CGIG_VTASMANIENSIS_RNASEQ_PRJNA515169

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

Injected into the adductor muscle with 7.5 x 10^7 CFU of the virulent Vibrio tasmaniensis LGP32 and sampled 8 h later

Control

Mock-injected with sterile seawater and sampled 8 h later (sample alias ‘anesthesis’)

Biological replication

6 libraries, each a pool of 30 spat: one mock and one V. tasmaniensis LGP32 pool from each of three independent infection experiments. Pools of 30 animals average out individual variation, so replication is at the level of experiments.

Phenotype interpretation

Virulent V. tasmaniensis LGP32 killed about 60% of oysters within 3 days, through phagocytosis-dependent hemocyte lysis requiring intracellular T6SS effectors. AREE records the 8 h whole-spat transcriptional response to infection, not survival per library.

Analysis status

raw_reanalysis_harmonized

Quality control and results

All 9 pooled libraries (223,876,435 read pairs) quantified with Salmon 2.3.4 against GCF_963853765.1/RS_2024_06; four runs from ENA FASTQs that match the manifest MD5s and five from NCBI .sra archives that match NCBI’s MD5s, converted with read counts checked against SRA. Mapping rates are 71.4-74.7% and flat across arms. Expressed-SNP allele frequencies at 2,126 sites show the pools are independent samples of one population: every pair differs by 0.074-0.100 against 0.056 for one RNA resequenced, with no closer similarity within an experiment (0.086 within, 0.085 between), so the experiment block absorbs non-genetic batch effects. ~ experiment + condition (3 v 3): 489 of 23,984 tested genes reach FDR < 0.05 (397 higher, 92 lower with LGP32); PC1 explains 61.7% of variance. The two virulent strains elicit a shared response: all 416 genes significant for both change in the same direction and log2 fold changes correlate 0.76. The top genes form an antibacterial inflammatory programme (interleukin 17-like, TNF receptor superfamily member 11A, Toll-like receptors, prostaglandin E2 receptor EP4, serum amyloid A, baculoviral IAP repeat proteins, coadhesin) with no interferon-pathway response, in line with the publication’s finding that all strains are recognized by the immune system; it reports 331 genes against mock across the four strains.

Limitations

  • The two AREE records from this study (the other is CGIG_VCRASSOSTREAE_RNASEQ_PRJNA515169, V. crassostreae J2-9) test against the same three mock-injected pools, so they carry the dependence group PRJNA515169_mock_pools and count as one replication group.
  • Replicate numbers in the sample aliases are taken to identify the independent infection experiment, as the publication describes one pool per condition per experiment; the model blocks on experiment (~ experiment + condition).
  • The mock control is an injection of sterile seawater, so the contrast isolates the response to the bacteria, not to injection; the study’s untreated oysters and its nonvirulent strains (V. tasmaniensis LMG20012T, V. crassostreae J2-8) are not used.
  • The publication reports 331 oyster genes modulated by Vibrio relative to mock across strains, analysed in the IHPE Galaxy pipeline; AREE quantifies against GCF_963853765.1/RS_2024_06 with Salmon and DESeq2.
  • ENA served the FASTQs at 0.05-0.35 MB/s in October 2026, so the five runs that had not arrived intact (SRR8551080, SRR8551081, SRR8551083, SRR8551087, SRR8551091: one mock, one J2-9 and all three LGP32 pools) were taken from NCBI .sra archives instead (CGIG_VIBRIO_RNASEQ_PRJNA515169_sra_locations.tsv). Each library comes from a single source.

Sources