Project description:G. sulfurreducens was cultured on a variety of different iron concentrations and differential expression analysis was used to identify the iron stimulon. Wild type G. sulfurreducens was cultured on fresh water media with trace concentrations of iron (iron sufficient condition) as well as no trace iron (iron deficient condition). It was also cultured in ferric citrate (iron excess condition) media
Project description:Fur is a transcriptional regulator whose activity is dependent on Fe(II) concentrations. Chromatin immunoprecipitation (ChIP) coupled to microarray analysis allowed for the identification of Fur binding sites within the G. sulfurreducens genome. Wild type G. sulfurreducnes was cultured on fresh water media (harvested during log phase), and ChIP was used to identify Fur binding regions.
Project description:We applied a ChIP-chip approach to elucidate the binding profiles of RNAP and RpoD experimentally under different growth conditions. This technique localizes DNA fragments within DNA-protein complexes enriched by chromatin immunoprecipitation using high-density oligonucleotide tilling arrays. A 21 ChIP-chip study using immunoprecipitated DNA (IP-DNA) from three culture conditions for RNAP and four culture conditions for RpoD. The high-density oligonucleotide tiling arrays used consisted of 381,174 oligonucleotide probes spaced 20 bp apart (30-bp overlap between two probes) across the G. sulfurreducens genome (NimbleGen). Experiments were conducted as three bioliogical replicates (different cultures).
Project description:This SuperSeries is composed of the following subset Series: GSE22497: Transcriptome analysis of Geobacter sulfurreducens under multiple growth conditions GSE22503: ChIP-chip of Geobacter sulfurreducens PCA with antibody against RNAP and RpoD under various conditions GSE22511: Genome-wide transcription start site determination of Geobacter sulfurreducens under multiple growth conditions Refer to individual Series
Project description:This SuperSeries is composed of the following subset Series: GSE21312: Gene expression in a Geobacter sulfurreducens strain adapted for faster Fe(III) oxide reduction grown with ferric citrate as an electron acceptor GSE21313: Gene expression in a Geobacter sulfurreducens strain adapted for faster Fe(III) oxide reduction grown with fumarate as an electron acceptor Refer to individual Series
Project description:We applied a ChIP-chip approach to elucidate the binding profiles of sigma factors (RpH, RpoN and RpoS) experimentally under different growth conditions. This technique localizes DNA fragments within DNA-protein complexes enriched by chromatin immunoprecipitation using high-density oligonucleotide tilling arrays. A 10 ChIP-chip study using immunoprecipitated DNA (IP-DNA) from three culture condtions against three alternative sigma factors . The high-density oligonucleotide tiling arrays used were consisted of 381,174 oligonucleotide probes spaced 20 bp apart (30-bp overlap between two probes) across the G.sulfurreducens genome (NimbleGen). Experiments were conducted as three bioliogical replicates (different cultures).
Project description:Geobacter sulfurreducens PCA was put under selective pressure for rapid Fe(III) oxide reduction. The resultant strain, V1, contained five confirmed mutations and reduced Fe(III) oxide 17 times faster. One of these five mutations inactivates dcuB, a fumarate/succinate antiporter necessary for growth with fumarate as an electron acceptor. V1 dcuB+ is a V1 strain containing a wild type copy of dcuB. Whole genome DNA microarray analysis was performed in order to determine which genes are up- or down-regulated in V1 dcuB+ compared to PCA, both grown with fumarate as an electron acceptor. Three biological replicates were hybridized in duplicate. Experimental (V1) was labeled with cy5, control (wild type PCA) was labeled with cy3.
Project description:To investigate the whole-genome gene expression difference between the wild-type and capsule deletion mutant in Klebsiella pneumoniae MGH 78578. The mutants analyzed in this study are further described in Huang T.W., Stapleton J.C., Chang H.Y., Tsai S.F., Palsson B.O., Charusanti P. Capsule removal via lambda-Red knockout system perturbs biofilm formation and fimbriae extression in Klesiella pneumoniae MGH 78578 (manuscript submission) A six chip study using total RNA recovered from three separate wild-type cultures and three separate cultures of a capsule deltion mutant of Klebsiella pneumoniae MGH 78578. The capsule gene cluster (KPN_02493 to KPN_02515) was entirely removed in the capsule deletion mutant. Each chip measures the expression level of 5,305 genes from Klebsiella pneumoniae MGH 78578 and the associated five plasmids (pKPN3, pKPN4, pKPN5, pKPN6 and pKPN7) with 50-mer oligo tiling array with 30-mer spacer.
Project description:Investigation of comprehensive information about the transcripts (boundary, level, etc.) across the entire G. sulfurreducens genome in mulitple growth conditions, including in biofilm and on electrode. A five array study using total RNA recovered from two separate culture conditions of G. sulfurreducens. G. sulfurreducens were harvested one week after growth on electrode or to form biofilm. The high-density oligonucleotide tiling arrays used consisted of 381,174 oligonucleotide probes spaced 20 bp apart (30-bp overlap between two probes) across the G. sulfurreducens genome (NimbleGen). Experiments were conducted as two (electrode) or three (biofilm) biological replicates (different cultures).
Project description:Investigation of whole genome changes in six serotypes of Actinobacillus pleuropneumoniae in control cultures compared to bacteria grown in media containg the iron chelator 2,2'-dipyridyl. A 48 chip study using total RNA recovered from four different control cultures and four different iron depleted cultures of Actinobacillus pleuropneumoniea serotype 1 (4074), serotype 2 (4226), serotype 3 (1421), serotype 5b(L209, serotype 6 (7712640) and serotype 7 (WF87).