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

Version 2.0
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, V2
Learn about Data Citation Standards.
Contact Owner Share
Dataset Metrics
2 Downloads
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 Winklhofer, M., Nilsson, G. E. & Lefevre, S. (2025). Long Non-Coding RNA Transcripts in Crucian Carp Brain - Annotation and Expression Patterns in Anoxia and Reoxygenation. bioRxiv, 2025.2009.2007.674702doi: 10.1101/2025.09.07.674702
License/Data Use Agreement

CC0 1.0

Table
Tree
Filter by
1 to 10 of 53 Files
00_README.txt
Plain Text - 46.4 KB
Published Oct 6, 2025
0 Downloads
MD5: f14eab473533997f872c4c18ca0f7ea4
Preview "00_README.txt"
01_Stringtie_cc_transcriptome_merged_gtf.txt
Plain Text - 291.3 MB
Published Oct 6, 2025
1 Download
MD5: 7adf79af0dddd1480e0f6a763214cd55
Preview "01_Stringtie_cc_transcriptome_merged_gtf.txt"
02_gffread_cc_transcripts_all_fa.txt
Plain Text - 649.7 MB
Published Oct 6, 2025
1 Download
MD5: e4cbc6a918f3b9131d494023dba80560
Preview "02_gffread_cc_transcripts_all_fa.txt"
03_CPAT_output_lncRNA_sense_ORF1.ORF_prob_tsv.txt
Plain Text - 11.6 MB
Published Oct 6, 2025
0 Downloads
MD5: 3e88cc402bdce7c3f781d2f5c485ec93
Preview "03_CPAT_output_lncRNA_sense_ORF1.ORF_prob_tsv.txt"
04_CNCI_output_lncRNA_index.txt
Plain Text - 6.6 MB
Published Oct 6, 2025
0 Downloads
MD5: 7d700b3808b55f90813fcfbfb020c539
Preview "04_CNCI_output_lncRNA_index.txt"
05_CPC2_output_lncRNA_codpot.txt
Plain Text - 10.5 MB
Published Oct 6, 2025
0 Downloads
MD5: e6314095b9a51ccc887075d9ba954a50
Preview "05_CPC2_output_lncRNA_codpot.txt"
06_feelnc_candidate_lncRNA.gtf_RF.txt
Plain Text - 1.4 MB
Published Oct 6, 2025
0 Downloads
MD5: f163cef8840a101b161ad4279dd1fa1a
Preview "06_feelnc_candidate_lncRNA.gtf_RF.txt"
07_common_lncRNA_csv.txt
Plain Text - 82.2 KB
Published Oct 6, 2025
0 Downloads
MD5: 1e495f0d409aabec73445ee771176eec
Preview "07_common_lncRNA_csv.txt"
08_lncRNA_classes.txt
Plain Text - 3.1 MB
Published Oct 6, 2025
0 Downloads
MD5: bf4471b40d29c79f8251107c2a856d6f
Preview "08_lncRNA_classes.txt"
10_DEG_Normoxia to Anoxia_lncrna_csv.txt
Plain Text - 14.5 MB
Published Oct 6, 2025
0 Downloads
MD5: d8b7a7799750b5257c3af341ceff6742
Preview "10_DEG_Normoxia to Anoxia_lncrna_csv.txt"
Edit File

This file has already been deleted (or replaced) in the current version. It may not be edited.

Restrict Access

Restricting limits access to published files. People who want to use the restricted files can request access by default. If you disable request access, you must add information about access to the Terms of Access field.

Learn about restricting files and dataset access in the User Guide.

Enable access request
You must enable request access or add terms of access to restrict file access.
Save Changes
Edit Embargo

The selected file or files have already been published. Contact an administrator to change the embargo date or reason of the file or files.
Edit Retention Period

The selected file or files have already been published. Contact an administrator to change the retention period date or reason of the file or files.
Delete Files

The file will be deleted after you click on the Delete button.

Files will not be removed from previously published versions of the dataset.

Select File(s)

Please select one or more files.

Share Dataset

Share this dataset on your favorite social media networks.

Continue
Dataset Citations

Citations for this dataset are retrieved from Crossref via DataCite using Make Data Count standards. For more information about dataset metrics, please refer to the User Guide.

Sorry, no citations were found.
Inaccessible Files Selected

The selected file(s) may not be downloaded because you have not been granted access or the file(s) have a retention period that has expired or the files can only be transferred via Globus.

You may request access to any restricted file(s) by clicking the Request Access button.

Ineligible Files Selected

The selected file(s) may not be transferred because you have not been granted access or the file(s) have a retention period that has expired or the files are not Globus accessible.

You may request access to any restricted file(s) by clicking the Request Access button.

Download Options

The files selected are too large to download as a ZIP.

You can select individual files that are below the 4.7 GB download limit from the files table, or use the Data Access API for programmatic access to the files.

Select File(s)

Please select a file or files to be downloaded.

Inaccessible Files Selected

The selected file(s) may not be downloaded because you have not been granted access or the file(s) have a retention period that has expired.

Click Continue to download the files you have access to download.

Ineligible Files Selected

Some file(s) cannot be transferred. (They are restricted, embargoed, with an expired retention period, or not Globus accessible.)

Click Continue to transfer the elligible files.

Delete Dataset

Are you sure you want to delete this dataset and all of its files? You cannot undelete this dataset.

Delete Draft Version

Are you sure you want to delete this draft version? Files will be reverted to the most recently published version. You cannot undelete this draft.

Unpublished Dataset Preview URL

Preview URL can only be used with unpublished versions of datasets.

Unpublished Dataset Preview URL

Are you sure you want to disable the Preview URL? If you have shared the Preview URL with others they will no longer be able to use it to access your unpublished dataset.

Delete Files

The file(s) will be deleted after you click on the Delete button.

Files will not be removed from previously published versions of the dataset.

Compute

This dataset contains restricted files you may not compute on because you have not been granted access.

Deaccession Dataset

Are you sure you want to deaccession? This is permanent and the selected version(s) will no longer be viewable by the public.

Deaccession Dataset

Are you sure you want to deaccession this dataset? This is permanent an it will no longer be viewable by the public.

Version Differences Details

Please select two versions to view the differences.

Version Differences Details
 
Version:
Last Updated:
Version:
Last Updated:
Select File(s)

Please select a file or files for access request.

Select File(s)

Embargoed files cannot be accessed. Please select an unembargoed file or files for your access request.

Edit Tags

Select existing file tags or create new tags to describe your files. Each file can have more than one tag.

Request Access

  You need to Log In to request access.

Dataset Terms

Please confirm and/or complete the information needed below in order to request access to files in this dataset.

This dataset is made available under the following terms. Please confirm and/or complete the information needed below in order to continue.

Our Community Norms as well as good scientific practices expect that proper credit is given via citation. Please use the data citation shown on the dataset page.

CC0 1.0

Preview Guestbook

Upon downloading files the guestbook asks for the following information.

Account Information

Package File Download

Use the Download URL in a Wget command or a download manager to download this package file. Download via web browser is not recommended. User Guide - Downloading a Dataverse Package via URL

https://dataverse.no/api/access/datafile/

Compute Batch
Clear Batch
Dataset Persistent Identifier Change Compute Batch
Compute Batch
Submit for Review

You will not be able to make changes to this dataset while it is in review.

Publish Dataset

Are you sure you want to republish this dataset?

Select if this is a minor or major version update.

Publish Dataset

This dataset cannot be published until University of Oslo is published by its administrator.

Publish Dataset

This dataset cannot be published until University of Oslo and DataverseNO are published.

Return to Author

Return this dataset to contributor for modification.

Add/Edit a Version Note
Styled Citation