Figure S1. Frequency of concordant alignments for RNA-Seq read pairs across five parameter sets for four different RNA-Seq datasets. Samples 1 and 2 are CG60. Samples 3 and 4 are CG102. Samples 1 and 3 are from plants harvested 24Â h into cold temperature exposure. Samples 2 and 4 are from plants grown only in control conditions. Parameter set details are given in Additional file 2: Table S2. (PDF 4 kb
Quantitative PCR plots of the selected expressed genes for technical validation. (TIF 114 kb
RNA-seq assembly results and expression analysis from various tissues. (XLSX 38411Â kb
Similarity analysis between two biological replicates of control and chilling-treated samples. (A) C...
Table S11. Genes from two GO categories with significant G x E terms in the analysis of plants with ...
Table S4. Number of genes significantly affected by factors at different false discovery rates (FDRs...
Table S9. GO terms enriched among genes only up-regulated in D4 and among genes up-regulated in both...
Figure S2. Molecular function GO terms over-represented (Fisher Test, Benjamini-Hochberg adjusted p-...
Figure S3. A plot of the proportion of mesophyll and bundle sheath cell-specific transcripts that ar...
Table S5. A master list of genes expressed within cold and recovery analyses. (CSV 4615 kb
Table S10. GO terms enriched amongst genes only downregulated in D4 and among genes downregulated in...
Table S7. Significantly enriched biological process, molecular function, and cellular component GO t...
Table S8. Transcript abundance estimates of genes from GO category GO:00424542, response to hydrogen...
The correlation analysis between RNA-seq-generated data and qRT-PCR confirmed results. (tif 102 KB
Differentially expressed genes/transcripts in at least one sample with 2 fold change and at p-value ...
Primer sequences used technical validation of expression data obtained from RNASeq. (XLSX 9 kb
Quantitative PCR plots of the selected expressed genes for technical validation. (TIF 114 kb
RNA-seq assembly results and expression analysis from various tissues. (XLSX 38411Â kb
Similarity analysis between two biological replicates of control and chilling-treated samples. (A) C...
Table S11. Genes from two GO categories with significant G x E terms in the analysis of plants with ...
Table S4. Number of genes significantly affected by factors at different false discovery rates (FDRs...
Table S9. GO terms enriched among genes only up-regulated in D4 and among genes up-regulated in both...
Figure S2. Molecular function GO terms over-represented (Fisher Test, Benjamini-Hochberg adjusted p-...
Figure S3. A plot of the proportion of mesophyll and bundle sheath cell-specific transcripts that ar...
Table S5. A master list of genes expressed within cold and recovery analyses. (CSV 4615 kb
Table S10. GO terms enriched amongst genes only downregulated in D4 and among genes downregulated in...
Table S7. Significantly enriched biological process, molecular function, and cellular component GO t...
Table S8. Transcript abundance estimates of genes from GO category GO:00424542, response to hydrogen...
The correlation analysis between RNA-seq-generated data and qRT-PCR confirmed results. (tif 102 KB
Differentially expressed genes/transcripts in at least one sample with 2 fold change and at p-value ...
Primer sequences used technical validation of expression data obtained from RNASeq. (XLSX 9 kb
Quantitative PCR plots of the selected expressed genes for technical validation. (TIF 114 kb
RNA-seq assembly results and expression analysis from various tissues. (XLSX 38411Â kb
Similarity analysis between two biological replicates of control and chilling-treated samples. (A) C...