Table S1. RNA-seq data used for the validation of gene models. Reads from 24 publically
available RNA-Seq runs (Table S1a) and reads from 23 published and unpublished RNA-Seq
runs (Table S1b) generated in our lab or through collaborations were used for our alignments.
Reads from each sample were aligned to the B73 RefGen_v2 using Tophat. Each alignment file
was merged using SAMtools. BEDtools was then used to intersect the merged alignment against
the genomic co-ordinates of our genes of interest. The .bam files were then loaded into
Integrative Genomics Viewer for computer graphical viewing.
Table S2a. Publically available RNA-Seq data
NCBI Zea
mays
PUBLIC
RNA-Seq
Sample
Detail
[link]
Study Details/Publication
[link]
Tissue/
Developmental
stage
Time of harvest/Details
Inbred line
SRR029369
link
Wang X et al.
Seedling shoots/
Vegetative
Seedlings were harvested after 14
d
B73
SRR029370
link
Wang X et al.
Seedling shoots/
Vegetative
Seedlings were harvested after 14
d
B73
SRR029371
link
Wang X et al.
Seedling shoots/
Vegetative
Seedlings were harvested after 14
d
B73
SRR029372
link
Wang X et al.
Seedling shoots/
Vegetative
Seedlings were harvested after 14
d
B73
SRR029373
link
Wang X et al.
Seedling shoots/
Vegetative
Seedlings were harvested after 14
d
B73
SRR029374
link
Wang X et al.
Seedling shoots/
Vegetative
Seedlings were harvested after 14
d
B73
SRR029375
link
Wang X et al.
Seedling shoots/
Vegetative
Seedlings were harvested after 14
d
B73
SRR029376
link
Wang X et al.
Seedling shoots/
Vegetative
Seedlings were harvested after 14
d
B73
SRR029377
link
Wang X et al.
Seedling roots/
Vegetative
Seedlings were harvested after 14
d
B73
SRR029378
link
Wang X et al.
Seedling roots/
Vegetative
Seedlings were harvested after 14
d
B73
SRR029379
link
Wang X et al.
Seedling roots/
Vegetative
Seedlings were harvested after 14
d
B73
SRR029380
link
Wang X et al.
Seedling roots/
Vegetative
Seedlings were harvested after 14
d
B73
SRR029381
link
Wang X et al.
Seedling roots/
Vegetative
Seedlings were harvested after 14
d
B73
SRR029382
link
Wang X et al.
Seedling roots/
Vegetative
Seedlings were harvested after 14
d
B73
SRR029383
link
Wang X et al.
Seedling roots/
Vegetative
Seedlings were harvested after 14
d
B73
SRR029384
link
Wang X et al.
Seedling roots/
Vegetative
SRR039507
link
Li, P et al.
Leaves (Tip)/
Vegetative
SRR039508
link
Li, P et al.
Leaves (Tip)/
Vegetative
SRR039505
link
Li, P et al.
Leaves (4 cm)/
Vegetative
SRR039506
link
Li, P et al.
Leaves (4 cm)/
Vegetative
SRR039503
link
Li, P et al.
Leaves (1 cm)/
Vegetative
SRR039504
link
Li, P et al.
Leaves (1 cm)/
Vegetative
SRR039501
link
Li, P et al.
Leaves (base)/
Vegetative
SRR039502
link
Li, P et al.
Leaves (base)/
Vegetative
Seedlings were harvested after 14
d
Leaf 3 at 9 days after planting 3
hours into the L period from
segment "mature" (1 cm below
the leaf three tip) - Tissue was
pooled from 15 seedlings
Leaf 3 at 9 days after planting 3
hours into the L period from
segment "mature" (1 cm below
the leaf three tip) - Tissue was
pooled from 15 seedlings
Leaf 3 at 9 days after planting 3
hours into the L period from
segment "maturing" (4 cm above
the leaf two ligule) - Tissue was
pooled from 15 seedlings
Leaf 3 at 9 days after planting 3
hours into the L period from
segment "maturing" (4 cm above
the leaf two ligule) - Tissue was
pooled from 15 seedlings
Leaf 3 at 9 days after planting 3
hours into the L period from
segment "transitional", (1 cm
below the leaf two ligule) - Tissue
was pooled from 15 seedlings
Leaf 3 at 9 days after planting 3
hours into the L period from
segment "transitional", (1 cm
below the leaf two ligule) - Tissue
was pooled from 15 seedlings
Leaf 3 at 9 days after planting 3
hours into the L period from
segment "basal" (1 cm above the
leaf three ligule) - Tissue was
pooled from 15 seedlings
Leaf 3 at 9 days after planting 3
hours into the L period from
segment "basal" (1 cm above the
leaf three ligule) - Tissue was
pooled from 15 seedlings
B73
B73
B73
B73
B73
B73
B73
B73
B73
Table S1b. Published and unpublished RNA-Seq data generated by the Grotewold lab and collaborators used in the maize
TFome collection
Plant Ontology Annotation
Embryo 14DAP. PO:0009009 plant embryo; PO:0001095
true leaf formation; PO:0007001 FR.01 early stage of fruit
ripening.
Embryo 14DAP. PO:0009009 plant embryo; PO:0001095
true leaf formation; PO:0007001 FR.01 early stage of fruit
ripening.
Tissue
Inbred line
Name
Embryo 14 DAP
B73
Embryo_Rep1
Embryo 14 DAP
B73
Embryo_Rep2
Silks (R1). PO:0006354 ear floret; PO:0009074 style;
PO:0007016 4 flowering.
Silks (P1-rr)
A619
Silks_Rep1
Silks (R1). PO:0006354 ear floret; PO:0009074 style;
PO:0007016 4 flowering.
Silks (P1-ww)
A619
Silks_Rep2
Pericarp 14DAP. PO:0009084 pericarp; PO:0007001
FR.01 early stage of fruit ripening.
Pericarp 14DAP (P1rr)
A619
Pericarp_14DAP_Rep1
Pericarp 14DAP. PO:0009084 pericarp; PO:0007001
FR.01 early stage of fruit ripening.
Pericarp 14DAP (P1ww)
A619
Pericarp_14DAP_Rep2
Pericarp 25DAP. PO:0009084 pericarp; PO:0007031
FR.02 mid stage of fruit ripening.
Pericarp 25DAP (P1rr)
A619
Pericarp_25DAP_Rep1
Pericarp 25DAP. PO:0009084 pericarp; PO:0007031
FR.02 mid stage of fruit ripening.
Pericarp 25DAP (P1ww)
A619
Pericarp_25DAP_Rep2
Aleurone 18DAP. PO:0005360 aleurone; PO:0007031
FR.02 mid stage of fruit ripening.
Aleurone 18DAP
B73
Aleurone_18DAP_Rep1
Aleurone 18DAP
B73
Aleurone_18DAP_Rep2
Endosperm 18DAP
B73
Endosperm_18DAP_Rep
1
Endosperm 18DAP
B73
Endosperm_18DAP_Rep
2
Aleurone 22DAP
B73
Aleurone_22DAP_Rep1
Aleurone 22DAP
B73
Aleurone_22DAP_Rep2
Endosperm 22DAP
B73
Endosperm_22DAP_Rep
1
Endosperm 22DAP
B73
Endosperm_22DAP_Rep
2
Immature ears
B73
Ears_Rep1
Immature ears
B73
Ears_Rep2
Immature tassels
B73
Tassels_Rep1
Immature tassels
B73
Tassels_Rep2
Immature tassels
Shoot apical
meristem + Immature
leaves P1-P4
Shoot apical
meristem + Immature
leaves P1-P4
B73
Tassels_Rep3
B73
SAM_Rep1
B73
SAM_Rep2
Aleurone 18DAP. PO:0005360 aleurone; PO:0007031
FR.02 mid stage of fruit ripening.
Endosperm 18DAP. PO:0009089 endosperm;
PO:0007031 FR.02 mid stage of fruit ripening;
PO:0007633 endosperm development stages.
Endosperm 18DAP. PO:0009089 endosperm;
PO:0007031 FR.02 mid stage of fruit ripening;
PO:0007633 endosperm development stages.
Aleurone 22DAP. PO:0005360 aleurone; PO:0007031
FR.02 mid stage of fruit ripening.
Aleurone 22DAP. PO:0005360 aleurone; PO:0007031
FR.02 mid stage of fruit ripening.
Endosperm 22DAP. PO:0009089 endosperm;
PO:0007031 FR.02 mid stage of fruit ripening;
PO:0007633 endosperm development stages.
Endosperm 22DAP. PO:0009089 endosperm;
PO:0007031 FR.02 mid stage of fruit ripening;
PO:0007633 endosperm development stages.
Pre-pollination Cob (R1). PO:0006505 central spike of
ear; PO:0007016 4 flowering
Pre-pollination Cob (R1). PO:0006505 central spike of
ear; PO:0007016 4 flowering
Immature Tassel (V13). PO:0020126 tassel; PO:0001007
pollen developmental stages; PO:0007104 LP.15 fifteen
leaves visible.
Immature Tassel (V13). PO:0020126 tassel; PO:0001007
pollen developmental stages; PO:0007104 LP.15 fifteen
leaves visible.
Immature Tassel (V13). PO:0020126 tassel; PO:0001007
pollen developmental stages; PO:0007104 LP.15 fifteen
leaves visible.
Stem and SAM (V3). PO:0020142 stem internode;
PO:0020148 shoot apical meristem; PO:0007065 LP.05
five leaves visible.
Stem and SAM (V3). PO:0020142 stem internode;
PO:0020148 shoot apical meristem; PO:0007065 LP.05
five leaves visible.