Project description:We have developed a computational approach that uses self-organizing maps for integrative genomic analysis. We utilize this approach to identify the single-cell chromatin and transcriptomic profiles during mouse pre-B cell differentiation.
Project description:We have developed a computational approach that uses self-organizing maps for integrative genomic analysis. We utilize this approach to identify the single-cell chromatin and transcriptomic profiles during mouse pre-B cell differentiation.
Project description:Ixodes species ticks are competent vectors of tick-borne viruses including tick-borne encephalitis and Powassan encephalitis. Tick saliva has been shown to facilitate and enhance viral infection. This likely occurs by saliva-mediated modulation of host responses into patterns favorable for viral infection and dissemination. Because of the rapid kinetics of tick-borne viral transmission, this modulation must occur as early as tick attachment and initiation of feeding. In this study, the gene expression profile of cutaneous bite-site lesions created by uninfected ticks were analyzed at 1, 3, 6, and 12 hours after Ixodes scapularis nymphal tick attachment to discover host pathways or responses potentially important in tick-borne viral establishment. Four milimeter ear biopsies from BALB/cJ mice infested with Ixodes scapularis nymphs were assayed using Affymetrix genechip 430A 2.0 arrays at 1, 3, 6, and 12 hours after infestation during a primary exposure. 3 mice were measured at each time point. Controls were 3 similarly housed but tick-free mice.
Project description:Ixodes species ticks are competent vectors of tick-borne viruses including tick-borne encephalitis and Powassan encephalitis. Tick saliva has been shown to facilitate and enhance viral infection. This likely occurs by saliva-mediated modulation of host responses into patterns favorable for viral infection and dissemination. Because of the rapid kinetics of tick-borne viral transmission, this modulation must occur as early as tick attachment and initiation of feeding. In this study, the gene expression profile of cutaneous bite-site lesions created by uninfected ticks were analyzed at 1, 3, 6, and 12 hours after Ixodes scapularis nymphal tick attachment to discover host pathways or responses potentially important in tick-borne viral establishment.
Project description:Singapore grouper iridovirus (SGIV) is the major agent that causes severe iridovirus diseases in grouper maricluture. Based on the genomic information, a DNA microarray, containing probes corresponding to 162 putative SGIV open reading frames (ORFs), was constructed to map the viral gene transcriptional profiles over the time course by establishing the models of SGIV-infected GS cells and SGIV-infected grouper. All the data from real-time RT-PCR, RT-PCR and dilution RT-PCR assays were confirmed with the findings of microarrays, which were clustered into groups with the similarity expression profiles by the Self-Organizing Maps (SOMs) approach. The microarray analysis showed that SGIV had big differential expression profiles in the special infected cells and organ and the viral DNA replication mechanisms were firstly prevented as an important strategy of the host defense during the natural course infection.Our studies firstly uncover the relative of a marine viral gene expression patterns between in vitro and in vivo infection, which provides a better understanding of SGIV transcription regulation and a greater degree shared with other iridoviruses on their repliaction and pathogenesis. Keywords: time course
Project description:We report the ChIP-seq analysis of multiple Xenopus transcription factors binding. Also, we report loss-of-function transcriptomic analysis of Tcf7l1 by RNA-seq at different developmental stages. These newly generated datasets are analyzed using self-organizing maps, along with previously published Xenopus genomic data.
Project description:The 10 samples below represent a study where gene expression levels were measured in 5 different parts of the rat brain under cocaine-treated (GSM4696, GSM4698 - GSM4701) and saline-treated control (GSM4702 - GSM4706) conditions. The regions studied were amygdala (amy), caudate putamen (cpu), nucleus acumbens (na), prefrontal cortex (cpu), and the ventral tegmental area (vta). The data were analyzed using two different computational techniques, viz. singular value decomposition (SVD) and self-organizing maps (SOM), to identify a common set of genes that were regulated by cocaine administration.
