Table S3A. Primer sequences for RT-qPCR expression analysis.

Gene / Product (bp) /

Forward primer

/

Reverse primer

ITGA11 / 73 / GCCGCCAGATCGTGTTTG / GGTGCTGCCTACAATGA
SULF1 / 105 / TGCTCAAAGTGACGGGTTCTT / TGTTTTCCCAACCTTATGCCTT
MFAP5 / 61 / TGCTGCATTCATCATCACCTC / CGTCTCCTCGTTGACTATTGACC
CTHRC1 / 80 / TTGGTGCTGGATTAGTGGATGT / CCATCCAGTAGAAGCATCTCCTTT
THBS2 / 78 / CGCTGTAGGTTTTGACGAGTTTG / TAGTCGTCGTCCCGGTCAGT
COL11A1 / 59 / ATGACTATGAGTATGGGGAAGCA / TGGGTCCCTCTGTTACACTTT
IGSF10 / 88 / AGCTTGACACGATTGCACATG / GCACCAGGCGGAGAAAGTT
PZP / 80 / GAGTCAGCCTGGAATGTAGCAA / GAAAAAGCATAGGCCAGCAATG
PDE3B / 70 / TGGGTCCCCTGTGTAACTCCTA / TCCTCTTCTGCTTCTAACCACTGA
CCDC102B / 71 / GTCAACATAATGATGAAATGCAAGAA / TTTGCTGTTTTGAGATTTGGATTC
CLU / 70 / ATCTTCTTGACTGTGGCATTTCCT / TGTGGTCCAGGGAAAGGTATG
FLRT3 / 72 / CAGTTAGCATAGAAGAGGGAGCATT / GGTGATTACGGGACAGGAAAAG
TMOD1 / 71 / TGTGACATTGCAGCGATCCT / CTGCTCAGGGCCTGGTAGTACT
GPR126 / 75 / TCTGTTGTCAGTTCTAAGCATGCA / AGCTAAATTCCTGACCTCTGTTCTG
SULF1(all 4 variants) / 70 / GAATGGTGCCTTTCTGAGTGTCT / CAGGCAGTGGAAGTGTGTTGA

Primers were designed using Primer-Blast and Primer Express Program (Invitrogen, Burlington, ON, Canada).


Table S3B. Correlation between microarray and RT-qPCR

Spearman's correlation Coefficient / P value
Transcript Cluster ID / Type / Gene Symbol / NFs / CAFs / NFs / CAFs
2425756 / up / COL11A1 / 0.78 / 0.75 / 0.0007 / 0.0012
3443226 / up / MFAP5 / 0.96 / 0.93 / P<0.0001 / < 0.0001
3102372 / up / SULF1 / 0.88 / 0.90 / P<0.0001 / < 0.0001
3630736 / up / ITGA11 / 0.99 / 0.94 / P<0.0001 / < 0.0001
2985781 / up / THBS2 / 0.13 / 0.68 / 0.6387 / 0.0058
3110317 / up / CTHRC1 / 0.41 / 0.76 / 0.1320 / 0.0011
2928461 / down / GPR126 / 0.30 / 0.77 / 0.2799 / 0.0008
3181240 / down / TMOD1 / 0.68 / 0.20 / 0.0050 / 0.4748
3321512 / down / PDE3B / 0.54 / 0.76 / 0.0378 / 0.0011
3792656 / down / CCDC102B / 0.57 / 0.88 / 0.0271 / < 0.0001
2701109 / down / IGSF10 / 0.52 / 0.81 / 0.0480 / 0.0002
3129065 / down / CLU / 0.28 / 0.65 / 0.3147 / 0.0089
3898355 / down / FLRT3 / 0.79 / 0.53 / 0.0005 / 0.0412
3443348 / down / A2M / 0.58 / 0.81 / 0.0238 / 0.0002

RT-qPCR was used to validate microarray results of 14 genes overlapped between NSCLC CAFs and stroma. Spearman’s rank-correlation and p-value were calculated in GraphPad Prism version 4 (GraphPad Software, Inc.; see also Supplmentary Figure S2).