paper01_emu-wing
Science Score: 57.0%
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✓CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
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✓DOI references
Found 4 DOI reference(s) in README -
○Academic publication links
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (4.0%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: Satovase
- Language: R
- Default Branch: main
- Size: 51.8 KB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 5
Metadata Files
README.md
paper01_emu-wing
This repository contains R codes used to perform analysis in Tsuboi, E., Ono, S.F., Cordeiro, I.R. et al. Immobilization secondary to cell death of muscle precursors with a dual transcriptional signature contributes to the emu wing skeletal pattern. Nat Commun 15, 8153 (2024). https://doi.org/10.1038/s41467-024-52203-x
Raw single-cell transcriptome sequencing data (FASTQ) of emu is available in the DNA Data Bank of Japan (Accession numbers: DRA014432 and DRA017391; Bioproject: PRJDB16987 and PRJDB13845).
Raw single-cell transcriptome sequencing data (FASTQ) of stage 24 (SRA accession numbers: SRR14570167 to SRR14570174) and stage 27 (SRA accession numbers: SRR14570175 to SRR14570178) were downloaded from the Sequence Read Archive (SRA). These data were previously published in Feregrino C, Tschopp P. Assessing evolutionary and developmental transcriptome dynamics in homologous cell types. Dev Dyn. 2022 Sep;251(9):1472-1489. https://doi.org/10.1002/dvdy.384
Preprocessing using cellranger
Emumakecellranger_count
Chickenmakecellranger_count
Creating figures using Seurat
Emu_stage20-21.R: Figure 3a, 3b, S9, S10, Supplymentary table 1
Emu_stage25.R: Figure 3d, 3e, 3g, 5a, S11, S12, Supplymentary table 2, Supplymentary table 3
Chicken_stage24.R: Figure S13a, S13b, S13d, Supplymentary table 4
Chicken_stage27.R: Figure S13e, S13f, S13h, Supplymentary table 5
License
This project is covered under the Apache 2.0 License.
Owner
- Login: Satovase
- Kind: user
- Repositories: 1
- Profile: https://github.com/Satovase
Citation (CITATION.cff)
cff-version: 1.1.0
message: "If you use this software, please cite it as below."
authors:
- family-names: Ono
given-names: Satomi
orcid: https://orcid.org/0009-0003-4386-3447
title: Immobilization secondary to cell death of muscle precursors with a dual transcriptional signature contributes to the emu wing skeletal pattern
version: 7
date-released: 2024-09-17