Bioproject ID: PRJNA508561

bioproject id PRJNA508561      to NCBI
key word Vaccine; Grass carps; Intestinal mucosal immunity; Intestinal tissue; Transcriptome; Proteome; EXPRESSION ANALYSIS; COMPLEMENT-SYSTEM; MOLECULAR-CLONING; MANNOSE-RECEPTOR; CATHEPSIN-S; CLASS-I; CATFISH; ANTIGEN; GENE; IDENTIFICATION
experiment type vaccine
publication Li J et al., "Integrated transcriptomic and proteomic analyses of grass carp intestines after vaccination with a double-targeted DNA vaccine of Vibrio mimicus", Fish and shell fish immunology, 2020; 98: 641-652.
description Understanding the Immune Mechanisms of Vibrio mimicus targeted epitopes gene vaccine by RNA-seq Technology
abstract Intestinal mucosal immunity plays a vital role against Vibrio mimicus infection because it is an enteric pathogen causing serious vibriosis in fish. In the previous studies, we developed an oral double-targeted DNA vaccine of V. mimicus and demonstrated that the vaccine could elicit significantly higher intestinal mucosal immune response than did naked DNA vaccine. But, little is known underlying regulatory molecular mechanisms of the enhanced intestinal mucosal immunity. Here the transcriptome and proteome in the intestines of the grass carps immunized or not with the double-targeted DNA vaccine were investigated by using RNA-seq and iTRAQ-coupled LC-MS/MS. Compared with the control group, a total of 5339 differentially expressed genes (DEGs) and 1173 differentially expressed proteins (DEPs) were identified in the immunized fish intestines. Subsequently, the integrated analysis between transcriptome and proteome data revealed that 250 DEPs were matched with the corresponding DEGs (named associated DEPs/DEGs) at both transcriptome and proteome levels. Fifty of all the associated DEPs/DEGs were immune-related and mainly enriched in phagosome, antigen-processing and presentation, complement and coagulation cascades, NLRs and MAPK signaling pathways via Gene Ontology and KEGG pathway analyses, which suggested the coordination of the five activated pathways was essential to the enhanced intestinal mucosal immune response in the immunized fish. The protein-protein interaction analysis showed that 60 of the 63 immune-related DEPs to form an integrated network. Additionally, randomly selected DEGs and DEPs were respectively validated by quantitative real-time RT-PCR and multiple reaction monitoring (MRM) assay, indicating that the both RNA-Seq and iTRAQ results in the study were reliable. Overall, our comprehensive transcriptome and proteome data provide some key genes and their protein products for further research on the regulatory molecular mechanisms underlying the enhanced intestinal mucosal immunity.

Sample Information

sample id sample name tissue strain treatment description
1. SRR8283944 Ib_2 intestin nan untreatment Control, replicate 2
2. SRR8283945 Ib_3 intestin nan untreatment Control, replicate 3
3. SRR8283946 Ia_3 intestin nan Immunized oral double-targeted DNA vaccine of V. mimicus Immunized group replicate 3
4. SRR8283947 Ib_1 intestin nan untreatment Control, replicate 1
5. SRR8283948 Ia_1 intestin nan Immunized oral double-targeted DNA vaccine of V. mimicus Immunized group replicate 1
6. SRR8283949 Ia_2 intestin nan Immunized oral double-targeted DNA vaccine of V. mimicus Immunized group replicate 2