A multi-scale analysis of bull sperm methylome revealed both species peculiarities and conserved tissue-specific features

Table 1 Samples and experiments

Experiment	Species	Breed/strain	Sample type	Sample number	Figures
LUMA	Cattle	Holstein	PBMCs	73	Fig. 1a
	Cattle	Belgian White Blue	Sperm, frozen	14	Fig. 1a-b, e
	Cattle	Holstein	Sperm, frozen	112	Fig. 1a-b, e
	Cattle	Montbéliarde	Sperm, frozen	41	Fig. 1a-b, e
	Cattle	Normande	Sperm, frozen	18	Fig. 1a-b, e
	Cattle	Montbéliarde	Sperm, frozen	6	Fig. 1c-d
	Cattle	Montbéliarde	Total blood	6	Fig. 1c
	Sheep	Ile-de-France	Sperm, frozen	5	Fig. 1c-d, e
	Sheep	Ile-de-France	Total blood	5	Fig. 1c
	Cattle	Montbéliarde	Sperm, fresh	6	Fig. 1d
	Sheep	Ile-de-France	Sperm, fresh	4	Fig. 1d
	Horse	Welsh	Sperm, fresh	2	Fig. 1e
	Pig	mixed	Sperm, fresh	3	Fig. 1e
	Mouse	C57Bl/6JOlaHsd	Sperm, fresh	2	Fig. 1e
	Human		Sperm, frozen	7	Fig. 1e
	Goat	Alpine	Sperm, frozen	2	Fig. 1e
Genotyping	Cattle	Montbéliarde	Sperm, fresh	2	Additional file 1: Figure S2
Genotyping	Cattle	Montbéliarde	Total blood	2	Additional file 1: Figure S2
MeDIP	Cattle	Holstein	Sperm, frozen	4	Figs. 2, 3, 4, 6
	Cattle	Holstein	Liver	4	Figs. 2, 3, 4, 6
	Cattle	Holstein	Fibroblasts	3	Figs. 2, 3, 4, 6
RRBS	Cattle	Holstein	Sperm, frozen	2	Figs. 2, 3, 5, 6
	Cattle	Holstein	Monocytes	2	Figs. 2, 3, 5, 6
	Cattle	Holstein	Fibroblasts	2	Figs. 2, 3, 5, 6

All the samples were independent, except for (i) the sperm and blood samples in Fig. 1c-d that were collected on the same bulls and rams, and (ii) two fibroblast samples and two livers that were collected on the same animals. Two independent amplifications of the same fibroblast cultures were used for MeDIP and RRBS. The sperm and blood DNA samples used for genotyping were the same as used for LUMA, Fig. 1c-d. PBMCs: peripheral blood mononuclear cells

ISSN: 1471-2164