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Table 1 Candidate genes used for real-time quantitative RT-PCR validation.

From: Transcript profiling of two alfalfa genotypes with contrasting cell wall composition in stems using a cross-species platform: optimizing analysis by masking biased probes

   t-test1 Ratio2  
Annotation Probe Set ID No mask Double- mask No mask Double- mask ΔΔCT3
Cell Wall-related Genes       
Chitinase Msa.3005.1.S1_at + + -2.8 -3.4 -2.2**
Peroxidase Mtr.40028.1.S1_at - + -4.5 -5.2 -2.2**
Chitinase Mtr.40130.1.S1_at + + -1.8 -2.1 -1.2**
Reversibly glycosylated polypeptide Mtr.4595.1.S1_at - + 0.8 2.4 1.9**
Cellulose synthase-like Mtr.45005.1.S1_at - + 0.8 1.1 0.3**
Endo-1,4-beta glucanase Mtr.31102.1.S1_at - + 0.9 1.1 1.1**
Xyloglucan endotransglusoxylase Mtr.6499.1.S1_at - + -0.7 -1.6 -1.3**
UDP-glucose dehydrogenase Msa.2895.1.S1_at + + 1.3 1.6 0.4*
Acetyl-CoA C-acetyltransferase Mtr.10429.1.S1_at - + -0.5 -2.7 -2.3**
Cinnamyl-alcohol dehydrogenase Mtr.8985.1.S1_at - + -0.3 -1.3 -0.9**
Caffeoyl-CoA O-methyltransferase Mtr.4850.1.S1_at - + -1.3 -2 -1.5**
Glycosyl hydrolase Mtr.2288.1.S1_at - + 0.4 2 0.6
UDP-glucosyl transferase Mtr.37847.1.S1_at + + 2.2 4.1 3.0**
Transcription Factors       
LOB gene family Mtr.28784.1.S1_at - + 1.8 2.4 1.2*
bZIP transcription factor Mtr.17513.1.S1_s_at + + 2.3 2.8 2.7**
C2H2 zinc finger family Mtr.972.1.S1_at - + 2 3.2 2.6**
C2H2 zinc finger family Mtr.50483.1.S1_at + + 1.6 1.5 1.0**
C2H2 zinc finger family Mtr.39849.1.S1_at - + -1.5 -2.8 -1.4**
Homeobox transcription factor Mtr.24122.1.S1_at + + -1 -1.3 -0.4
Homeobox transcription factor Mtr.46916.1.S1_at - + -0.9 -1.9 -1.1**
Homeobox transcription factor Mtr.38132.1.S1_a_at - + -0.6 -1 -0.7**
JUMONJI family Mtr.17177.1.S1_at - + 2 2.1 3.0**
MYB transcription factor Mtr.42648.1.S1_at - + 0.6 2.4 1.0**
NAC transcription factor Mtr.14808.1.S1_at - + -0.9 -1.2 -0.7*
PHD finger family Mtr.39174.1.S1_at - + -1.1 -1.9 -0.2
Zinc finger family Mtr.33527.1.S1_at + + 3.2 3.6 2.7**
WRKY family Mtr.23120.1.S1_s_at + + 3.8 3.4 3.8**
WRKY family Mtr.12866.1.S1_at - + 2.1 2.2 2.2**
Signal Transduction Genes       
Transducin family Mtr.11654.1.S1_at - + 0.8 2.1 1.8
FAR1-related Mtr.47127.1.S1_at + + 3 3 2.1**
MAP kinase Mtr.5102.1.S1_at + + -1.3 -1.7 -0.8**
Receptor-like kinase Mtr.1545.1.S1_at - + 0.7 2.5 4.2**
Receptor-like kinase Mtr.9480.1.S1_at + + 1.3 1.5 0.4
Receptor-like kinase Mtr.3024.1.S1_at - + 0.6 2.1 2.2**
  1. 1+ indicates genes that were detected as differentially-expressed between PES internodes of genotypes 252 and 1283 after a t-test (p < 0.001, FDR < 0.05, ≥2-fold difference) using the GeneChip data with no masking or after double-masking.
  2. 2Log2 (252PES/1283PES) value obtained from the GeneChip data with no masking or after double-masking.
  3. 3ΔΔCT = [CT(1283PES) - CT(18s)] — [CT(252PES) - CT(18s)] from real-time quantitative RT-PCR data. CT18s rRNA values were stable in the tissues examined and were used to normalize data. *,** indicates probe sets that were detected as differentially expressed after a t-test (P < 0.01 or P < 0.001) respectively, The t-test of the real-time quantitative RT-PCR data for PES internodes of genotypes 252 and 1283 was performed with ΔCT values (12 data points = 2 plates × 3 wells × 2 genotypes).