CGIG_OSHV1_RNASEQ_PRJNA593309

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

48 h after the start of cohabitation with OsHV-1 muVar-injected donor oysters at 21 C

Control

Same 21 C tanks sampled at 0 h, when donors were added (uninfected baseline)

Biological replication

6 libraries, one whole 8-month-old oyster per tank: three at 0 h and three at 48 h, the same three 21 C tanks sampled at both times.

Phenotype interpretation

At 21 C survival 14 days after cohabitation was 52.4%, and OsHV-1 DNA had reached high levels in all three oysters sampled at 48 h. AREE records the whole-oyster transcriptional response to infection, not survival per library.

Analysis status

raw_reanalysis_harmonized

Quality control and results

All 12 downloaded libraries (96,206,490 read pairs) quantified with Salmon 2.3.4 against GCF_963853765.1/RS_2024_06; this record’s six map 49.2-56.0% (0 h 51.5-56.0%, 48 h 49.2-54.3%). Expressed-SNP allele frequencies at 801 sites show each of the six libraries is a different diploid oyster (34-44% heterozygous sites; all pairs differ by 0.28 or more against 0.03 for one RNA resequenced). ~ condition (3 v 3): 846 of 14,555 tested genes reach FDR < 0.05 (663 higher, 183 lower at 48 h); the tank-paired model ~ tank + condition gives 1,025. PC1 explains 44.6% of variance. The response is the expected antiviral programme: all 12 significant interferon-pathway genes rise, with interferon regulatory factor 2, an MDA5-like helicase, baculoviral IAP repeat proteins and E3 ubiquitin ligases. The publication reports 1,413 genes at 48 h against 0 h with edgeR on the Ensembl genome.

Limitations

  • The 0 h and 48 h oysters come from the same three tanks. The primary model is unpaired (~ condition); a tank-paired model (~ tank + condition) is kept as a sensitivity analysis.
  • One whole oyster per tank was sequenced at each time point, with three replicate tanks per temperature (45 l tanks), so libraries are tank-level replicates and the contrast has three tanks per arm.
  • The two AREE records from this study use different oysters but the same three 21 C tanks (the 21 C 12 h oysters of CGIG_HEAT_RNASEQ_PRJNA593309 and the 21 C 0 h and 48 h oysters of CGIG_OSHV1_RNASEQ_PRJNA593309), so both carry the dependence group PRJNA593309_21C_tanks and count as one replication group.
  • The BioSamples give a collection date of 2019-05-19, but the publication dates the experiment to May 2016; the experimental groups follow the sample aliases (Cg_<CTR | OsHV>hpc_), which agree with the publication’s design.
  • The study also deposited libraries at 26 C and at 24 and 96 h; the publication does not analyse the 26 C libraries, and AREE uses only the time points of its two contrasts.
  • The publication aligned reads with STAR to the Ensembl oyster genome v9.38 and tested with edgeR; AREE quantifies against GCF_963853765.1/RS_2024_06 with Salmon and DESeq2.

Sources