Table 3. Most highly expressed genes in MGT, SC, LCMEC, MFG and mMEC transcriptome in Jersey and Normande cows expressed in RPKM values (reads per kilo base per million mapped reads). Green color represents the most highly expressed genes, red color represents the lowest expressed genes and the different color tones are intermediate values.

	MGT		SC	LCMEC		MFG		mMEC
Gene	Jersey	Normande	Jersey	Jersey	Normande	Jersey	Normande	Jersey	Normande
CSN2	207305	145263	156130	105065	179820	76891	45571	13651	2591
CSN3	72233	87335	30208	51838	84031	15602	18689	1877	1991
CSN1S1	39736	45340	24903	25982	50297	11528	7652	956	710
CSN1S2	12056	32973	4010	9093	29740	2156	4592	206	551
LALBA	5619	6537	3056	2706	11139	2693	1719	43	42
GLYCAM1	4035	8346	3579	2668	10633	1758	2995	119	90
BLG	3231	2407	6835	2697	5925	3854	707	121	84
SPP1	1406	1036	6975	845	1301	927	6250	10680	992
RPS17	1374	366	3164	120	90	2183	916	118	69
TCTP	937	1098	2724	974	917	2451	2656	1320	42
PTMA	893	123	2876	401	104	1843	392	3345	28
MFGE8	705	186	576	75	84	95	49	177	2
CD36	486	691	264	322	673	56	112	65	27
SCD	265	459	44	222	570	39	98	4	6
FABP4	171	527	138	182	103	90	123	5	4
FRIH	127	134	1898	121	87	779	3400	2165	53
RL19	519	358	1351	348	405	1142	717	255	16
RS12	412	152	1172	516	186	66	66	1379	84
CD68	3	3	1108	7	4	84	62	1755	46
RS17	157	117	117	1577	433	87	119	1499	33
B2MG	171	156	766	482	265	97	1055	84	21
PLIN2	57	65	77	75	73	994	8195	38	23
TUBA1B	46	39	38	35	37	59	46	1625	53
HMOX1	4	0.2	1	0.09	0.04	7	3	1073	54
S100A11	33	4	2	10	5	51	10	936	57
RL10	36	4	34	32	35	45	33	668	53

MGT: mammary gland tissue; SC: milk somatic cells; LCMEC: laser microdissected mammary epithelial cells; MFG: milk fat globules; mMEC: antibody- captured milk mammary epithelial cells. Jersey data provided correspond to mean values of the two analyzed Jersey cows.