7 protocols
AccessionType
normalization data transformation protocol
The analyses of the wheat roots transcriptome profiling involved 3 main-steps: 1) sequential mapping of reads to different reference datasets (UniGene-EST of T. aestivum, MicroRNAs-databank of T. aestivum and A. brasilense genome sequence); 2) de novo assembly of unmapped reads; and 3) mapping of unmapped reads to de novo assembled ESTs. The libraries were mapped to T. aestivum and A. brasilense sequence references using CLC Genomics Workbench 4.8, with a tolerance of 2 mismatches, and minimum length fraction of 0.9 to A. brasilense and 0.8 to T. aestivum and minimum similarity fraction of 0.8 for both. The unmapped reads were pooled and de novo assembled using CLC Genomics Workbench 4.8.
nucleic acid extraction protocol
RNAqueous (Ambion)
nucleic acid sequencing protocol
Fragment Multiplexing
nucleic acid sequencing protocol
Fragment Multiplexing
treatment protocol
T. aestivum seeds were surface-sterilized and germinated (in water agar plates) at 30 degrees C for 12 h under darkness. Germinated seedlings were transferred to sterile glass tubes containing 25 mL Hoagland nutrient solution (two seedlings per tube) and cultivated at 26 degrees C under 14 h light/10 h darkness for 24 h. Each tube were then inoculated with 0.25 mL of A. brasilense solution grown until optical density (600 nm) of 1.0. The inoculated seedlings were incubated for 3 days at 26 degrees C under 14 h light/10 h darkness.
nucleic acid library construction protocol
SOLiD Total RNA-Seq Kit (barcoded by Transcriptome Multiplexing Kit) (Life Technologies)
growth protocol
T. aestivum seeds were surface-sterilized and germinated (in water agar plates) at 30 degrees C for 12 h under darkness. Germinated seedlings were transferred to sterile glass tubes containing 25 mL Hoagland's nutrient solution (two seedlings per tube) and cultivated at 26 degrees C under 14 h light/10 h darkness for 24 h. In each tube were then added 0.25 mL of sterile Hoagland's nutrient solution and incubated for 3 days at 26 degrees C under 14 h light/10 h darkness.