Skip to main content

Table 3 Differentially methylated 3Kb regions between Holstein and Angus cultures as determined by MIRA-Seq and gene expression data for annotated genes

From: Differential responsiveness of Holstein and Angus dermal fibroblasts to LPS challenge occurs without major differences in the methylome

     RNA-Seq fold changec
FCa Chr Genomic coordinates Geneb Hour 0 Hour 2 Hour 8
−2.9 1 8811701–8814700 ADAMTS5 - - - - - -
4.2 1 4686501–4689500 LOC100848874 - - - - - -
2.0 1 8325701–8328700 LOC526789 - - - - - -
−3.4 2 88463334–88466333 - - - - - - - -
−3.4 2 88469334–88472333 - - - - - - - -
2.6 2 18491734–18494733 OSBPL6 - - 1.4 1.5
2.0 5 116626706–116629705 FBLN1 - - - - - -
2.3 6 5529182–5532181 - - - - - - - - -
−8.3 7 18532846–18535845 LOC100337044 - - - - - -
2.9 8 23178787–23181786 LOC100300143 - - - - - -
−2.6 8 34929387–34932386 - - - - - - - -
−2.7 8 78669587–78672586 - - - - - - - -
−2.8 8 12568687–12571686 - - - - - - - -
−4.0 8 79335787–79338786 NTRK2 - - - - - -
−2.6 8 98801087–98804086 - - - - - - - -
−2.6 9 20444051–20447050 - - - - - - - -
−2.7 9 93571151–93574150 - - - - - - - -
−4.0 9 88292251–88295250 ULBP1 - - - - - -
−2.7 10 32127701–32130700 - - - - - - - -
2.1 12 51081922–51084921 - - - - - - - -
−2.5 13 64236797–64239796 ASIP −14.0 −15.2 −13.4
2.8 13 48576797–48579796 LRRN4 - - - - - -
2.6 14 36500947–36503946 - - - - - - - - -
2.1 15 53581057–53584156 LOC100336675 - - - - - -
−2.3 15 9012857–9015856 - - - - - - - -
−7.5 15 27535857–27538856 - - - - - - - -
−2.8 15 55516557–55519556 SERPINH1 - - - - - -
−2.4 17 7224294–7227293 MAB21L2 - - - - - -
2.2 17 17977294–17980293 MAML3 - - - - - -
−2.8 18 60220698–60223697 LOC100848332 - - - - - -
−3.6 18 63217498–63220497 LOC783134 - - - - - -
3.4 18 33452798–33455797 - - - - - - - -
2.4 19 42556475–42559474 - - - - - - - -
2.3 19 62858675–62861674 AXIN2 - - - - - -
−2.4 19 43381475–43384474 CNTNAP1 - - 1.8 2.0
−3.6 19 23655275–23658274 HIC1 - - 1.7 - -
2.2 19 42109475–42112474 KRTAP9-2 - - - - - -
2.4 19 62705675–62708674 RGS9 2.0 2.1 2.5
4.8 23 49777993–49780992 - - - - - - - - - - - -
2.8 24 59112931–59115930 CCBE1 −2.3 −2.2 −1.8
2.4 24 62388931–62391930 - - - - - - - - - - - -
2.5 25 27266601–27269600 - - - - - - - - - - - -
2.4 26 23658031–23661030 C26H10orf26 - - - - - - 1.4
−2.4 26 16776031–16779030 LOC100848660 - - - - - - - - -
3.2 27 23720367–23723366 - - - - - - - - - - - -
−2.4 X 63726195–63729194 LOC100848206 2.4 2.6 2.3
2.1 X 111529495–111532494 LOC516666 - - - - - - - - -
2.1 X 128195395–128198394 - - - - - - - - - - - -
−2.6 X 55935095–55938094 - - - - - - - - - - - -
  1. aData obtained by MIRA-Seq and presented as fold difference in read count of methylated regions. Positive fold change indicates higher methylation levels in Holstein cultures while negative values are higher methylation in Angus cultures
  2. bDMRs with an associated gene indicate that some portion of the 3Kb region falls within an annotated gene, while - - indicates DMRs that are intergenic. Bolded gene names indicate that the discovered DMR fell within the promoter region of that gene (-2500 to +500bp from gene transcription start site)
  3. cPositive values indicate greater expression in Holstein cultures as compared to Angus