SRX129687 B73-ear SRP011480 Immature, unpollinated ear tips were harvested ~68 days after planting (depending on the maturity rate of each line). Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. Ear sizes ranged from 0.5 inch to 3 inch, only the tip (the top 1/3 ~1/5 of each ear) was collected. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300531 B73-ear RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129688 B73-root SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300531 B73-root RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129689 B73-shoot SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300531 B73-shoot RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129690 B73-tassel SRP011480 Immature tassels before emerging were harvested approximately at 60 days after planting (depending on the maturity rate of each line) Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300531 B73-tassel RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129692 B97-ear SRP011480 Immature, unpollinated ear tips were harvested ~68 days after planting (depending on the maturity rate of each line). Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. Ear sizes ranged from 0.5 inch to 3 inch, only the tip (the top 1/3 ~1/5 of each ear) was collected. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300533 B97-ear RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129693 B97-root SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300533 B97-root RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina Genome Analyzer IIx SRX129694 B97-shoot SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300533 B97-shoot RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129695 B97-tassel SRP011480 Immature tassels before emerging were harvested approximately at 60 days after planting (depending on the maturity rate of each line) Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300533 B97-tassel RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129698 CML103-ear SRP011480 Immature, unpollinated ear tips were harvested ~68 days after planting (depending on the maturity rate of each line). Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. Ear sizes ranged from 0.5 inch to 3 inch, only the tip (the top 1/3 ~1/5 of each ear) was collected. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300536 CML103-ear RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129699 CML103-root SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300536 CML103-root RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129700 CML103-shoot SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300536 CML103-shoot RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129703 CML103-tassel SRP011480 Immature tassels before emerging were harvested approximately at 60 days after planting (depending on the maturity rate of each line) Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300536 CML103-tassel RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129708 CML228-ear SRP011480 Immature, unpollinated ear tips were harvested ~68 days after planting (depending on the maturity rate of each line). Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. Ear sizes ranged from 0.5 inch to 3 inch, only the tip (the top 1/3 ~1/5 of each ear) was collected. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300543 CML228-ear RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129709 CML228-root SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300543 CML228-root RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129710 CML228-shoot SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300543 CML228-shoot RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129711 CML228-tassel SRP011480 Immature tassels before emerging were harvested approximately at 60 days after planting (depending on the maturity rate of each line) Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300543 CML228-tassel RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129712 CML247-ear SRP011480 Immature, unpollinated ear tips were harvested ~68 days after planting (depending on the maturity rate of each line). Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. Ear sizes ranged from 0.5 inch to 3 inch, only the tip (the top 1/3 ~1/5 of each ear) was collected. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300544 CML247-ear RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129713 CML247-root SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300544 CML247-root RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129715 CML247-shoot SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300544 CML247-shoot RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129716 CML247-tassel SRP011480 Immature tassels before emerging were harvested approximately at 60 days after planting (depending on the maturity rate of each line) Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300544 CML247-tassel RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129717 CML277-ear SRP011480 Immature, unpollinated ear tips were harvested ~68 days after planting (depending on the maturity rate of each line). Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. Ear sizes ranged from 0.5 inch to 3 inch, only the tip (the top 1/3 ~1/5 of each ear) was collected. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300546 CML277-ear RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129719 CML277-root SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300546 CML277-root RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129720 CML277-shoot SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300546 CML277-shoot RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129721 CML277-tassel SRP011480 Immature tassels before emerging were harvested approximately at 60 days after planting (depending on the maturity rate of each line) Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300546 CML277-tassel RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129722 CML322-ear SRP011480 Immature, unpollinated ear tips were harvested ~68 days after planting (depending on the maturity rate of each line). Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. Ear sizes ranged from 0.5 inch to 3 inch, only the tip (the top 1/3 ~1/5 of each ear) was collected. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300548 CML322-ear RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129723 CML322-root SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300548 CML322-root RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129724 CML322-shoot SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300548 CML322-shoot RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129725 CML322-tassel (NSF-CNV) SRP011480 Immature tassels before emerging were harvested approximately at 60 days after planting (depending on the maturity rate of each line) Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300548 CML322-tassel RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129726 CML333-ear SRP011480 Immature, unpollinated ear tips were harvested ~68 days after planting (depending on the maturity rate of each line). Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. Ear sizes ranged from 0.5 inch to 3 inch, only the tip (the top 1/3 ~1/5 of each ear) was collected. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300549 CML333-ear RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129727 CML333-root SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300549 CML333-root RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129728 CML333-shoot SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300549 CML333-shoot RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129729 CML333-tassel SRP011480 Immature tassels before emerging were harvested approximately at 60 days after planting (depending on the maturity rate of each line) Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300549 CML333-tassel RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129730 CML52-ear SRP011480 Immature, unpollinated ear tips were harvested ~68 days after planting (depending on the maturity rate of each line). Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. Ear sizes ranged from 0.5 inch to 3 inch, only the tip (the top 1/3 ~1/5 of each ear) was collected. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300550 CML52-ear RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129731 CML52-root SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300550 CML52-root RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129732 CML52-shoot SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300550 CML52-shoot RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129733 CML52-tassel SRP011480 Immature tassels before emerging were harvested approximately at 60 days after planting (depending on the maturity rate of each line) Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300550 CML52-tassel RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129734 CML69-ear SRP011480 Immature, unpollinated ear tips were harvested ~68 days after planting (depending on the maturity rate of each line). Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. Ear sizes ranged from 0.5 inch to 3 inch, only the tip (the top 1/3 ~1/5 of each ear) was collected. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300551 CML69-ear RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129735 CML69-root SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300551 CML69-root RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129736 CML69-shoot SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300551 CML69-shoot RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129737 CML69-tassel SRP011480 Immature tassels before emerging were harvested approximately at 60 days after planting (depending on the maturity rate of each line) Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300551 CML69-tassel RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129742 Hp301-ear SRP011480 Immature, unpollinated ear tips were harvested ~68 days after planting (depending on the maturity rate of each line). Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. Ear sizes ranged from 0.5 inch to 3 inch, only the tip (the top 1/3 ~1/5 of each ear) was collected. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300556 Hp301-ear RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129743 Hp301-root SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300556 Hp301-root RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129744 Hp301-shoot SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300556 Hp301-shoot RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129745 Hp301-tassel SRP011480 Immature tassels before emerging were harvested approximately at 60 days after planting (depending on the maturity rate of each line) Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300556 Hp301-tassel RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129746 IL14H-ear SRP011480 Immature, unpollinated ear tips were harvested ~68 days after planting (depending on the maturity rate of each line). Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. Ear sizes ranged from 0.5 inch to 3 inch, only the tip (the top 1/3 ~1/5 of each ear) was collected. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300557 IL14H-ear RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129747 IL14H-root SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300557 IL14H-root RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129748 IL14H-shoot SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300557 IL14H-shoot RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129749 IL14H-tassel SRP011480 Immature tassels before emerging were harvested approximately at 60 days after planting (depending on the maturity rate of each line) Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300557 IL14H-tassel RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129750 Ki11-ear SRP011480 Immature, unpollinated ear tips were harvested ~68 days after planting (depending on the maturity rate of each line). Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. Ear sizes ranged from 0.5 inch to 3 inch, only the tip (the top 1/3 ~1/5 of each ear) was collected. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300558 Ki11-ear RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129751 Ki11-root SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300558 Ki11-root RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129752 Ki11-shoot SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300558 Ki11-shoot RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129753 Ki11-tassel SRP011480 Immature tassels before emerging were harvested approximately at 60 days after planting (depending on the maturity rate of each line) Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300558 Ki11-tassel RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129754 Ki3-ear SRP011480 Immature, unpollinated ear tips were harvested ~68 days after planting (depending on the maturity rate of each line). Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. Ear sizes ranged from 0.5 inch to 3 inch, only the tip (the top 1/3 ~1/5 of each ear) was collected. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300559 Ki3-ear RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129755 Ki3-root SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300559 Ki3-root RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129756 Ki3-shoot SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300559 Ki3-shoot RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129757 Ki3-tassel SRP011480 Immature tassels before emerging were harvested approximately at 60 days after planting (depending on the maturity rate of each line) Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300559 Ki3-tassel RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129759 Ky21-ear SRP011480 Immature, unpollinated ear tips were harvested ~68 days after planting (depending on the maturity rate of each line). Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. Ear sizes ranged from 0.5 inch to 3 inch, only the tip (the top 1/3 ~1/5 of each ear) was collected. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300561 Ky21-ear RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129760 Ky21-root SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300561 Ky21-root RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129761 Ky21-shoot SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300561 Ky21-shoot RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129762 Ky21-tassel SRP011480 Immature tassels before emerging were harvested approximately at 60 days after planting (depending on the maturity rate of each line) Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300561 Ky21-tassel RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129765 M162W-ear SRP011480 Immature, unpollinated ear tips were harvested ~68 days after planting (depending on the maturity rate of each line). Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. Ear sizes ranged from 0.5 inch to 3 inch, only the tip (the top 1/3 ~1/5 of each ear) was collected. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300564 M162W-ear RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129767 M162W-root SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300564 M162W-root RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129768 M162W-shoot SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300564 M162W-shoot RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129769 M162W-tassel SRP011480 Immature tassels before emerging were harvested approximately at 60 days after planting (depending on the maturity rate of each line) Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300564 M162W-tassel RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129770 M37W-ear SRP011480 Immature, unpollinated ear tips were harvested ~68 days after planting (depending on the maturity rate of each line). Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. Ear sizes ranged from 0.5 inch to 3 inch, only the tip (the top 1/3 ~1/5 of each ear) was collected. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300566 M37W-ear RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129771 M37W-root SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300566 M37W-root RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129772 M37W-shoot SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300566 M37W-shoot RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129773 M37W-tassel SRP011480 Immature tassels before emerging were harvested approximately at 60 days after planting (depending on the maturity rate of each line) Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300566 M37W-ear RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129774 Mo17-ear SRP011480 Immature, unpollinated ear tips were harvested ~68 days after planting (depending on the maturity rate of each line). Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. Ear sizes ranged from 0.5 inch to 3 inch, only the tip (the top 1/3 ~1/5 of each ear) was collected. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300568 Mo17-ear RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129776 Mo17-root SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300568 Mo17-root RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129777 Mo17-shoot SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were done with the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen protocol. Total RNA was eluted twice with 30 ul RNase free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 101 7 101 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300568 Mo17-shoot RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129778 Mo17-tassel SRP011480 Immature tassels before emerging were harvested approximately at 60 days after planting (depending on the maturity rate of each line) Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300568 Mo17-tassel RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129780 Mo18W-ear SRP011480 Immature, unpollinated ear tips were harvested ~68 days after planting (depending on the maturity rate of each line). Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. Ear sizes ranged from 0.5 inch to 3 inch, only the tip (the top 1/3 ~1/5 of each ear) was collected. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300570 Mo18W-ear RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129781 Mo18W-root SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300570 Mo18W RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129782 Mo18W-shoot SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300570 Mo18W-shoot RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129783 Mo18W-tassel SRP011480 Immature tassels before emerging were harvested approximately at 60 days after planting (depending on the maturity rate of each line) Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300570 Mo18W-tassel RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129785 Ms71-fieldear SRP011480 Immature, unpollinated ear tips were harvested ~68 days after planting (depending on the maturity rate of each line). Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. Ear sizes ranged from 0.5 inch to 3 inch, only the tip (the top 1/3 ~1/5 of each ear) was collected. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300572 Ms71-fieldear RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129786 Ms71-root SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300572 Ms71-root RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129787 Ms71-shoot SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300572 Ms71-shoot RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129788 NC350-ear SRP011480 Immature, unpollinated ear tips were harvested ~68 days after planting (depending on the maturity rate of each line). Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. Ear sizes ranged from 0.5 inch to 3 inch, only the tip (the top 1/3 ~1/5 of each ear) was collected. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300573 NC350-ear RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129789 NC350-root SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300573 NC350-root RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129790 NC350-shoot SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300573 NC350-shoot RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129791 NC350-tassel SRP011480 Immature tassels before emerging were harvested approximately at 60 days after planting (depending on the maturity rate of each line) Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300573 NC350-tassel RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129792 NC358-ear SRP011480 Immature, unpollinated ear tips were harvested ~68 days after planting (depending on the maturity rate of each line). Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. Ear sizes ranged from 0.5 inch to 3 inch, only the tip (the top 1/3 ~1/5 of each ear) was collected. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300574 NC358-ear RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129793 NC358-root SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300574 NC358-root RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129794 NC358-shoot SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300574 NC358-shoot RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129795 NC358-tassel SRP011480 Immature tassels before emerging were harvested approximately at 60 days after planting (depending on the maturity rate of each line) Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300574 NC358-tassel RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129796 Oh43-ear SRP011480 Immature, unpollinated ear tips were harvested ~68 days after planting (depending on the maturity rate of each line). Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. Ear sizes ranged from 0.5 inch to 3 inch, only the tip (the top 1/3 ~1/5 of each ear) was collected. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300575 Oh43-ear RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129797 Oh43-root SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300575 Oh43-root RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129798 Oh43-shoot SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300575 Oh43-shoot RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129799 Oh43-tassel SRP011480 Immature tassels before emerging were harvested approximately at 60 days after planting (depending on the maturity rate of each line) Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300575 Oh43-tassel RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129800 Oh7B-ear SRP011480 Immature, unpollinated ear tips were harvested ~68 days after planting (depending on the maturity rate of each line). Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. Ear sizes ranged from 0.5 inch to 3 inch, only the tip (the top 1/3 ~1/5 of each ear) was collected. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300576 Oh7B-ear RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129801 Oh7B-root SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300576 Oh7B-root RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129802 Oh7B-shoot SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300576 Oh7B-shoot RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129803 Oh7B-tassel SRP011480 Immature tassels before emerging were harvested approximately at 60 days after planting (depending on the maturity rate of each line) Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300576 Oh7B-tassel RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129804 P39-ear SRP011480 Immature, unpollinated ear tips were harvested ~68 days after planting (depending on the maturity rate of each line). Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. Ear sizes ranged from 0.5 inch to 3 inch, only the tip (the top 1/3 ~1/5 of each ear) was collected. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300577 P39-ear RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129805 P39-root SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300577 P39-root RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129806 P39-shoot SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300577 P39-shoot RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129807 P39-tassel SRP011480 Immature tassels before emerging were harvested approximately at 60 days after planting (depending on the maturity rate of each line) Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300577 P39-tassel RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129808 Tx303-ear SRP011480 Immature, unpollinated ear tips were harvested ~68 days after planting (depending on the maturity rate of each line). Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. Ear sizes ranged from 0.5 inch to 3 inch, only the tip (the top 1/3 ~1/5 of each ear) was collected. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300578 Tx303-ear RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129809 Tx303-root SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300578 Tx303-root RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129810 Tx303-shoot SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300578 Tx303-shoot RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129811 Tx303-tassel SRP011480 Immature tassels before emerging were harvested approximately at 60 days after planting (depending on the maturity rate of each line) Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300578 Tx303-tassel RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129812 Tzi8-ear SRP011480 Immature, unpollinated ear tips were harvested ~68 days after planting (depending on the maturity rate of each line). Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. Ear sizes ranged from 0.5 inch to 3 inch, only the tip (the top 1/3 ~1/5 of each ear) was collected. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300579 Tzi8-ear RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129813 Tzi8-root SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300579 Tzi8-root RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129814 Tzi8-shoot SRP011480 10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300579 Tzi8-shoot RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX129815 Tzi8-tassel SRP011480 Immature tassels before emerging were harvested approximately at 60 days after planting (depending on the maturity rate of each line) Samples from three plants of each inbred/line were pooled for homogenization in liquid nitrogen and RNA extraction. All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp. SRS300579 Tzi8-tassel RNA-Seq TRANSCRIPTOMIC PCR 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000