Impact of neonatal iron deficiency on hippocampal DNA methylation and gene transcription in a porcine biomedical model of cognitive development

Table 1 DM sites associated with DEGs

Gene	Chr	Start	Stop	Strand	Control expression (FPKM)	Iron deficient expression (FPKM)	Log2 fold change	CpG site	% Methylation difference
AK5	6	125,964,963	126,223,426	−	220.095	108.314	−1.02291	126,222,882	27.13 %
COL18A1	13	218,086,392	218,088,850	+	6.0639	16.1761	1.41555	218,086,634	46.84 %
ENSSSCG00000010493	14	116,376,967	116,425,960	−	0.787778	2.73519	1.79578	116,377,431	25.47 %
SV2B	7	93,628,494	93,828,585	−	61.2676	31.3412	−0.967065	93,828,414	29.24 %
UNC5B	14	80,010,893	80,098,908	+	7.68495	12.5631	0.709085	80,060,756	34.05 %
VWF	5	67,005,340	67,078,256	+	2.61282	9.17948	1.81281	67,050,813	−39.15 %
HS6ST2	X	124,748,953	125,078,245	−	21.3711	8.641	−1.30639	125,076,126	25.18 %
HTR2C	X	108,566,657	108,871,722	+	3.18817	6.73597	1.07916	108,591,537	37.11 %
HTR2C	X	108,566,657	108,871,722	+	3.18817	6.73597	1.07916	108,591,463	−35.23 %
HTR2C	X	108,566,657	108,871,722	+	3.18817	6.73597	1.07916	108,564,261	−25.29 %
HTR2C	X	108,566,657	108,871,722	+	3.18817	6.73597	1.07916	08,564,264	−37.58 %
Gene	Chr	Start	Stop	Strand	Control expression (FPKM)	Iron deficient expression (FPKM)	Log2 fold change	Non-CpG site	% Methylation difference
MICALL2	3	1,066,675	1,085,568	−	2.73823	6.46233	1.23881	1,084,014	44.53 %

The first 11 lines represent DM CpG sites associated with DEGs, while the last line represents a single DM non-CpG site associated with a DEG. % methylation difference is the observed change in methylation in the deficient group relative to the control group. Log2 fold changes are the observed change in expression in the deficient group relative to the control group. Expression levels are represented as fragments per kilobase of transcript per million fragments mapped (FPKM)

ISSN: 1471-2164