NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE236409 Query DataSets for GSE236409
Status Public on Jul 01, 2024
Title Identification and characterization of long non-coding RNAs in intestinal immune regulation of largemouth bass, Micropterus salmoides, under acute heat stress
Organism Micropterus salmoides
Experiment type Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary Long noncoding RNAs (lncRNAs) are non-protein coding RNAs with a length of more than 200 bp, which play a vital regulatory role in intestinal immunity. Exposure to high temperature leads to death in many fish species, which is implicated in fish enteritis. Our study showed that fish enteritis was induced by acute heat stress. To date, which lncRNAs are participated in this process is still unclear. In the present study, based on the intestinal sequencing data of largemouth bass Micropterus salmoides, a total of 347,351,492 clean reads were generated from six cDNA libraries. Among them, 3399 novel lncRNA transcripts from 2488 lncRNA genes were identified. As expected, these lncRNAs exhibited shorter transcript lengths than protein-coding genes similar to those lncRNAs reported from other fish species. In total, 216 novel lncRNAs were differentially expressed (DE) in largemouth bass intestine (absolute log2 fold change > 2 and p-value < 0.05) and that 210 neighboring genes were cis-regulated by these DE-lncRNAs. An analysis of GO/KEGG enrichment showed that most of these cis-genes seemed to be significantly enriched in immune regulation (p < 0.05) and lncRNA MSTRG.8573 had an important role in regulating jak-stat signaling pathway during this process. Through this study, we showed a catalog of novel DE-lncRNAs involved in the occurrence of enteritis in largemouth bass under acute heat stress, which could provide some useful references by regulating lncRNAs to solve the heat stress-induced fish enteritis for further studies.
 
Overall design 120 healthy fish were randomly divided into two groups, and respectively maintained at two temperatures, 26℃ and 34℃, with three parallels in each group. After 9h (determined by our pre-experiment), 9 fish samples were taken from the 26℃ group (control group) and 34°C group (9h_HS group) with 3 fish per parallel, respectively. As soon as the intestine samples were collected, they were quickly frozen in liquid nitrogen, and then preserved at -80℃ for RNA extraction.
 
Contributor(s) Yan D, Gan L
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Jul 03, 2023
Last update date Jul 01, 2024
Contact name Lei Gan
E-mail(s) lgan3@gzu.edu.cn
Phone 15026676513
Organization name Guizhou university
Department college of animal science
Street address Guizhou University, Guiyang, Guizhou, People’s Republic of China
City Guiyang
ZIP/Postal code 550025
Country China
 
Platforms (1)
GPL33547 Illumina HiSeq 4000 (Micropterus salmoides)
Samples (6)
GSM7532594 Control1
GSM7532595 Control2
GSM7532596 Control3
Relations
BioProject PRJNA990768

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
GSE236409_gene_expression.addAnno.txt.gz 2.8 Mb (ftp)(http) TXT
GSE236409_lncRNA_expression.addAnno.txt.gz 115.1 Kb (ftp)(http) TXT
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