Project description:The RIL population used in this study is derived from a cross between parental lines B73 and H99, followed by 12 generations of self-pollination. In total 142 RILs were generated and 223 markers were used for mapping these RILs (Marino et al. (2009) Mol Genet Genomics, 281:163-179). The transcriptome of a randomly chosen subset of 103 RILs was analyzed in this study using RNA-seq.
Project description:In this study we used a maize multiparental advanced generation intercross (MAGIC) population, originating from nine parental lines (A632, B73, B96, F7, H99, HP301, Mo17, W153R and CML91) followed by 6 generations of self-pollination. A subset of 94 lines was chosen randomly from the set of 529 lines that was genotyped and phenotyped in the field (Dell'Aqua et al (2015) Genome Biology, 16:167) and sampled for RNA seq of proliferative tissue of growing leaf.
Project description:Following the domestication of maize over the past 10,000 years, breeders have exploited the extensive genetic diversity of this species to mold its phenotype to meet human needs. The extent of structural variation, including copy number variation (CNV) and presence/absence variation (PAV), which are thought to contribute to the extraordinary phenotypic diversity and plasticity of this important crop, have not been elucidated. Whole-genome, array-based, comparative genomic hybridization (CGH) revealed a level of structural diversity between the inbred lines B73 and Mo17 that is unprecedented among higher eukaryotes. A detailed analysis of altered segments of DNA conservatively estimates that there are several hundred CNV sequences among the two genotypes, as well as several thousand PAV sequences that are present in B73 but not Mo17. Haplotype-specific PAVs contain hundreds of single-copy, expressed genes that may contribute to heterosis and to the extraordinary phenotypic diversity of this important crop.
Project description:(1) The identification of genes that are transcriptionally regulated in response to exposure to hypoxia (~0.2% oxygen) in H99 (WT) and strains CM092 and CM098. (2) The identification of genes that are differentially-regulated in the strain CM093 compared to H99 (WT) Keywords: hypoxia response, comparative transcriptional hybridization
Project description:We measured protein translation (by ribosome profiling) and RNA levels (by polyA-enriched RNA-seq) in Cryptococcus neoformans strain H99 and Cryptococcus neoformans strain JEC21. This is the first transcriptome-wide map of translation in this species complex.
Project description:Comparison of transcriptional profiles of WT Cryptococcus neoformans (H99) and strain CM126 (pRPL2b-GAT201) which overexpresses the transcription factor GAT201 using a ribosomal protein promoter Keywords: Genetic modification
Project description:H99 derived 2 ug/mL uniconazole adaptors: Approximately 1 million cells of Crypotoccus neoformans lab strain H99 were spread on YPD-agar plate supplemented with 2 ug/mL uniconazole. After 5 days incubation of the plate at 30℃, randomly 30 adaptors were chosen. 21 adaptors were resistant and were sequenced. H99 derived 0.25 ug/mL uniconazole adaptors: Cells of H99 were adjusted to 2500 cells/mL. The culture was supplemented with 0.25 ug/mL uniconazole. After 72 h incubation, the culture was washed, diluted and approximately 200 cells were spread on YPD-agar plate. Randomly 95 colonies were tested for resistance to uniconazole. One colony (TJ3832) was resistant and was sequenced.
