CGIG_VIBRIO12H_RNASEQ_PRJNA852380
Primary-analysis sample count: 6. The counted unit and independent experimental units are described under Biological replication; counts may represent animals, pools or libraries.
Treatment
Exposed to Vibrio and sampled 12 h later (species, dose and route not stated in the metadata)
Control
Unexposed control oysters
Biological replication
6 digestive-gland libraries: 3 controls and 3 at 12 h after Vibrio exposure. Each library is a pool by expressed-SNP genotype; pool size is not recorded.
Phenotype interpretation
No phenotype is deposited; AREE records the digestive-gland transcriptional response to Vibrio exposure.
Analysis status
raw_reanalysis_harmonized
Quality control and results
All 18 digestive-gland libraries (426,745,884 read pairs) quantified with Salmon 2.3.4 against GCF_963853765.1/RS_2024_06 from NCBI .sra archives that match NCBI’s MD5s; mapping 74.8-77.4% and flat across groups. Expressed-SNP allele frequencies at 2,640 sites show all libraries are independent pools from one population: pools differ as much within a group as between groups (0.189 against 0.190, 0.046 for one RNA resequenced), so time is not confounded with genetic background. The response builds over time (85, 138, 236, 1,233 and 3,296 genes at FDR < 0.05 at 1, 3, 6, 12 and 24 h); the 1-6 h contrasts are not harmonized, to avoid several correlated records on one control set. ~ condition (3 v 3): 1,233 of 20,757 tested genes reach FDR < 0.05 (859 higher, 374 lower at 12 h); PC1 explains 41.4% of variance. The top genes form an antibacterial programme (TNF receptor, MyD88, prostaglandin E2 receptor EP4, Toll-like receptors) that replicates the independent PRJNA515169 Vibrio records: 225 genes are significant in both this record and the V. crassostreae J2-9 record, 223 of them in the same direction (207 of 208 for V. tasmaniensis LGP32), with log2 fold changes correlated 0.33-0.35 across about 15,000 genes.
Limitations
- No publication is linked. The Vibrio species, dose and exposure route are not recorded; the submitting group’s 2022 study (Liu et al., Fish Shellfish Immunol 131:1027-1039) used Vibrio mediterranei, and a 2025 study describes digestive-gland data after V. parahaemolyticus at 12 and 24 h, but neither is confirmed to be this dataset.
- The two AREE records from this study (12 h and 24 h) test against the same three control libraries, so they carry the dependence group PRJNA852380_controls and count as one replication group.
- Groups come from the SRA sample names (control1-3, V
h_ ), which agree with the BioSample replicate attributes. - All runs come from NCBI .sra archives checked against NCBI’s MD5s, with read counts checked against the NCBI spot counts on conversion.