Replication Data for: Long Non-Coding RNA Transcripts in Crucian Carp Brain – Annotation and Expression Patterns in Anoxia and Reoxygenation

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Winklhofer, Magdalena; Nilsson, Göran E.; Lefevre, Sjannie, 2025, "Replication Data for: Long Non-Coding RNA Transcripts in Crucian Carp Brain – Annotation and Expression Patterns in Anoxia and Reoxygenation", https://doi.org/10.18710/1EIOVF, DataverseNO, V1

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Description	The dataset contains the supplementary material that was created to identify and investigate long non-coding RNA (lncRNA) in the whole brain tissues of crucian carp (Carassius carassius), i.e. the annotation of lncRNAs with the four algorithms (FEELnc, CNCI, CPAT and CPC2), the result of differential expression analysis of the identified lncRNAs, and the characterization of predicted interaction partners and results from analysis of their differential gene expression. All raw RNA sequencing data are deposited in the NCBI Sequence Read Archive (SRA) under BioProject ID PRJNA386629 (http://www.ncbi.nlm.nih.gov/bioproject/386629). The genome sequence and annotation data were obtained from DataverseNO (https://doi.org/10.18710/GXMSUH). The scripts are available in the GitHub repository LncRNA (https://github.com/MagdalenaWinklhofer/LncRNA.git).
Subject	Medicine, Health and Life Sciences
Keyword	genome annotation, long non-coding RNA, anoxia, fish
Related Publication	Submitted
License/Data Use Agreement	CC0 1.0

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	00_README.txt Plain Text - 31.5 KB Published Sep 15, 2025 0 Downloads MD5: 528b91ae454cad711c46c969f1b60e26	Preview "00_README.txt" Access File File Access Public Download Options Plain Text Download Metadata Data File Citation EndNote XML RIS BibTeX
	01_Stringtie_cc_transcriptome_all_gtf.txt Plain Text - 255.9 MB Published Sep 15, 2025 0 Downloads MD5: 971dfc938a85433e5dd7ec116b1b6497	Preview "01_Stringtie_cc_transcriptome_all_gtf.txt" Access File File Access Public Download Options Plain Text Download Metadata Data File Citation EndNote XML RIS BibTeX
	02_gffread_cc_transcripts_all_fa.txt Plain Text - 572.0 MB Published Sep 15, 2025 0 Downloads MD5: acbb823cfa496c8923b1029760485ef4	Preview "02_gffread_cc_transcripts_all_fa.txt" Access File File Access Public Download Options Plain Text Download Metadata Data File Citation EndNote XML RIS BibTeX
	03_feelnc_candidate_lncRNA_all.gtf_RF.txt Plain Text - 5.8 MB Published Sep 15, 2025 0 Downloads MD5: 830e6643e84a347890ed6020d9e069b0	Preview "03_feelnc_candidate_lncRNA_all.gtf_RF.txt" Access File File Access Public Download Options Plain Text Download Metadata Data File Citation EndNote XML RIS BibTeX
	04_CNCI_output_lncRNA_index.txt Plain Text - 6.5 MB Published Sep 15, 2025 0 Downloads MD5: e679908c9166514e155b8e02a6d8d0c8	Preview "04_CNCI_output_lncRNA_index.txt" Access File File Access Public Download Options Plain Text Download Metadata Data File Citation EndNote XML RIS BibTeX
	05_CPAT_output_lncRNA_sense_ORF1.ORF_prob_tsv.txt Plain Text - 12.0 MB Published Sep 15, 2025 0 Downloads MD5: 3872b7c4a2568f5810925ba5997d0d02	Preview "05_CPAT_output_lncRNA_sense_ORF1.ORF_prob_tsv.txt" Access File File Access Public Download Options Plain Text Download Metadata Data File Citation EndNote XML RIS BibTeX
	06_CPC2_output_lncRNA_codpot_all.txt Plain Text - 10.8 MB Published Sep 15, 2025 0 Downloads MD5: bfc39262178f7d3a27e204c6b91c3824	Preview "06_CPC2_output_lncRNA_codpot_all.txt" Access File File Access Public Download Options Plain Text Download Metadata Data File Citation EndNote XML RIS BibTeX
	07_DEG_Normoxia to Anoxia_lncrna_csv.txt Plain Text - 469.6 KB Published Sep 15, 2025 0 Downloads MD5: 443dd561b30fcfe1d40dbe07620da517	Preview "07_DEG_Normoxia to Anoxia_lncrna_csv.txt" Access File File Access Public Download Options Plain Text Download Metadata Data File Citation EndNote XML RIS BibTeX
	08_DEG_Normoxia to Reoxygenation_lncrna_csv.txt Plain Text - 420.6 KB Published Sep 15, 2025 0 Downloads MD5: 1a560b3d5ed349ea220ce8ec73e8f7d1	Preview "08_DEG_Normoxia to Reoxygenation_lncrna_csv.txt" Access File File Access Public Download Options Plain Text Download Metadata Data File Citation EndNote XML RIS BibTeX
	09_DEG_Anoxia to Reoxygenation_lncrna_csv.txt Plain Text - 120.9 KB Published Sep 15, 2025 0 Downloads MD5: 7c45d1ceb063cfc15d2e4ab771a169bc	Preview "09_DEG_Anoxia to Reoxygenation_lncrna_csv.txt" Access File File Access Public Download Options Plain Text Download Metadata Data File Citation EndNote XML RIS BibTeX

Citation Metadata

Persistent Identifier	doi:10.18710/1EIOVF
Publication Date	2025-09-15
Title	Replication Data for: Long Non-Coding RNA Transcripts in Crucian Carp Brain – Annotation and Expression Patterns in Anoxia and Reoxygenation
Author	Winklhofer, Magdalena (University of Oslo) Nilsson, Göran E. (University of Oslo) Lefevre, Sjannie (University of Oslo) - ORCID: 0000-0003-0865-0561
Point of Contact	Use email button above to contact. Lefevre, Sjannie (University of Oslo) Winklhofer, Magdalena (University of Oslo)
Description	The dataset contains the supplementary material that was created to identify and investigate long non-coding RNA (lncRNA) in the whole brain tissues of crucian carp (Carassius carassius), i.e. the annotation of lncRNAs with the four algorithms (FEELnc, CNCI, CPAT and CPC2), the result of differential expression analysis of the identified lncRNAs, and the characterization of predicted interaction partners and results from analysis of their differential gene expression. All raw RNA sequencing data are deposited in the NCBI Sequence Read Archive (SRA) under BioProject ID PRJNA386629 (http://www.ncbi.nlm.nih.gov/bioproject/386629). The genome sequence and annotation data were obtained from DataverseNO (https://doi.org/10.18710/GXMSUH). The scripts are available in the GitHub repository LncRNA (https://github.com/MagdalenaWinklhofer/LncRNA.git).
Subject	Medicine, Health and Life Sciences
Keyword	genome annotation long non-coding RNA anoxia fish
Related Publication	Submitted Winklhofer, M., Nilsson, G. E. & Lefevre, S. (2015). Long Non-Coding RNA Transcripts in Crucian Carp Brain - Annotation and Expression Patterns in Anoxia and Reoxygenation. bioRxiv, 2025.2009.2007.674702 doi: 10.1101/2025.09.07.674702 https://doi.org/10.1101/2025.09.07.674702
Producer	University of Oslo (UiO) https://www.uio.no/english/
Funding Information	Research Council of Norway: 324260 Sigma2: NN8014K Sigma2: NS8014K
Distributor	University of Oslo (UiO) https://dataverse.no/dataverse/uio
Depositor	Nilsson, Sjannie Lefevre
Deposit Date	2025-03-10
Date of Collection	Start Date: 2023-01-01 ; End Date: 2025-03-01
Data Type	transcript annotation; transcript sequences
Software	FASTQC, Version: 0.11.8 TrimGalore, Version: 0.3.3 HISAT2, Version: 2.2.1 SAMtools, Version: 1.17 StringTie, Version: 2.2.1 GFFread, Version: 0.9.0 CPC2, Version: 1.0.1 Biopython, Version: 1.81 CPAT, Version: 3.0.4 CNCI, Version: 2 FEELnc, Version: 0.2.1 Subread, Version: 2.0.3 DESeq2, Version: 1.40 goseq, Version: 1.52
Related Material	https://github.com/MagdalenaWinklhofer/LncRNA.git
Related Dataset	https://doi.org/10.18710/GXMSUH; http://www.ncbi.nlm.nih.gov/bioproject/386629

Life Sciences Metadata

Organism	Other
Other Organism	Carassius carassius

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