Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1017805 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Chaperones have essential role in assist nascent peptides folding, prevent proteins aggregation and maintain cellular protein homeostasis. Considering spatial and temporal features of chaperones regulating in vivo, changes in single or combined chaperone-depleted E.coli strain is needed to be put into understand at transcriptional level. Here, we utilized expression microarrays to investigate global transcriptional response upon deletion of single or multiple chaperones in E. coli for understanding the transcriptional network affected by chaperones. To identify prokaryotic expression profiles in deletion of chaperones, several E.coli mutants were constructed in the following: Z116 (△tig 37℃), Z125(△dnaK37℃), Z625(△tig△dnaK 37℃ or 30℃), Z629(△tig△dnaK 30℃), NM (C-domain of tig was deleted 37℃), MC (N-domain of tig was deleted 37℃), NC (M-domain of tig was deleted 37℃). Two types of cDNA mixtures containing Cy3-labeled (or Cy5-labeled) control DNA (from BW25113) and Cy5-labeled (or Cy3-labeled) DNA targets (from mutant strain) were hybridized with E.coli microarrays in a dye-swap strategy.
2015-06-18 | GSE69912 | GEO
Project description:Chaperones have essential role in assist nascent peptides folding, prevent proteins aggregation and maintain cellular protein homeostasis. Considering spatial and temporal features of chaperones regulating in vivo, changes in single or combined chaperone-depleted E.coli strain is needed to be put into understand at transcriptional level. Here, we utilized expression microarrays to investigate global transcriptional response upon deletion of single or multiple chaperones in E. coli for understanding the transcriptional network affected by chaperones. To identify prokaryotic expression profiles in deletion of chaperones, several E.coli mutants were constructed in the following: Z116 (△tig 37℃), Z125(△dnaK37℃), Z625(△tig△dnaK 37℃ or 30℃), Z629(△tig△dnaK 30℃), NM (C-domain of tig was deleted 37℃), MC (N-domain of tig was deleted 37℃), NC (M-domain of tig was deleted 37℃). Two types of cDNA mixtures containing Cy3-labeled (or Cy5-labeled) control DNA (from BW25113) and Cy5-labeled (or Cy3-labeled) DNA targets (from mutant strain) were hybridized with E.coli microarrays in a dye-swap strategy. E.coli gene expression data of chaperone DnaK deletant compared control WT (BW25113). Please note that other mutant microarray data will be added in the future.
2015-06-18 | E-GEOD-69912 | biostudies-arrayexpress
Project description:E.coli and Synechococcus elongatus PCC 7942 WT and a Mutant werde cultivated under standard growth conditions (37 or 28 degree C) and then heat shocked in a heat bath for 15 min at 58 degree C. (OD600 0.6 or 0.750 0.5). 50 mL of cells were harvested before and after treatment. Cell pellets were extracted with 20% or 80% MeOH. n=5.
Column: Kinetex C18, 1.7 um EVO C18 100A, 50x2.1 mm. 500uL, 10min, 5-99%, DDA, Top5
2024-02-04 | MSV000094005 | MassIVE
Project description:E.coli and Synechococcus elongatus PCC 7942 WT and a Mutant werde cultivated under standard growth conditions (37 or 28 degree C) and then heat shocked in a heat bath for 15 min at 58 degree C. (OD600 0.6 or 0.750 0.5). 50 mL of cells were harvested before and after treatment. Cell pellets were extracted with 20% or 80% MeOH. n=5.
Column: Kinetex C18, 1.7 um EVO C18 100A, 50x2.1 mm. 500uL, 10min, 5-99%, DDA, Top5
2024-02-04 | MSV000094005 | GNPS
Project description:The histone chaperones play an important role in chromatin assembly and disassembly during replication and transcription. We assessed the global roles of histone chaperones in Saccharomyces cerevisiae. Microarray transcriptional analyses indicate that histone chaperones have their own specific target genes, and various histone chaperones have partially overlapping functions during transcriptional regulation. Histone deacetylase inhibitor TSA and histone chaperones Asf1, Vps75 and Rtt106 can function in parallel pathways to regulate transcription. Moreover, TSA can specifically antagonize histone chaperone Chz1-mediated telomere anti-silencing. This study demonstrates that a mutual cross-talk mechanism exists between histone chaperones and histone deacetylation in transcriptional regulation. All yeast strains used in this study are listed in the paper (Table S1). CHZ1, NAP1, ASF1, VPS75 and RTT106 genes were deleted individually by homologous recombination in BY4742 (WT) by using a previously described in (Wan, Y. et al. MCB, 2009) PCR-based procedure. The strains were cultured at 30°C in YPD (1% yeast extract, 2% peptone, 2% glucose) media. For TSA treatments, WT and deletion mutants were grown to mid-log phase (OD600=0.5), TSA (Sigma-Aldrich) was then added to the yeast cultures at a final concentration of 10 ?M and cells were cultured for additional hour.Total RNA was isolated by hot acid phenol extraction protocol as previously described in Wan, Y. et al. MCB, 2009. Microarray labeling and hybridization reactions were performed as previously described in Wan, Y. et al. MCB, 2009 and Wan, Y. et al. NAR, 2010. Two color microarrays, comparing RNA from the experimental conditions (deletion mutations grown in YPD, WT and deletion mutations grown in YPD with TSA treatment) to RNA from the control WT cells grown in glucose-containing medium (YPD), were performed using Agilent whole-genome S. cerevisiae arrays.
2011-06-28 | E-GEOD-30228 | biostudies-arrayexpress
Project description:Transcriptome comparison of E.coli W3110 (wild type), hha, ydgT, hns, stpA, hha_ydgT double and hns_stpA double mutant cells
2013-04-04 | E-MEXP-3811 | biostudies-arrayexpress
Project description:Listeria monocytogenes ATCC19115, post-subculture under 37 degree celsius
| PRJDB3370 | ENA
Project description:We have analyzed changes in gene expression, histone 3 lysine 4 dimethyl (H3K4me2) and histone 3 lysine 37 trimethyl (H3K27me3) levels in the embryonic cortex at E17.5 resulting from conditional deletion of BAF complex - i.e., double knockout of BAF155 and BAF170, in late cortical progenitors utilizing Cre expression under human GFAP (hGFAP) promoter (dcKO_hGFAP-Cre). Moreover, we also analyzed gene expression in WT E17.5 cortex treated with vehicle and Wnt inhibitor together with that of in dcKO_hGFAP-Cre cortex treated with Wnt inhibitor. Gene expression studies were conducted by RNA-Seq and histone marks were analyzed by ChIP-Seq.
2018-04-22 | GSE106711 | GEO
Project description:Escherichia coli release Extracellular Vesicles (EVs) which carry diverse molecular cargo. Pathogenic E.coli EVs contain virulence factors which assist during infection in the host in different mechanisms.The RNA cargo of E.coli EVs has not been assessed in their effect in the host. We used microarray data to asses and compare the global response of bladder cells to EV-RNA from pathogenic E.coli (Uropathogenic UPEC 536) and non-pathogenic E. coli (probiotic Nissle 1917)
2020-07-08 | GSE148711 | GEO