Agave americana

RNA-Seq of Agave americana: young leaf at 6 pm

"Two-year-old plants of Agave americana ?marginata? were grown under day/night temperatures of 25/15degreeC, day/night relative humidities of 45/75%, photoperiod of 12 h with a photosynthetic photon flux (PPF, 400 to 700 nm) of 540 ?mol m-2 s-1. A total of 15 samples were collected, including eight mature leaf samples collected at 6 am, 9 am, 12 pm, 3 pm, 6 pm, 9 pm, 12 am and 3 am, respectively; three young leaf samples collected at 3 am, 12 pm, and 6 pm, respectively; and four non-leaf samples (i.e., meristem, rhizome, root, stem) collected at 9 am. Total RNA was extracted from each of the 15 samples. For each individual RNA sample, a strand-specific sequencing library was constructed as described (Wang et al. 2011; Zhong et al. 2011). mRNA was purified by Oligo(dT)25 Dynabeads and fragmented at 94degreeC for 5 min, with an average RNA fragment length of ~230 nt. Sequencing was performed in a v3 flowcell on an Illumina HiSeq 2000 sequencer, using the TruSeq Paired-End Cluster Kit v3 (Illumina PE-401-3001) and the TruSeq SBS HS Kit v3 200 cycles (Illumina FC-401-3001). The sequence reads from all the 15 RNA samples were pooled to form one mixed library. The reads were filtered on the following criteria: (1) a Q20 quality cutoff; and (2) not containing Ns.Reference:Wang L, Si Y, Dedow LK, Shao Y, Liu P, Brutnell TP. 2011. A low-cost library construction protocol and data analysis pipeline for Illumina-based strand-specific multiplex RNA-seq. PloS one 6(10): e26426. Zhong S, Joung J-G, Zheng Y, Chen Y-r, Liu B, Shao Y, Xiang JZ, Fei Z, Giovannoni JJ. 2011. High-throughput illumina strand-specific RNA sequencing library preparation. Cold Spring Harbor Protocols 2011(8): pdb. prot5652."

{'tissue': 'YoungLeaf_06pm', 'cultivar': 'marginata', 'dev_stage': 'Young', 'biosamplemodel': 'Plant', 'biomaterial_provider': 'Xiaohan Yang'}

RNA-Seq of Agave americana: young leaf at 12 pm

"Two-year-old plants of Agave americana ?marginata? were grown under day/night temperatures of 25/15degreeC, day/night relative humidities of 45/75%, photoperiod of 12 h with a photosynthetic photon flux (PPF, 400 to 700 nm) of 540 ?mol m-2 s-1. A total of 15 samples were collected, including eight mature leaf samples collected at 6 am, 9 am, 12 pm, 3 pm, 6 pm, 9 pm, 12 am and 3 am, respectively; three young leaf samples collected at 3 am, 12 pm, and 6 pm, respectively; and four non-leaf samples (i.e., meristem, rhizome, root, stem) collected at 9 am. Total RNA was extracted from each of the 15 samples. For each individual RNA sample, a strand-specific sequencing library was constructed as described (Wang et al. 2011; Zhong et al. 2011). mRNA was purified by Oligo(dT)25 Dynabeads and fragmented at 94degreeC for 5 min, with an average RNA fragment length of ~230 nt. Sequencing was performed in a v3 flowcell on an Illumina HiSeq 2000 sequencer, using the TruSeq Paired-End Cluster Kit v3 (Illumina PE-401-3001) and the TruSeq SBS HS Kit v3 200 cycles (Illumina FC-401-3001). The sequence reads from all the 15 RNA samples were pooled to form one mixed library. The reads were filtered on the following criteria: (1) a Q20 quality cutoff; and (2) not containing Ns.Reference:Wang L, Si Y, Dedow LK, Shao Y, Liu P, Brutnell TP. 2011. A low-cost library construction protocol and data analysis pipeline for Illumina-based strand-specific multiplex RNA-seq. PloS one 6(10): e26426. Zhong S, Joung J-G, Zheng Y, Chen Y-r, Liu B, Shao Y, Xiang JZ, Fei Z, Giovannoni JJ. 2011. High-throughput illumina strand-specific RNA sequencing library preparation. Cold Spring Harbor Protocols 2011(8): pdb. prot5652."

{'tissue': 'YoungLeaf_12pm', 'cultivar': 'marginata', 'dev_stage': 'Young', 'biosamplemodel': 'Plant', 'biomaterial_provider': 'Xiaohan Yang'}

RNA-Seq of Agave americana: mixed tissue

"Two-year-old plants of Agave americana “marginata” were grown under day/night temperatures of 25/15degreeC, day/night relative humidities of 45/75%, photoperiod of 12 h with a photosynthetic photon flux (PPF, 400 to 700 nm) of 540 µmol m-2 s-1. A total of 15 samples were collected, including eight mature leaf samples collected at 6 am, 9 am, 12 pm, 3 pm, 6 pm, 9 pm, 12 am and 3 am, respectively; three young leaf samples collected at 3 am, 12 pm, and 6 pm, respectively; and four non-leaf samples (i.e., meristem, rhizome, root, stem) collected at 9 am. Total RNA was extracted from each of the 15 samples. For each individual RNA sample, a strand-specific sequencing library was constructed as described (Wang et al. 2011; Zhong et al. 2011). mRNA was purified by Oligo(dT)25 Dynabeads and fragmented at 94degreeC for 5 min, with an average RNA fragment length of ~230 nt. Sequencing was performed in a v3 flowcell on an Illumina HiSeq 2000 sequencer, using the TruSeq Paired-End Cluster Kit v3 (Illumina PE-401-3001) and the TruSeq SBS HS Kit v3 200 cycles (Illumina FC-401-3001). The sequence reads from all the 15 RNA samples were pooled to form one mixed library. The reads were filtered on the following criteria: (1) a Q20 quality cutoff; and (2) not containing Ns.Reference:Wang L, Si Y, Dedow LK, Shao Y, Liu P, Brutnell TP. 2011. A low-cost library construction protocol and data analysis pipeline for Illumina-based strand-specific multiplex RNA-seq. PloS one 6(10): e26426. Zhong S, Joung J-G, Zheng Y, Chen Y-r, Liu B, Shao Y, Xiang JZ, Fei Z, Giovannoni JJ. 2011. High-throughput illumina strand-specific RNA sequencing library preparation. Cold Spring Harbor Protocols 2011(8): pdb. prot5652."

{'tissue': 'Mixed_1', 'cultivar': 'marginata', 'biosamplemodel': 'Plant', 'biomaterial_provider': 'Xiaohan Yang'}