NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE168454 Query DataSets for GSE168454
Status Public on Mar 08, 2021
Title De Novo Profiling of Long Non-Coding RNAs Involved in MC-LR-Induced Liver Injury in Whitefish: Discovery and Perspectives
Organism Coregonus lavaretus
Experiment type Expression profiling by high throughput sequencing
Summary Microcystin-LR (MC-LR) is a potent hepatotoxin for which a substantial gap in knowledge persists regarding the underlying molecular mechanisms of liver toxicity and injury. Although long non-coding RNAs (lncRNAs) have been extensively studied in model organisms, our knowledge concerning the role of lncRNAs in liver injury is limited. Given that lncRNAs show low levels of sequence conservation, their role becomes even more unclear in non-model organisms without an annotated genome, like whitefish (Coregonus lavaretus). The objective of this study was to discover and profile aberrantly expressed polyadenylated lncRNAs that are involved in MC-LR-induced liver injury in whitefish. Using RNA sequencing (RNA-Seq) data, we de novo assembled a high-quality whitefish liver transcriptome. This enabled us to find 94 differentially expressed (DE) putative evolutionary conserved lncRNAs, such as MALAT1, HOTTIP, HOTAIR or HULC, and 4429 DE putative novel whitefish lncRNAs, which differed from annotated protein-coding transcripts (PCTs) in terms of minimum free energy, guanine-cytosine (GC) base-pair content and length. Additionally, we identified DE non-coding transcripts that might be 3′ autonomous untranslated regions (3′UTRs) of mRNAs. We found both evolutionary conserved lncRNAs as well as novel whitefish lncRNAs that could serve as biomarkers of liver injury.
 
Overall design A total number of 52 individuals from the RNA-Seq of the whole project were used in order to assemble the reference transcriptome. However, 13 individuals from the project were used to assess MC-LR effects on expression of non-coding transcripts using RNA-Seq. RNA-Seq included four control samples (PBS_1d). Each treatment group (the dose of MC-LR 100 μg·kg−1 of body mass) included three individuals.
 
Contributor(s) Florczyk M, Brzuzan P, Woźny M
Citation(s) 33477898
BioProject PRJNA481245
Submission date Mar 08, 2021
Last update date Mar 08, 2021
Contact name Maciej Florczyk
E-mail(s) maciej.florczyk@uwm.edu.pl
Organization name University of Warmia and Mazury in Olsztyn
Street address Słoneczna 45G
City Olsztyn
ZIP/Postal code 10-709
Country Poland
 
Platforms (1)
GPL29821 Illumina HiSeq 4000 (Coregonus lavaretus)
Samples (13)
GSM5140639 RNA-Seq of Coregonus lavaretus after PBS injection – individual no. 52
GSM5140640 RNA-Seq of Coregonus lavaretus after PBS injection – individual no. 55
GSM5140641 RNA-Seq of Coregonus lavaretus after PBS injection – individual no. 58

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE168454_Cla_novel_lncRNAs.fasta.gz 646.5 Kb (ftp)(http) FASTA
GSE168454_deseq2_NOVEL_ncRNA_1d.csv.gz 76.9 Kb (ftp)(http) CSV
GSE168454_deseq2_NOVEL_ncRNA_6d.csv.gz 269.8 Kb (ftp)(http) CSV
GSE168454_deseq2_NOVEL_ncRNA_9d.csv.gz 178.5 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap