Figure S1: Flow chart describing construction of the probe sets used in this study.
Figure S2: Representative tissues used in this study. Tissues collected are
indicated by arrows and numbers wherever needed. Black lines indicate places the
tissues were cut from an organ.
Figure S3: Quality of the three biological replicates for each of the sixty tissues
used in the study. (a) Pair-wise Pearson’s correlation (r) was calculated for all three
pairs of biological replicates for each tissue. (b) Frequency distribution of Pearson’s
correlations for the 180 pair-wise combinations.
Figure S4: Expression of previously studied genes follows the expected
expression patterns. (a-b) opaque2 and shrunken2 are involved in starch
biosynthetic pathway (Schmidt, et al. 1990, Schultz and Juvik 2004). (c) LEAFY
COTYLEDON1 (LEC1) encodes a transcription factor involved in embryogenesis
(Lotan, et al. 1998). (d) ramosa2 encodes a transcription regulator of inflorescence
formation (Bortiri et al. 2006). (e) ribulose bisphosphate carboxylase/oxygenase
activase is an activator of Rubisco (Portis 1992). (f) ZmTIP-3 is a root-specific
aquaporin gene (Lopez, et al. 2004).
Figure S5: GO Slim enrichment of the non-expressed genes.
Figure S6: GO Slim enrichment of constitutively expressed genes. Only enriched
categories of biological processes are shown.
Figure S7: GO Slim enrichment of stably expressed genes
Figure S8: Identification of stably expressed genes. To identify these genes, the
expressed genes were ranked based on their coefficient of variation (CV) value. (a)
The relative expression levels of five genes used as reference for expression
experiments across the 60 tissues. Relative expression was calculated by dividing
the expression a gene in a given tissue by the average expression of that gene in
all the tissues. (b) Relative expression of 20 most stably expressed genes (CV ≤
15.0%) in the current study.
Figure S9: Up-regulation of selected genes in the base (a) and tip (b) of
developing leaf. The genes were selected based on differential expression
between base and tip of developing maize leaves reported in a recent study (Li, et
al. 2010).
Figure S10: Heat map global gene expression. Hierarchical clustering was
performed to cluster vegetative tissues (a) and seed tissues (b) based on
expression of 30,892 probe sets. Red, yellow, and blue colors indicate high,
medium, and low levels of gene expression, respectively.
Table S1: Details of the maize tissues included in the genome-wide gene
expression atlas of inbred line B73.
Table S2: Pearson's correlation coefficients for biological replicates.
Table S3: List of most stably expressed genes.
Table S4: List of tissue specific genes.