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Table 1 Differentially accessible regions in the dorsal root ganglion following either CCI or CFA

From: Global gene expression and chromatin accessibility of the peripheral nervous system in animal models of persistent pain

Locationa Chromatin accessibility Distance to nearest gene (bp) Gene Full gene name Gene expression
CCI versus Naïve CFA versus Naïve CCI versus Naïve CFA versus Naïve
Log2FC p-value Log2FC p-value Log2FC FDR Log2FC FDR
chr17:11683581-11684211 − 1.06 6.34E-05 − 0.99 1.64E-04 34 Msx2 Msh homeobox 2 n.s. n.s.
chr1:92513274-92513499 − 1.00 2.72E-04 -1.01 8.90E-05 261576 Tshz3 Teashirt zinc finger homeobox 3 n.s. n.s.
chr8:47237180-47237538 − 0.99 2.34E-05 − 0.97 8.26E-04 − 129442 Grik4 Glutamate ionotropic receptor kainate type subunit 4 0.669 3.30E-06 0.672 7.20E-06
chr6:144123384-144123972 − 0.95 4.70E-04 − 0.71 8.53E-05 − 82 Wdr60 WD repeat domain 60 − 0.415 3.08E-02 − 0.499 1.33E-02
chrX:70596272-70597179 − 0.95 1.45E-04 − 0.80 1.87E-04 149 Dlg3 Discs large MAGUK scaffold protein 3 − 0.599 1.19E− 03 − 0.674 6.12E− 04
chr19:34760039-34760205 − 0.94 7.18E-04 -0.64 3.23E-04 881 Nr3c2 Nuclear receptor subfamily 3, group C, member 2 n.s. n.s.
chr2:88365560-88366693 − 0.77 8.32E-04 -0.61 4.17E-04 21600 Rbis Ribosomal biogenesis factor n.s. − 0.501 2.48E-03
chr17:5634167-5634689 − 0.77 6.58E-04 -0.88 8.48E-04 123043 Agtpbp1 ATP/GTP binding protein 1 0.669 5.58E-13 0.572 1.23E-09
chr2:239413846-239414572 − 0.75 3.34E-04 -0.68 6.17E-04 − 673 Cxxc4 CXXC finger protein 4 n.s. n.s.
chr3:97720973-97722482 − 0.71 8.27E-04 -0.70 8.61E-04 − 2173 Mpped2 Metallophosphoesterase domain containing 2 n.s. n.s.
chr16:23432936-23433376 0.71 3.99E-04 0.71 4.94E-04 − 276331 Sh2d4a SH2 domain containing 4A n.s. n.s.
chr14:93768297-93768703 0.75 8.15E-04 1.00 1.86E-04 − 1272606 Cobl Cordon-bleu WH2 repeat protein n.s. n.s.
chr3:117326358-117326776 0.86 1.07E-04 0.87 1.87E-04 − 8645 Slc24a5 Solute carrier family 24 member 5 n.s. n.s.
chr7:72282656-72283204 0.87 5.84E-04 1.00 2.38E-05 − 489510 Mtdh Metadherin n.s. n.s.
chr7:76825894-76826308 0.95 4.39E-04 0.75 4.20E-04 -45284 Rrm2b Ribonucleotide reductase regulatory TP53 inducible subunit M2B 0.318 2.54E-02 0.534 1.15E-04
chr8:68261923-68262408 1.07 2.15E-05 0.81 8.92E-04 20424 Map2k5 Mitogen activated protein kinase kinase 5 n.s. n.s.
chr14:48665324-48665682 1.10 9.99E-04 0.96 6.22E-04 − 60542 Arap2 ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2 0.401 1.31E-03 0.800 2.69E-11
chr2:104740823-104741617 1.11 9.13E-05 0.67 7.82E-05 − 3223 Cp Ceruloplasmin n.s. n.s.
chr7:69057806-69058124 1.20 2.80E-04 1.14 8.43E-04 46985 LOC500846 Hypothetical protein LOC500846 n.s. n.s.
chr15:48090366-48090685 1.20 2.14E-04 1.10 1.15E-04 59452 Kif13b Kinesin family member 13B − 1.372 6.53E-35 − 0.864 8.10E-14
chr5:75716406-75716663 1.22 1.09E-04 0.88 2.39E-04 − 39951 Lpar1 Lysophosphatidic acid receptor 1 − 0.759 1.35E-16 − 0.759 5.95E-16
chr11:1269991-1270529 1.26 3.86E-05 0.69 8.21E-04 − 487306 Epha3 Eph receptor A3 n.s. n.s.
chr12:17820620-17821049 1.41 4.21E-05 0.81 9.32E-04 55600 LOC498155 LRRGT00167 n.s. n.s.
chr12:3340812-3341234 1.49 1.11E-04 0.83 4.64E-04 − 514790 Clec4m C-type lectin domain family 4 member M n.s. n.s.
chr13:10820032-10820423 1.58 1.21E-05 0.86 6.03E-04 1340233 Olr1065 Olfactory receptor 1065
chr12:8713579-8713997 1.58 2.56E-04 1.31 2.98E-05 − 11748 Slc46a3 Solute carrier family 46, member 3 n.s. 0.777 1.20E-02
chr15:75876479-75876957 1.79 2.13E-05 0.83 8.63E-04 1860057 Pcdh9 Protocadherin 9 0.778 1.29E-10 0.871 1.50E-12
chr8:4288257-4288665 3.64 5.15E-08 2.03 1.25E-04 − 31769 Vom2r18 Vomeronasal 2 receptor, 18 n.s. n.s.
chr8:4322772-4323450 3.88 7.77E-09 2.35 5.51E-05 2729 Vom2r17 Vomeronasal 2 receptor, 17
chr8:4337259-4338234 5.59 2.35E-09 3.45 5.54E-04 17365 Vom2r17 Vomeronasal 2 receptor, 17
chr8:4292048-4292933 5.64 2.72E-08 4.01 1.42E-04 − 27739 Vom2r18 Vomeronasal 2 receptor, 18 n.s. n.s.
  1. CCI chronic constriction injury, CFA complete Freund's adjuvant, n.s. not significant, FDR false discovery rate, FC fold change
  2. aGenome coordinates provided are for the rat genome assembly, rn6