Table 1 Details on qPCR primers.

From: Systematic evaluation of RNA quality, microarray data reliability and pathway analysis in fresh, fresh frozen and formalin-fixed paraffin-embedded tissue samples

Gene symbol Species   Primer sequence Product size Primer efficiency
Gapdh rat forward (5′ end) 5′-TGTGAAGCTCATTTCCTGGTA-3′ 88 bp 105%
reverse (5′ end) 5′-TTACTCCTTGGAGGCCATGT-3′
forward (3′ end) 5′-GTCGGTGTGAACGGATTTG-3′ 85 bp 113%
reverse (3′ end) 5′-TGATGGCAACAATGTCCACT-3′
Pgk1 rat forward (5′ end) 5′-AAAGGATCAAGGCTGCTGTC-3′ 74 bp 110%
reverse (5′ end) 5′-GCTCATAAGCACAACCGACT-3′
forward (3′ end) 5′-GCCTGTGAAAGGAAGTGAGC-3′ 98 bp 113%
reverse (3′ end) 5′-CCGTTATTTCCATGCTGTCA-3′
Actb rat forward (5′ end) 5′-AGGCCAACCGTGAAAAGATG-3′ 101 bp 112%
reverse (5′ end) 5′-ACCAGAGGCATACAGGGACAA-3′
forward (3′ end) 5′-GATTACTGCCCTGGCTCCTA-3′ 90 bp 111%
reverse (3′ end) 5′-AGGATAGAGCCACCAATCCA-3′
Gfap rat Rn_Gfap_1_SG QuantiTect Primer Assay (QT00195517, Qiagen)
Atrn rat forward 5′-GTTCGGAGGGAACACACACA-3′ 98 bp 105%
reverse 5′-ACCATCGGTCACAAGCAATG-3′
Mbp rat forward 5′-AGAACATTGTGACACCTCGTA-3′ 110 bp 123%
reverse 5′-GTAGCCAAATCCTGGCTTCT-3′
Mag rat forward 5′-CAGACCATCCAACCTTCTGTA-3′ 108 bp 118%
reverse 5′-AGTTGGGAATGTCTCCTGATT-3′
Cx3cr1 rat forward 5′-TGCTCAGGACCTCACCAT-3′ 101 bp 117%
reverse 5′-CCACGATGTCACCCAAATAA-3′
GAPDH human forward (5′ end) 5′-ATATTGTTGCCATCAATGACCC-3′ 121 bp 92%
reverse (5′ end) 5′-ATGACAAGCTTCCCGTTCTC-3′
forward (3′ end) 5′-CATTTCCTGGTATGACAACGA-3′ 120 bp 95%
reverse (3′ end) 5′-CTTCCTCTTGTGCTCTTGCT-3′
G6PD human forward (5′ end) 5′-GACATCCGCAAACAGAGTG-3′ 146 bp 87%
reverse (5′ end) 5′-GCATTCATGTGGCTGTTGA-3′
forward (3′ end) 5′-ACCTACGGCAACAGATACA-3′ 141 bp 97%
reverse (3′ end) 5′-CAGCAGTGGGGTGAAAATAC-3′
SDHA human forward (5′ end) 5′-GGCAGGGTTTAATACAGCAT-3′ 126 bp 95%
reverse (5′ end) 5′-TAGAAATGCCACCTCCAGTT-3′
forward (3′ end) 5′-AAGGTGCGGATTGATGAGTA-3′ 150 bp 97%
reverse (3′ end) 5′-TTTGTCGATCACGGGTCTAT-3′
ACTB human forward 5′-GCACCACACCTTCTACAATGAG-3′ 123 bp 90%
reverse 5′-AAGGTCTCAAACATGATCTGGG-3′
PGK1 human forward 5′-TGCTGGACAAAGTCAATGAG-3′ 109 bp 93%
reverse 5′-GCTCCCTCTTCATCAAACAG-3′
CASP1 human forward 5′-TGATGCTATTAAGAAAGCCCAC-3′ 72 bp 103%
reverse 5′-GAAACATTATCTGGTGTGGAAGAG-3′
IL1R1 human forward 5′-AGACAAGGCCTTCTCCAAGA-3′ 102 bp 121%
reverse 5′-CGTTCCTTGCATTTATCAGCCTC-3′
AIF1 human forward 5′-TGAGCCAAACCAGGGATTTA-3′ 99 bp 93%
reverse 5′-CGTCTAGGAATTGCTTGTTGA-3′
IL18 human forward 5′-CCTTTAAGGAAATGAATCCTCCTG-3′ 95 bp 117%
reverse 5′-CATCTTATTATCATGTCCTGGGAC-3′
TLR3 human forward 5′-TCATCCAACAGAATCATGAGAC-3′ 115 bp 85%
reverse 5′-CTTCATGGCTAACAGTGCAC-3′
HMBS human forward 5′-AGCCCAAAGATGAGAGTGAT-3′ 95 bp 103%
reverse 5′-TACGAGGCTTTCAATGTTGC-3′
CX3CR1 human forward 5′-CCAGTGGGGCCTTCA-3′ 100 bp 81%
reverse 5′-ACCACGATGTCCCCAATATAA-3′
ITGAM human forward 5′-TCAGTGGTGCCTGCAA-3′ 100 bp 104%
reverse 5′-GACATAAGGTCAAGGCTGTTA-3′
  1. Gapdh, glyceraldehyde-3-phosphate dehydrogenase; Pgk1, phosphoglycerate kinase 1; Actb, actin beta; Gfap, glial fibrillary acidic protein; Atrn, attractin; Mbp, myelin basic protein; Mag, myelin-associated glycoprotein; Cx3cr1, chemokine (C-X3-C motif) receptor 1; G6pd, glucose-6-phosphate dehydrogenase; Sdha, succinate dehydrogenase complex flavoprotein subunit A; Casp1, caspase 1; Il1r1, interleukin 1 receptor, type I; Aif1, allograft inflammatory factor 1; Il18, interleukin 18; Tlr3, toll-like receptor 3; Hmbs, hydroxymethylbilane synthase; Itgam, integrin alpha M.