Table 1.

Gene of interest expression levels, fold change (FC) and associated P values measured in Haemonchus contortus recovered from vaccinated and control sheep.

	Gene ID	Mean Counta	logFCb DESeq2	adj. Pc DESeq2	logFCb voom	adj. Pc voom	Correlation with FEC29d	WormBase ParaSite Gene Description	Caenorhabditis elegans orthologue	Candidate Gene Name	GenBank Acc. Number
Top differentially expressed (DE)	HCOI00569100	24.21	−2.39	2.40E−13	−5.16	4.55E−03	0.63 (0.05)	Glycoside hydrolase domain containing protein [U6P060]	n/a	n/a	n/a
	HCOI01945600	2000.03	2.02	2.33E−16	2.39	9.83E−04	−0.64 (0.05)	Peptidase A1 domain containing protein [U6PP66]	pcl, Bace	n/a	n/a
	HCOI01623600	23.12	2.03	2.05E−09	4.21	6.77E−03	−0.79 (0.01)	n/a	n/a	n/a	n/a
	HCOI01283800	38840.11	2.15	3.58E−15	2.79	1.28E−03	−0.76 (0.01)	Peptidase C1A domain containing protein [U6P6R9]	CtsB1	n/a	n/a
	HCOI01549900	1104.78	2.20	6.42E−16	2.86	1.31E−03	−0.73 (0.02)	Protease inhibitor I4 domain containing protein [U6PNP0]	srp-1,2,3,6,7,8	n/a	n/a
	HCOI01736400	2678.92	2.49	4.60E−31	3.01	7.91E−05	−0.81 (0.004)	n/a	CtsB1	n/a	n/a
Vaccine Antigen	HCOI01993300	4049.71	0.30	3.09E−01	0.32	3.46E−01	n/a	Propeptide domain containing protein [U6PXI5]	n/a	pep-2	AJ577754.1
	HCOI01993500	13499.65	0.34	2.65E−01	0.35	3.06E−01	n/a	Propeptide and Peptidase A1 domain containing protein [U6PQD5]	n/a	pep-1	AF079402.1
	HCOI00348800	8859.39	0.47	1.56E−02	0.51	1.14E−01	n/a	Peptidase M13 domain containing protein [U6NMI3]	n/a	mep-2	AF080117.1
	HCOI01333400	9325.90	0.59	3.88E−02	0.62	1.64E−01	n/a	Peptidase M13 domain containing protein [U6PHP6]	nep-9, nep-20	mep-3	AF080172.1
	HCOI02032800	2207.13	0.71	1.25E−02	0.90	5.97E−02	n/a	Peptidase M1 domain containing protein [U6PYE0]	T07F10.1	h11	FJ481146.1
	HCOI00308300	18250.90	0.73	4.82E−04	0.78	5.85E−02	n/a	Peptidase M13 domain containing protein [U6NME0]		mep-1	AF102130.1
	HCOI00631000	5690.45	0.77	2.40E−04	0.81	5.97E−02	n/a			mep-4	AF132519.1
Housekeeping genes	HCOI00909100	5753.25	−0.41	5.29E−01	−0.60	3.93E−01	n/a	Nematode fatty acid retinoid binding domain containing protein [U6NYW0]	n/a	far	CDJ86885.1
	HCOI00117100	1379.12	0.08	9.64E−01	0.07	7.96E−01	n/a	Superoxide dismutase [Cu-Zn] [U6NGP5]	n/a	sod	CDJ80830.1
	HCOI01760600	24868.64	0.08	8.59E−01	0.08	7.92E−01	n/a	Glyceraldehyde-3-phosphate dehydrogenase (inferred by orthology to a human protein) [Source:UniProtKB;Acc:P04406]	n/a	gpd	CDJ92718.1
	HCOI01743600	194.02	0.13	9.13E−01	0.14	7.28E−01	n/a	RNA recognition motif domain containing protein [U6NLP1]	n/a	ncbp	CDJ82645.1
	HCOI01464300	974.31	0.32	3.24E−01	0.35	3.06E−01	n/a	DNA-directed RNA polymerase [U6PFA6]	n/a	ama	CDJ91461.1

^aMean count indicates the mean transcript count across the pools.

^blog-FC in expression as measured by DeSeq2 or voom accordingly.

^cP values adjusted for multiple testing.

^dCorrelation between transcript expression level and faecal egg count (FEC) at 29 day p.i.