Project description:These samples are being analyzed by the Duke-UNC-Texas-EBI ENCODE consortium. Expression from these cell types will compared to three whole genome open chromatin methodologies: DNaseI hypersensitivity (DNase-seq), Formaldehyde-Assisted Isolation of Regulatory elements (FAIRE-seq), and Chromatin Immunoprecipitation (ChIP-seq) . For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
Project description:The “Spanish influenza” of 1918 claimed an unprecedented number of lives, yet the determinants of virulence for this virus are still not fully understood. Here, we used functional genomics and an in vitro human lung epithelial cell infection model to define the global host transcriptional response to the eight-gene 1918 virus. To better understand the role of the 1918 virus NS1 gene, we evaluated the host response to A/Texas/36/91 (a seasonal isolate of human influenza virus) and a reassortant of A/Texas/36/91 containing the 1918 NS1 gene.
Project description:The M-bM-^@M-^\Spanish influenzaM-bM-^@M-^] of 1918 claimed an unprecedented number of lives, yet the determinants of virulence for this virus are still not fully understood. Here, we used functional genomics and an in vitro human lung epithelial cell infection model to define the global host transcriptional response to the eight-gene 1918 virus. To better understand the role of the 1918 virus NS1 gene, we evaluated the host response to A/Texas/36/91 (a seasonal isolate of human influenza virus) and a reassortant of A/Texas/36/91 containing the 1918 NS1 gene. A549 cells were infected at a MOI=2 with either A/Texas/36/91 (Tx/91) or A/Texas/36/91 (Tx/91) containing the NS1 gene from r1918 influenza. Virus was allowed to bind to cells for 1 h at 4M-BM-0C in serum-free infection medium supplemented with trypsin (1 g/ml). Mock-infected cells were treated with allantoic fluid instead of virus. Three replicate wells were used for each infection condition at each time point. Cells were harvested for array analysis at 2, 6, and 24hr post-infection. Cells from three individual cultures were pooled for each condition for microarray.
Project description:The vast majority of traditional almond varieties are self-incompatible and the level of variability of the species is very high, resulting in a highly heterozygosity genome. Therefore, information on the different haplotypes is particularly relevant to understand the genetic basis of trait variability in this species. However, although reference genomes for several almond varieties exist, none of them is phased and has genome information at the haplotype level. Here we present a phased assembly of genome of the almond cv. Texas. Our analysis shows that the “Texas” genome has a high degree of heterozygosity, both as SNPs, short indels, and structural variants (SV) level. Many of the SVs are due to heterozygous Transposable Element (TE) insertions, and in many cases they also contain genic sequences. In addition to the direct consequences of this genic variability on the presence/absence of genes, our results show that variants located close to genes tend to be associated with allele-specific gene expression (ASE), which highlights the importance of heterozygous SVs in almond.
