Table 1.

Libraries description and construction method.

	Library	Type	Origin	Status of infection	Presence of symbiont	Description	Number of individuals / bacteriomes sampled and pooled (quantity of RNA used from samples)
Host response to pathogen	SSH1	Subtraction	Whole larvae	infected	no	Salmonella+ vs. Salmonella-	Salmonella -: 10 uninfected aposymbiotic larvae (10µg)
	SSH2	Subtraction	Whole larvae	Not infected	no	Salmonella- vs. Salmonella+	Salmonella +: 15 infected aposymbiotic larvae: 5 collected 3h after infection (3.33µg), 5 after 6h (3.33µg) and 5 after 12h (3.33µg)
Host response to symbiont	SSHA	Subtraction	Bacteriome	Not infected	yes	With symbiont vs. without symbiont	With symbiont: 200 symbiotic bacteriomes (10 µg)
	SSHB	Subtraction	Bacteriome	Not infected	no	Without symbiont vs. with symbiont	Without symbiont: 640 aposymbiotic bacteriomes (10 µg)
	SO	Non-normalized	Bacteriome	Not infected	yes	Pool of bacteriomes with symbiont	170 symbiotic bacteriomes (10µg)
	AO	Non-normalized	Bacteriome	Not infected	no	Pool of bacteriomes without symbiont	578 aposymbiotic bacteriomes (10 µg)
	NOR	Normalized	Whole larvae	infected	yes	Pool of Symbiotic Larvae / Aposymbiotic larvae / Aposymbiotic larvae infected during 3h, 6h and 12h	10 uninfected aposymbiotic larvae (2µg) / 10 uninfected symbiotic larvae (2µg) / 15 infected aposymbiotic larvae: 5 collected after 3h of infection (2µg), 5 after 6h (2µg) and 5 after 12h (2µg)