Project description:Perennial plants alternate between periods of active growth and periods of dormancy. Prerequisite to bud dormancy is the formation of an apical bud. Short day photoperiod in the fall induces bud formation in poplar. Transgenic plants overexpressing the bZIP transcription factor FD do not stop growing and do not form a bud. In order to better understand the molecular events leading to bud formation, we used microarrays to compare the transcriptomes of shoot tips of poplars overexpressing FD and wild type plants (1) grown under long day conditions and (2) collected after 3 weeks under short day conditions
Project description:Transcriptional profiling of an Fd-GOGAT1/GLU1 mutant in Arabidopsis thaliana reveals a multiple stress response and extensive reprogramming of the transcriptome Glutamate plays a central position in the synthesis of a variety of organic molecules in plants and is synthesised from nitrate through a series of enzymatic reactions. Glutamate synthases catalyse the last step in this pathway and two types are present in plants: NADH- or ferredoxin-dependent. Here we report a genome wide microarray analysis of the transcriptional reprogramming that occurs in leaves and roots of the A. thaliana mutant glu1-2 knocked-down in the expression of Fd-GOGAT1 (GLU1; At5g04140), one of the two genes of A. thaliana encoding ferredoxin-dependent glutamate synthase.
Project description:This experiment set contains the raw data for 8 arrays that were used in the genomic typing of the pre- and post-mouse H. pylori strains SS1 and SS2000. 10700 is the pre-mouse clinical isolate of SS1 and PMSS2000 is the pre-mouse clinical isolate of SS2000. gDNA from these strains were labeled and hybridized to H. pylori microarrays as described in Salama et al. {Salama et al. 2000 PNAS 97:14668-73}. In each case the test gDNA sample was labeled with Cy5 (red) and this was hybridized with Cy3 (green) labeled reference DNA of equal amount. The reference DNA consisted of equal amounts of gDNA from the two H. pylori strains used to make the H. pylori microarray, 26695 and J99. This data was used for the manuscript: L. J. Thompson, S. J. Danon, J.E. Wilson, J. L. O'Rourke, N. R. Salama, S. Falkow, H. Mitchell, and A. Lee. (2004) Chronic Helicobacter pylori infection in C57BL/6 and BALB/c mice using SS1 and a newly identified mouse-adapted strain (SS2000). Infect. Immun. (in press).
Project description:Current high-throughput single-cell RNA sequencing (scRNA-seq) methods are incompatible with paraformaldehyde (PFA) fixation, a common cell/tissue preservation and viral inactivation technique, which has prevented transcriptomic analysis of rare cells that require protein staining and enrichment. Here we present FD-seq, a method for high-throughput RNA sequencing of PFA-fixed, stained and FACS-sorted single cells. We used FD-seq to address two important questions in virology. First, by analyzing a rare population of cells supporting herpesvirus reactivation, we identified TMEM119 to mediate reactivation of Kaposi’s sarcoma-associated herpesvirus (KSHV), a tumor virus. Second, we studied the innate immune activation in cells infected with the coronavirus OC43, which causes the common cold and also serves as a safer model pathogen for SARS-CoV-2 studies. We found that pro-inflammatory cytokine induction, which is a major contributor to the severe pathogenicity in SARS-CoV-2-infected individuals, is primarily driven by uninfected or lowly infected bystander cells that are exposed to the virus but fail to express high level of viral genes. FD-seq is a simple method that is suitable for characterizing the transcriptome of rare cell populations of interest, and for studying high-containment biological samples such as SARS-CoV-2-infected cells after PFA inactivation.