Plant Molecular Biology

Primer Library for Arabidopsis

This primer library contains 96 sets of gene-specific primers that can be used for expression profiling of 96 genes, of which 93 are Arabidopsis pathogen-inducible genes and 3 are housekeeping genes (see Appendix). It is designed for expression analysis of Arabidopsis defense response genes by quantitative RT-PCR (Q-RT-PCR). The pathogen-inducible genes are selected based on a search of an Arabidopsis database and microarray analysis (see Appendix for the list of Primer names). The housekeeping genes, Actin-2, CBP (nuclear cap-binding protein) 20, and Ubiquitin, are selected based on their expression patterns.
  • Packaged in a 96-well plate format.
  • Each well contains a lyophilized set of forward and reverse primers for a specific gene.
  • Each primer set allows for 200 RT-PCR reactions (20-25 µl reaction volume).
  • Suitable for one-step or two-step RT-PCR.
  • Works for both real time and end-point time RT-PCR analysis.
The specificity and amplification efficiency of all primers have been validated using pathogen-infected Arabidopsis leaf samples and Sigma's SYBR® Green Quantitative RT-PCR Kit (QR0100)
(See Figures 1 & 2).

Data Analysis
Figure 1. Real-time quantification of a defense-response gene expression.
The expression level of the defense gene was highly induced in pathogen treated samples (32 folds of increase) compared to the untreated sample; whereas the internal control actin-2 gene has the same expression level (same CT value) in both samples.
 
Figure 2. Real-time RT-PCR amplification of all 96 selected genes in pathogen treated and untreated Arabidopsis leaves.
Many genes are induced in pathogen treated samples as indicated by reduced CT values. The CT for pathogen treated sample ranged from cycle 23 to 31, whereas the CT from untreated control ranged from cycle 27 to 33. The data was normalized against control gene amplifications (Table 1).
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Table 1
Expression patterns upon Pseudomonas syringae (Pst or expressing avrRpm1) infection in Arabidopsis leaves at different time points.
Expression Pst/1hr Rpm/1hr Rpm/3hr Rpm/8hr Pst/24hr Rpm/24hr Wound/3hr
Up 13 3 52 56 64 59 10
Down 14 10 4 3 4 5 44
Unchanged 66 80 37 34 25 29 39
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Appendix
Lists of primer sets in the primer library.
Well # Primer Name Amplicon Length (bp)   Well # Primer Name Amplicon Length (bp)   Well # Primer Name Amplicon Length (bp)
A1 At2g32680 210   C9 At1g03220 245   F5 At2g40000 177
A2 At3g56710 150   C10 At1g21250 179   F6 At5g20230 210
A3 At4g02380 150   C11 At5g26920 203   F7 At2g02930 189
A4 At5g60900 164   C12 At4g17500 156   F8 At4g38540 189
A5 At1g18890 242   D1 At5g47200 249   F9 At2g45680 217
A6 At3g16530 156   D2 At4g17490 175   F10 At2g40140 159
A7 At5g44420 152   D3 At3g50770 179   F11 At4g39890 190
A8 At4g04490 158   D4 At3g26820 199   F12 At4g26070 226
A9 At4g11830 151   D5 At4g23150 175   G1 At2g13790 225
A10 At2g44790 186   D6 At1g65970 225   G2 At2g32210 169
A11 At1g10140 213   D7 At4g24340 199   G3 At4g11370 213
A12 At4g12720 160   D8 At1g28480 197   G4 At4g34390 189
B1 At3g04720 228   D9 At1g73800 151   G5 At5g47910 207
B2 At5g18470 223   D10 At2g47130 175   G6 At4g39670 174
B3 At2g28210 184   D11 At4g37520 228   G7 At5g59820 170
B4 At2g31880 159   D12 At2g35980 163   G8 At2g35660 223
B5 At3g59700 157   E1 At3g57260 221   G9 At2g38470 250
B6 At4g16650 229   E2 At3g57240 200   G10 At4g11280 228
B7 At5g60900 194   E3 At2g14610 166   G11 At3g28210 152
B8 At4g23180 238   E4 At4g11890 177   G12 At4g37260 163
B9 At5g45110 175   E5 At4g23130 176   H1 At3g52430 172
B10 AT2g14560 150   E6 At4g16260 240   H2 At2g39400 169
B11 At4g36950 195   E7 At3g16530 156   H3 At5g33340 266
B12 At4g14400 161   E8 At3g46090 216   H4 At5g33350 361
C1 At3g56400 216   E9 At4g03450 197   H5 At1g67980 217
C2 AT2g31180 236   E10 At1g13470 245   H6 At3g25882 216
C3 AT4g25390 182   E11 At5g10760 247   H7 At2g45220 192
C4 At1g47510 179   E12 At5g27600 171   H8 At1g05100 164
C5 At2g22270 196   F1 At1g02920 213   H9 At1g66700 245
C6 At3g04640 217   F2 At2g14560 151   H10 CBP20(At5g44200) 409
C7 At2g32200 161   F3 At4g04490 160   H11 Actin-2(At3g18780) 257
C8 At1g05430 166   F4 At1g24140 193   H12 UBC(At5g25760) 217
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Related Products
Product Code Product Name
Quantity
C3615 Control Primer Set for Arabidopsis Actin-2 Gene 1 Set
C3240 Control Primer Set for Arabidopsis UBC Gene 1 Set
C3115 Control Primer Set for Arabidopsis CBP20 Gene 1 Set
QR0100 SYBR® Green Quantitative RT-PCR Kit 1 Kit
J3520 JumpStart™ RED HT RT PCR Kit 40 Reactions
200 Reactions
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