Table 1:

Primerand Run methods for qRT-PCR

Target Gene	Forward Primer (5’−3’)	Reverse Primer (5’−3’)	Run Method
BM5eco gaga	CCAATGTGTCCATGTCATTT	CTTTCTCTCTCTGCTCATCGC	95°C for 8 min, followed by 80 cycles of 94°C for 15 sec, 63°C for 45 sec, and 72°C for 15 sec.
BMSdefb	CCTTTTCCTTTATCGACACT	ACCAGGGGGGGAATACCTCG
β-actina	AGAGGGAAATCGTGCGTGAC	CAATAGTGATGACCTGGCCGT
IFN-αc	ATGGCTAGGCTCTGTGCTTTTCCTC	AGGGCTCTCCAGACTTCTGCTCTG	95°C for 3 min, followed by 40 cycles of 95°C for 30 sec, 65°C for 30 sec, and 72°C for 30 sec.
IFN-βc	TTGCCATCCAAGAGATGCTCCAGA	TCAGAAACACTGTCTGCTGGTGGA
“gp120f	TGA GCC AAT TCC CAT ACA TTA TTG	CCT GTT CCA TTG AAC GTC TTA TTA TTA C	95 °C for 10’, followed by 40 cycles of 95 °C for 30 sec, 59 °C for 1 min, and 72 °C for lmin, and then followed by a denaturation step: 95 °C for 1 min, 59 °C for 30 sec, 95 °C for 30 sec.
iNOsd	TGGTGGTGACAAGCACATTTG	CATTGGAAGTGAAGCGTTTCG	95°C for 15 sec, followed by 40 cycles of 95°C for 15 sec and 60°C for 1 min.
CCL2/MCP-1d	GTATGTCTGGACCCATTCCTTC	GCTGTAGTTTTTGTCACCAAGC
CCL3/MIP-1αd	CAGCCAGGTGTCATTTTCCT	AGGCATTCAGTTCCAGGTCA
CCL5/RANTESd	AGCTGCCCTCACCATCATC	CTCTGGGTTGGCACACACTT
11-12 p40d	CCATTGAACTGGCGTTGGAAG	CGGGTCTGGTTTGATGATGTCC
TNF- αa	TGAACTTCGGGGTGA TCGGTC	AGC CTTGTC CCTTGAAG AGAAC
IFN-ϓd	GCCATCAGCAACAAC ATAAGC	CAGCAGCGACTCCTTTT CC
CXCL10d	TTTCTGCCTCATCCTGCTG	CTCATCATTCTTTTTCATCGTG
GAPDHd	ACCACCATGGAGAAG GC	GGCATGGACTGTGGTCA TGA
CCL4e	GTCTCATAGTAATCCA TCACAAAGC	CTCTCTCTCCTCTTGCTC GT	95°C for 30 sec then 40 cycles of 95°C for 3 sec and 60°C for 30 sec, with fast ramp speed
CD11be	TGTCCAGATTGAAGC CATGA	CCACAGTTCACACTTCT TTCAG
GFAPe	AACCGCATCACCATT CCTG	GCATCTCCACAGTCTTT ACCA
Synapto-physine	CAGACAGGAAACACA TGCAAG	TCTCCTTGAACACGAAC CATAG
MAP-2e	AACAGCTAATCTGCCACCTTC	GTGACTTTATCCTTCGCCTGT
GAPDHe	GTGGAGTCATACTGGAACATGTAG	AATGGTGAAGGTCGCTGTG

[Citation: a=(Cook et al. 2003), b=(Giese et al. 1994), c=(Kundu et al. 2013), d=(Chrismiddlehi et al. 2009), e=PrimeTime® Primers from IDT (Coralville, IA, CA), f=(Kaul lab, personal communication)].