Yeast genomic DNA: SH6484 vs. FY834
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE19876 | GEO | 2010/05/17
SECONDARY ACCESSION(S): PRJNA121973
REPOSITORIES: GEO
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Project description:To detect genome amplification or deletion of genome reconstructed strain SH6484 compare to parental strain FY833. SH6484 genome was reconstructed using PCS technology. Keywords: Comparative genomic hybridization SH6484 vs. FY834. There are no biological replicates.
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Project description:Hybridization of amplified genomic DNA against unamplified genomic DNA using three different amplification methods to assess the bias introduced by amplification alone. Keywords: genomic DNA
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Project description:Klebsiella pneumoniae poses significant threat to global health. Detailed investigation to the nature of its interaction to human epithelial cells is still lacking. OmpR is an important regulator to the expression of major outer membrane protein genes, ompF and ompC. Here, we exploited the recently described dual RNA-seq to simultaneously measure genome-wide expression of host and pathogen two hours into infection. By comparing OmpR deleted strain to its wildtype parental strain, we, simultaneously, reconstructed OmpR regulon and deletion effect to host response.
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Project description:Despite being one of the first eukaryotic transcriptional regulatory elements identified, the sequence of a native TATA box and its significance remain elusive. Applying criteria associated with TATA boxes we queried several Saccharomyces genomes and arrived at the consensus TATA(A/T)A(A/T)(A/G). Approximately 20% of yeast genes contain a TATA box. Strikingly, TATA box-containing genes are associated with responses to stress, are highly regulated, and preferentially utilize SAGA rather than TFIID when compared to TATA-less promoters. Transcriptional regulation in yeast appears to be mechanistically bipolar, possibly reflecting a need to balance inducible stress-related responses with constitutive housekeeping functions. A strain containing amino terminal HA-tagged TBP and its parental untagged counterpart BY4741 (Resgen) were grown at 23?C in CSM to OD600 = 0.8-1.0. Cultures were shifted to 37?C for 5 minutes (to mimic heat treatments used elsewhere (Huisinga and Pugh, 2004)), then crosslinked at 23?C with 1% formaldehyde. ChIP was performed as described previously (Strahl-Bolsinger et al., 1997) with the some modification. Following cell disruption with glass beads, the chromatin was partially purified by centrifugation (Kurdistani and Grunstein, 2003). HA-TBP was immunopurified with 12CA5 antibody. After elution and reversal of the crosslinks, samples were subjected to non-specific amplification, labeling, and array hybridization as described (Bohlander et al., 1992; Chitikila et al., 2002). The amplification procedure was modified as follows. Following 15 round B amplification cycles, DNA was purified via QIAquick PCR Purification kit. Ten cycles were used in round C. Intergenic microarrays were generated by PCR amplification of entire intergenic regions of all yeast genes, then spotted onto glass slides. Spot intensities were filtered to remove any signal that was less then one standard deviation above local background. Three replicates were performed and their log2 ratios (enriched/input) were averaged. Keywords = Chromatin Immunoprecipitation Keywords = genome-wide binding Keywords: other
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Project description:A major goal of biology is the construction of networks that predict complex system behavior. We combine multiple types of molecular data, including genotypic, expression, transcription factor binding site (TFBS), and protein-protein interaction (PPI) data previously generated from a number of yeast experiments in order to reconstruct causal gene networks. Networks based on different types of data are compared using metrics devised to assess the predictive power of a network. A network reconstructed by integrating genotypic, TFBS and PPI data is shown to be the most predictive. This network is used to predict causal regulators responsible for hot spots of gene expression activity in a segregating yeast population. The network is also shown to elucidate the mechanisms by which causal regulators give rise to larger-scale changes in gene expression activity. Predictions are prospectively validated to provide direct experimental evidence that predictive networks can be constructed by integrating multiple, appropriate data types. Keywords: allele replacement Allele replacement strains were created in two backgrounds: BY (BY4724 and BY4742), and RM11-1a, and compared to the parental type (BY4716 and RM11-1a). BY7g, BY9g, BY11g are BY4716, while RM7g, RM9g, and RM11g are RM11-1a. YAD350 is a MKT1 D30G replacement strain in BY4742 background. YLK804 is a SAL1-RM allele in BY4724 and YLK806 is a SAL1-BY allele in RM11-1a. All strains were grown in YNB + 2% glucose, with leucine, lysine, and uracil. YAD350 was also grown with histidine.
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