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

DOI

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).

FASTQC, 0.11.8

TrimGalore, 0.3.3

HISAT2, 2.2.1

SAMtools, 1.17

StringTie, 2.2.1

GFFread, 0.9.0

CPC2, 1.0.1

Biopython, 1.81

CPAT, 3.0.4

CNCI, 2

FEELnc, 0.2.1

Subread, 2.0.3

DESeq2, 1.40

goseq, 1.52

Identifier
DOI https://doi.org/10.18710/1EIOVF
Related Identifier IsCitedBy https://doi.org/10.1101/2025.09.07.674702
Metadata Access https://dataverse.no/oai?verb=GetRecord&metadataPrefix=oai_datacite&identifier=doi:10.18710/1EIOVF
Provenance
Creator Winklhofer, Magdalena; Nilsson, Göran E.; Lefevre, Sjannie ORCID logo
Publisher DataverseNO
Contributor Lefevre, Sjannie; Winklhofer, Magdalena; University of Oslo
Publication Year 2025
Funding Reference Research Council of Norway 324260 ; Sigma2 NN8014K ; Sigma2 NS8014K
Rights CC0 1.0; info:eu-repo/semantics/openAccess; http://creativecommons.org/publicdomain/zero/1.0
OpenAccess true
Contact Lefevre, Sjannie (University of Oslo); Winklhofer, Magdalena (University of Oslo)
Representation
Resource Type transcript annotation; Dataset
Format text/plain
Size 32211; 268365784; 599771645; 6042169; 6861109; 12598647; 11332787; 480910; 430712; 123802; 82113; 71471; 34172; 1798198; 20122311; 29641388; 43888165; 43887089; 29641145; 29640380; 43885170; 43895846; 29643532; 29641609; 43888615; 43891117; 29642523; 43888435; 29641365; 29641971; 43888716; 43889148; 29641806; 43883482; 29640081; 43894768; 29643734; 43892185; 29642850; 29643673; 43895184; 29641711; 43889416; 29641786; 43889462; 29642244; 43890809; 43895007; 29643808; 43892497; 29642347
Version 1.0
Discipline Life Sciences; Medicine