Table 2.

Immune challenge transcriptome experiments

Experiment	Host Life Stage	Challenge Method	Host Stock	Challenge Type	Challenge Species	Sample Collection Post-Challenge	Citation
CVBAC-A	Veliger larvae	Laboratory	Mixed stock	Bacterial	Probionts Phaeobacter inhibens S4 and Bacillus pumilus RI06–95, or pathogenic Vibrio coralliilyticus RE22	6 h (RE22, RI, S4) or 24 h (S4, RI)	Modak et al., 2020 [52]
CVBAC-B	Veliger larvae	Hatchery	Mixed stock	Bacterial	Probionts Phaeobacter inhibens S4 and Bacillus pumilus RI06–95	5, 12, 16 d	Modak et al., 2020 [52]
CVBAC-C Res., CVBAC-C Sus.	Juvenile	Laboratory	Comparison of susceptible and resistant families	Bacterial	Aliiroseovarius crassostreae	1,5,15, 30 d	McDowell et al., 2014 [38]
CVPMA Tol., CVPMA Sus.	Adult	Laboratory	Comparison of susceptible and tolerant families	Parasitic	Perkinsus marinus	36 h, 7 d, 28 d	Proestou and Sullivan, 2020 [53]
CGBAC-A	Adult	Laboratory	Mixed stock	Bacterial	V. anguillarum, V. tubiashii, V. aestuarianus, V. alginolyticus-1, V. alginolyticus-2, Micrococcus luteus, LPS	12 h	Zhang et al. 2015 [3]
CGBAC-B	Juvenile	Laboratory	Mixed stock	Bacterial	Pathogenic and non-pathogenic V. tasmaniensis (LGP32) and V. crassostreae (J2–9)	8 h	Rubio et al. 2019 [54]
CGOSHV1-A Res., CGOSHV1-A Sus.	Juvenile	Field	Comparison of susceptible and resistant families	Viral	OsHV-1	0, 6, 12, 24, 48, 60, 72 h	de Lorgeril et al., 2018 [55]
CGOSHV1-B	Juvenile	Laboratory	Susceptible stock	Viral	OsHV-1	0, 6, 12, 24, 48, 120 h	He et al., 2015 [15]

Oyster transcriptome datasets were selected from publicly available data (NCBI SRA) from bacterial, parasitic, and viral challenges from a range of life stages (larval, juvenile, adult) and challenge methods (experimental and natural). Experiments were coded by their species (CV = C. virginica, CG = C. gigas), experimental challenge (BAC = bacterial, PMA = Perkinsus marinus, OSHV-1 = OsHV-1) and a letter code when there were multiple experiments of that type (A, B, C)