CGIG_VIBRIO24H_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 24 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 24 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): 3,296 of 20,792 tested genes reach FDR < 0.05 (1,816 higher, 1,480 lower at 24 h); PC1 explains 51.0% of variance. The response broadens beyond the 12 h antibacterial programme (25 heat shock protein genes significant, superoxide dismutase [Cu-Zn] lower), and agreement with the PRJNA515169 Vibrio records is weaker (about 95% of shared significant genes in the same direction; log2FC r = 0.14-0.18), consistent with a later systemic stage.

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, Vh_), 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.

Sources