genomes, cc transcriptome, ve, model, GFFread, tools · Report a mismatch
  3. [3] § Materials and methods › Differential expression of DElncRNA interaction partners ↔ 7_create_feature_count_matrix/7_1_featurecount_lncrna_lncpartner_gene.sh, the whole file · a weak match · score 0.78 · countReadPairs, featureCounts, gene_id, Subread, matrix, BAM · Report a mismatch
  4. [4] § Materials and methods › Differential expression of lncRNAs ↔ 7_create_feature_count_matrix/7_1_featurecount_lncrna_all.sh, the whole file · a weak match · score 0.77 · countReadPairs, featureCounts, transcript_id, chimeric, Subread, BAM · Report a mismatch
  5. [5] § Materials and methods › Differential expression of lncRNAs ↔ 7_create_feature_count_matrix/7_1_featurecount_lncrna_lncpartner_transcipt.sh, the whole file · a weak match · score 0.76 · countReadPairs, featureCounts, transcript_id, chimeric, Subread, BAM · Report a mismatch
  6. [6] § Materials and methods › Differential expression of DElncRNA interaction partners ↔ 7_create_feature_count_matrix/7_1_featurecount_lncrna_all.sh, the whole file · a weak match · score 0.73 · countReadPairs, featureCounts, Subread, matrix, BAM, score · Report a mismatch
  7. [7] § Materials and methods › Prediction and characterization of lncRNA interaction partners ↔ 10_lncRNA_classification/5_1_3_feelnc_classifier.sh, the whole file · a weak match · score 0.71 · FEELnc classifier module, lncRNA_classes.txt, carcar_annotation_v5.gtf · Report a mismatch
  8. [8] § Materials and methods › Pre-Processing of RNAseq reads and transcriptome assembly ↔ 4_gffread/gffread.sh, lines 1 to 27 · score 0.65 · ccar genome v1, crucian carp, 262scaffolds, command, fasta, gtf · Report a mismatch
  9. [9] § Materials and methods › Pre-Processing of RNAseq reads and transcriptome assembly ↔ 4_gffread/gffread_transcript_all.sh, lines 1 to 27 · score 0.64 · ccar genome v1, crucian carp, 262scaffolds, command, fasta, gtf · Report a mismatch
  10. [10] § Results › Classification of differentially expressed LncRNAs and the nearby genes ↔ 9_3_number_of_genes_degs/9_3_number_of_genes.ipynb, lines 205 to 248 · score 0.54 · median length, DELncRNA, density, bp, kb, LncRNAs · Report a mismatch
  11. [11] § Materials and methods › Prediction and characterization of lncRNA interaction partners ↔ 10_lncRNA_classification/10_1_classification.ipynb, lines 11 to 22 · score 0.52 · lncRNA_classes.txt, FEELnc classifier, transcripts · Report a mismatch

Paper

Loaded from Europe PMC by your browser; OSCR does not store it: doi.org · Europe PMC

The paper is loaded when this pane is shown.

The authors' code

Shell · 83 lines · 2.4 KB · no license · 2 matches

  1. #!/bin/bash
  3. #SBATCH --account=nn8014k
  4. #SBATCH --job-name=featurecounts_cc
  5. #SBATCH --time=25:00:00
  6. #SBATCH --mem-per-cpu=4G
  7. #SBATCH --ntasks=1
  8. #SBATCH --cpus-per-task=4
  9. #SBATCH --array=0-17
  12. # load the needed modules
  13. ml load Subread/2.0.3-GCC-11.2.0
  15. # show me the loaded modules in a list
  16. ml list
  18. # change directory to the program script
  19. cd /cluster/work/users/magdalena/lncrna/7_featurecounts/
  21. # additional settings
  22. set -o errexit # Exit the script on any error
  23. set -o nounset # Treat any unset variables as an error
  25. # Commands for the program (alignment of the reads to the genome)
  26. echo running featureCounts
  28. input=("A1.bam" \
  29. "A2.bam" \
  30. "A3.bam" \
  31. "A4.bam" \
  32. "A5.bam" \
  33. "A6.bam" \
  34. "N14.bam" \
  35. "N15.bam" \
  36. "N16.bam" \
  37. "N17.bam" \
  38. "N18.bam" \
  39. "N21.bam" \
  40. "R10.bam" \
  41. "R11.bam" \
  42. "R12.bam" \
  43. "R13.bam" \
  44. "R8.bam" \
  45. "R9.bam" )
  47. output=("cc_counts_A1.txt" \
  48. "cc_counts_A2.txt" \
  49. "cc_counts_A3.txt" \
  50. "cc_counts_A4.txt" \
  51. "cc_counts_A5.txt" \
  52. "cc_counts_A6.txt" \
  53. "cc_counts_N14.txt" \
  54. "cc_counts_N15.txt" \
  55. "cc_counts_N16.txt" \
  56. "cc_counts_N17.txt" \
  57. "cc_counts_N18.txt" \
  58. "cc_counts_N21.txt" \
  59. "cc_counts_R10.txt" \
  60. "cc_counts_R11.txt" \
  61. "cc_counts_R12.txt" \
  62. "cc_counts_R13.txt" \
  63. "cc_counts_R8.txt" \
  64. "cc_counts_R9.txt" )
  67. featureCounts \
  68. -T 4 -O -C -p --countReadPairs -s 2 -t exon -g transcript_id \
  69. -a /cluster/projects/nn8014k/magdalena/LncRNA/3_stringtie/3_1_create_transcriptome_all/cc_transcriptome_all.gtf \
  70. -o /cluster/work/users/magdalena/lncrna/7_featurecounts/${output[$SLURM_ARRAY_TASK_ID]}\
  71. /cluster/work/users/magdalena/lncrna/2_hisat_alignment/${input[$SLURM_ARRAY_TASK_ID]}
  75. # T: threads
  76. # O: creates a summary statsitsics file
  77. # C: Exclude chimeric fragments from fragment counting. (should be excluded)
  78. # p: It allows reads to be assigned to multiple features if they have the same best alignment score.
  79. # s: Specifies the strandedness of the reads - 2 = assumes hat the reads are from the second strand (reverse strand).
  80. # t: Specifies the feature type to be counted
  81. # g: Specifies the attribute used to group reads. In this case, counts will be associated with unique gene IDs.
  83. # settings were talked about with Sjannie

7_1_featurecount_lncrna_all.sh at commit e2dc79f, no license · at the source

Overview

Authors: Magdalena Winklhofer1,2, Göran Erik Nilsson1, Sjannie Lefevre1
ORCID iDs: Magdalena Winklhofer, Göran Erik Nilsson, Sjannie Lefevre
  1. Section for Physiology and Cell Biology, Department of Biosciences, University of Oslo, Oslo, Norway
  2. Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
Institutions: University of Oslo (Norway)
Journal: RNA biology, volume 23, issue 1, pages 1-21
Dates: accepted 5 March 2026; published online 10 March 2026; in print December 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1080/15476286.2026.2643366 · PMID 41804966 · PMCID PMC13023002 · OpenAlex W7134832456
Open access: gold, a free copy (OpenAlex)
Status: code verified (how the code is found and verified)
Categories: genetics / omics (modality), cellular / molecular (subfield)
Methods: Statistics, Smoothing, state filtering, decompositions, Machine learning, Preprocessing, Connectivity
Keywords: Gene expression, next-generation RNA sequencing, fish, hypoxia, comparative animal physiology, mRNA abundance
MeSH: Brain*, Carps*, Gene Expression Regulation*, Hypoxia*, Oxygen*, RNA, Long Noncoding*, Animals, Gene Expression Profiling, Molecular Sequence Annotation, RNA, Messenger, Transcriptome (* major topic)
Topic: Physiological and biochemical adaptations (Ecology, Environmental Science), according to OpenAlex
Funding: Research Council of Norway FRIPRO (261864, 324260); University of Oslo; Research Council of Norway FRIMEDBIO (231260)
Citations: cited by 1 paper (Europe PMC); 53 references in the paper

Abstract

Long non-coding RNAs (lncRNAs) regulate diverse cellular processes, yet their role in anoxia-induced transcriptomic changes in crucian carp (Carassius carassius) – a species that endures months without oxygen at low temperatures – remains unclear. Because existing genome annotations focus on protein-coding genes, we aimed to annotate lncRNAs in crucian carp, assess their potential for involvement in mRNA regulation during anoxia and reoxygenation, and characterize differentially regulated lncRNAs and nearby putative interaction partners (IPs). Using next-generation RNA sequencing of the brain across normoxia, anoxia, and reoxygenation (n = 10 per group), we assembled 145,264 transcripts with a reference-guided approach. With CPC2, CNCI, CPAT, and FEELnc, we identified 6072 lncRNAs. Anoxia elicited a robust transcriptomic response: 56,440 transcripts were differentially expressed (adjusted p-value < 0.05; |log2(fold change)| > 0.38), including 1321 lncRNAs. FEELnc classification highlighted proximal RNA transcripts suggestive of cis-acting lncRNA functions. Most (60%) DElncRNA – IP interaction sites were intergenic, predominantly on the same strand within intergenic subtypes, with many features nested within genic contexts. Notably, log2-fold changes in RNA abundance of predicted DE IPs positively correlated with those of their corresponding DElncRNAs. These results provide a comprehensive lncRNA annotation for crucian carp and reveal extensive lncRNA co-expression with nearby genes during anoxia and reoxygenation, supporting a potential cis-regulatory role in the adaptive transcriptomic response to oxygen deprivation.

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

Repository

Its files are read in the Code ↔ Paper reader above, with 11 matches between paragraphs and lines of code.

MagdalenaWinklhofer/LncRNA

License: none: the authors keep all their rights
State: the link answers, verified on 30 September 2026
Evidence: files inventoried
Commit: e2dc79fadcb408db3525b0a153de6e1abfd9237c, 5 March 2025
Languages: Shell (23), Jupyter (20)
Size: 54 files, 43 scripts
Software Heritage: not archived
Found in: “Data availability statement”
Holds: README, 20 notebooks
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: pandas (20 files), NumPy (13 files), Matplotlib (12 files), seaborn (11 files), SciPy (3 files), Subread (featureCounts) (3 files), BCFtools (2 files), Biopython (2 files), SAMtools (2 files), scikit-learn (2 files), FastQC (1 file), statsmodels (1 file)
Availability: 1 check, the latest on 30 September 2026: the link answers
  • 30 September 2026: the link answers
44 files
At the source: github.com/MagdalenaWinklhofer/LncRNA.git

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

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;
  • 43 scripts, each with its path and the digest of its content;
  • 11 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

All raw RNA sequencing data from batch 1 dataset are deposited in the NCBI Sequence Read Archive (SRA) under BioProject Accession PRJNA386629 (https://www.ncbi.nlm.nih.gov/sra/SRP107188). The batch 2 dataset is deposited in the NCBI SRA under BioProject Accession PRJNA1163668 (https://www.ncbi.nlm.nih.gov/sra/SRP533984). The genome sequence and annotation data were obtained from DataverseNO (https://doi.org/10.18710/GXMSUH). Supplementary Material for the present study has been deposited in DataverseNO (https://doi.org/10.18710/1EIOVF), and scripts are available in the GitHub repository LncRNA (https://github.com/MagdalenaWinklhofer/LncRNA.git). Any further underlying data will be made available upon reasonable request.

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, 30 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 3 authors, 6 keywords, 11 MeSH terms, 3 funders, 50 references.

Cite

This paper

Winklhofer, M., Nilsson, G. E., & Lefevre, S. (2026). Long non-coding RNA transcripts in crucian carp brain - annotation and expression patterns in anoxia and reoxygenation. RNA biology, 23(1), 1-21. https://doi.org/10.1080/15476286.2026.2643366

BibTeX

@article{winklhofer2026long,
author = {Winklhofer, Magdalena and Nilsson, Göran Erik and Lefevre, Sjannie},
title = {{Long non-coding RNA transcripts in crucian carp brain - annotation and expression patterns in anoxia and reoxygenation}},
journal = {RNA biology},
year = {2026},
month = mar,
volume = {23},
number = {1},
pages = {1--21},
publisher = {Taylor \& Francis},
issn = {1547-6286},
doi = {10.1080/15476286.2026.2643366},
url = {https://doi.org/10.1080/15476286.2026.2643366},
pmid = {41804966},
pmcid = {PMC13023002}
}

RIS

TY - JOUR
AU - Winklhofer, Magdalena
AU - Nilsson, Göran Erik
AU - Lefevre, Sjannie
TI - Long non-coding RNA transcripts in crucian carp brain - annotation and expression patterns in anoxia and reoxygenation
T2 - RNA biology
J2 - RNA Biol
PY - 2026
DA - 2026/03/25
VL - 23
IS - 1
SP - 1
EP - 21
SN - 1547-6286
PB - Taylor & Francis
DO - 10.1080/15476286.2026.2643366
UR - https://doi.org/10.1080/15476286.2026.2643366
LA - en
ER -

CSL-JSON

{
"id": "10.1080/15476286.2026.2643366",
"type": "article-journal",
"title": "Long non-coding RNA transcripts in crucian carp brain - annotation and expression patterns in anoxia and reoxygenation",
"container-title": "RNA biology",
"author": [
{
"family": "Winklhofer",
"given": "Magdalena"
},
{
"family": "Nilsson",
"given": "Göran Erik"
},
{
"family": "Lefevre",
"given": "Sjannie"
}
],
"container-title-short": "RNA Biol",
"volume": "23",
"issue": "1",
"page": "1-21",
"DOI": "10.1080/15476286.2026.2643366",
"PMID": "41804966",
"PMCID": "PMC13023002",
"ISSN": "1547-6286",
"publisher": "Taylor & Francis",
"URL": "https://doi.org/10.1080/15476286.2026.2643366",
"language": "en",
"issued": {
"date-parts": [
[
2026,
3,
25
]
]
}
}

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

Similar papers

The papers with a page that share the most with this one: the tools found in their code, their categories, datasets, cited references and authors, the rarest counting most.

[1] doi:10.1038/s41597-024-03380-3 [code]
Long non-coding RNAs expression and regulation across different brain regions in primates.
Journal: Scientific data
In common: Biopython, SAMtools, seaborn, 3 other tools, genetics / omics, 7 references
[2] doi:10.1093/bioinformatics/btag592 [code]
Network-based stratification of allele-specific expression reveals patient subgroups in Huntington's disease.
Journal: Bioinformatics (Oxford, England)
In common: FastQC, Subread (featureCounts), BCFtools, 7 other tools, genetics / omics, 1 reference
[3] doi:10.1038/s42003-026-10957-8 [code]
Brain defence by the extracellular matrix protein Cochlin.
Journal: Communications biology
In common: Subread (featureCounts), BCFtools, Biopython, 8 other tools, cellular / molecular
[4] doi:10.1038/s41422-022-00719-6 [code]
Single-cell epigenome analysis reveals age-associated decay of heterochromatin domains in excitatory neurons in the mouse brain.
Journal: Cell research
In common: FastQC, Subread (featureCounts), Biopython, 6 other tools, genetics / omics, cellular / molecular, 1 reference
[5] doi:10.1016/j.xgen.2022.100177 [code]
Dual genome-wide coding and lncRNA screens in neural induction of induced pluripotent stem cells.
Journal: Cell genomics
In common: FastQC, Subread (featureCounts), Biopython, 6 other tools, genetics / omics, cellular / molecular
[6] doi:10.21203/rs.3.rs-9927928/v1 [code]
Genome-wide and allele-resolved maps of the radial architecture of the mouse genome
Journal: Research Square (preprint)
In common: FastQC, Subread (featureCounts), BCFtools, 5 other tools, genetics / omics, 1 reference
[7] doi:10.1038/s41467-026-71432-w [code]
MeCP2 gene dosage-dependent neurodevelopmentally restricted defects arise by aberrant activation of cell fate-determining bivalent genes.
Journal: Nature communications
In common: FastQC, Subread (featureCounts), SAMtools, 7 other tools, cellular / molecular
[8] doi:10.1038/s41467-025-59115-4 [code]
Large-scale transcriptomic analyses of major depressive disorder reveal convergent dysregulation of synaptic pathways in excitatory neurons.
Journal: Nature communications
In common: FastQC, Subread (featureCounts), BCFtools, 5 other tools, genetics / omics, cellular / molecular
[9] doi:10.1038/s41467-025-57286-8 [code]
Cryptic mitochondrial DNA mutations coincide with mid-late life and are pathophysiologically informative in single cells across tissues and species.
Journal: Nature communications
In common: Subread (featureCounts), BCFtools, SAMtools, 6 other tools, cellular / molecular, 1 reference
[10] doi:10.1126/sciadv.ady5085 [code]
Decoder-FFPE-seq enables sensitive, genome-wide spatial transcriptomics of archival tissues at single-cell resolution.
Journal: Science advances
In common: BCFtools, Biopython, SAMtools, 5 other tools, genetics / omics, cellular / molecular, 1 reference

Contribute

The authors of this paper can claim it, correct its record and validate its tracing map, and the maintainers of its code (its owner, or a public member of its organization) correct what it says of their repository; anyone signed in can ask for its removal. Every request goes to OSCR's own machine, which answers it; your account page follows them.

Sign in with ORCID to claim this paper as one of its authors, correct its record or validate its tracing map: when the paper's metadata lists your ORCID iD, you are recognized at once. Maintainers of its code: sign in with GitHub, then claim the repository on your account page.

Add the badge to the code's README

OSCR: the badge of this paper

If you are an author or a maintainer of this paper's code, you can add this badge. It says what OSCR knows of the paper (its code, its validated tracing map) and links the code to this page. Paste one of these snippets under the README's title. Keep the two marks around it, so that the badge can be replaced in place and is never added twice. OSCR changes nothing in your repository.

Markdown
<!-- oscr-badge:start -->
[![OSCR](https://openscicode.org/badge/doi/10.1080/15476286.2026.2643366.svg)](https://openscicode.org/badge/doi/10.1080/15476286.2026.2643366)
<!-- oscr-badge:end -->
reStructuredText
.. oscr-badge:start

.. image:: https://openscicode.org/badge/doi/10.1080/15476286.2026.2643366.svg
   :target: https://openscicode.org/badge/doi/10.1080/15476286.2026.2643366
   :alt: OSCR

.. oscr-badge:end
HTML
<!-- oscr-badge:start -->
<a href="https://openscicode.org/badge/doi/10.1080/15476286.2026.2643366"><img src="https://openscicode.org/badge/doi/10.1080/15476286.2026.2643366.svg" alt="OSCR"></a>
<!-- oscr-badge:end -->

On GitHub, open the README, choose Edit (the pencil), paste the snippet under the title, then "Commit changes".

If you choose to, you can have the badge kept up to date for you, with oscr badge --write from the command line or with the GitHub Action in your repository's workflows. Every other form and option (a card, AsciiDoc, LaTeX, shields.io) is on the badge page.

Request its removal

To ask OSCR to remove this record, the copies of its authors' scripts or its tracing map, use the removal request page: signed in, you say who you are, what to remove and why, then review and confirm the request. Published rules decide every request (how).

Discussion, reproductions, activity

Discussion: code errors and mismatches between the code and the paper about this paper and its code, from readers and its authors, beside the paper and its tracing map.

Report a mismatch between the code and the paper · Report a code error (signed in)

Reproductions: reports from readers who ran the authors' code and did not get the paper's result, what they ran, with which environment, commit and data.

Report a reproduction failure (signed in)

Versions of its code: the releases of its code tied to a version of this paper (the preprint, the accepted manuscript, the version of record…), each with the tracing map versioned with it.

Activity: what happens around this paper: new versions of its record, its map's validation, discussions and reproductions. It opens with sign-in.