Similar Datasets
Project description:The transcriptional regulator MucR was identified as highly attenuated in a mutagenesis screen conducted by this laboratory. MucR has been described as a key regulator of exopolysaccharide synthesis in closely related Rhizobials soil symbionts. The goal of this study was to apply custom Brucella melitensis oligonucleotide microarrays to identify the regulatory targets of MucR. These studies revealed that MucR's regulation of exopolysaccharide synthesis is also conserved in Brucella melitensis and is also a key regulator of iron sequestering/storage and denitrification. Keywords: Microarray comparison of a genetically modified organism compared to wild type.
2010-04-23 | GSE13647 | GEO
Project description:The transcriptional regulator MucR was identified as highly attenuated in a mutagenesis screen conducted by this laboratory. MucR has been described as a key regulator of exopolysaccharide synthesis in closely related Rhizobials soil symbionts. The goal of this study was to apply custom Brucella melitensis oligonucleotide microarrays to identify the regulatory targets of MucR. These studies revealed that MucR's regulation of exopolysaccharide synthesis is also conserved in Brucella melitensis and is also a key regulator of iron sequestering/storage and denitrification. Keywords: Microarray comparison of a genetically modified organism compared to wild type. There are 3 biological replicates isolated from Brucella melitensis wild type 16M and from 16M∆mucR.
2010-04-23 | E-GEOD-13647 | biostudies-arrayexpress
Project description:Non-coding RNA (sRNA) are playing a key role in gene expression in bacteria. In general, sRNA regulates gene expression by base-pairing with ribosome binding sites to block translation. The modification of the ribosome trafficking generally affects mRNA stability. However, few examples have been described in bacteria where sRNA binding are mainly affected translation without modifying mRNA stability. In order to identify such targets in B. subtilis, we developed a pulsed-SILAC method allowing to label new protein synthesis after a short expression of the sRNA. We applied it to the best characterized sRNA in this bacteria, namely RoxS. RoxS sRNA was previously shown to interfere with the expression of genes encoding enzymes of the central metabolism to control the NAD/NADH ratio in B. subtilis.
2023-01-18 | MSV000091084 | MassIVE
Project description:MicroRNAs (miRNAs) are short noncoding RNA molecules regulating the expression of mRNAs. Target identification of miRNAs is computationally difficult due to the relatively low homology between miRNAs and their targets. We provide data here utilizing an experimental approach to identify targets of mmu-miR-378-3p, where mmu-miR-378-3p was overexpressed and silenced in NIH-3T3 murine fibroblasts and compared to control RNA transfected cells (RISC-free siRNA). Expression of mRNAs was profiled and differentially expressed genes following either treatment as compared to control transfected cells were identified. In this way we identified 491 significantly differentially expressed genes with more than 1.4 fold change in either comparison. One of the putative targets Akt-1 was subsequently confirmed by luciferase reporter assay.
2012-08-08 | GSE34873 | GEO
Project description:au07-04_vip1 - per8::vip micro-array - VIP1 early targets - estradiol-induced expression of VIP1-YFP and VIP1_D-YFP; 3h estradiol treatment. First comparison: non-induced versus induced. Second comparison: VIP1 lines versus YFP control line Keywords: treated vs untreated comparison
2009-01-23 | GSE13094 | GEO
Project description:miR-145 is downregulated in multiple cancers. The introduction of miR-145 could alleviate the tumor burden in the pancreatic cancer mouse model. However, how miR-145 mediates the tumor suppression is still an open question. In this study, we aimed to identify the targets of miR-145 using a SILAC approach.
2014-10-28 | PXD001260 | Pride
Project description:A glucocorticoid-regulated BBM protein (35S:BBM-GR) was used in combination with microarray analysis to identify genes directly activated by BBM. We employed the system described by (Lloyd et al., 1994) in which dexamethasone (DEX) and cycloheximide (CHX) are applied together to respectively, induce nuclear localization of the BBM-GR protein and prevent translation of the primary targets mRNAs. In this way it is possible to identify direct targets of a transcriptional activator by comparing gene expression profiles between DEX+CHX-treated transgenic and wild-type tissues. The ability of the 35S:BBM GR construct to induce somatic embryogenesis in Arabidopsis seedlings was determined by phenotypic observation of 35S:BBM GR seeds germinated and grown in the presence of 10 µM dexamethasone (DEX). As in 35S:BBM seedlings, we observed somatic embryo formation on the cotyledons, first leaves and shoot meristem of DEX-treated 35S:BBM GR seedlings. We identified a set of 20 genes (including BBM itself) and our analysis indicates that BBM directly activates a signaling pathway comprising transcription factors and other signaling molecules, but which does not initially include genes known to induce somatic embryogenesis, such as LEC1, LEC2 or WUS. The functions of the BBM target genes are unknown, however a number of them have recently been identified in microarray screens for meristem-expressed genes. The identification of BBM-interacting partners and downstream targets provides new tools for unraveling pathways related to plant cell growth and organogenesis. Keywords: transcriptional activation To identify candidate BBM targets, we treated 4 day old 35S:BBM-GR seedlings for 8 hours with 10 µM DEX in the presence of 10 µM CHX and compared the mRNA population from these seedlings using Arabidopsis Operon microarrays (http://www.ag.arizona.edu/microarray/) to that of 4 day old wild-type seedlings treated in the same way. The seed batches used in this analysis showed 100% EFS when grown continuously on media with 10 µM DEX. Four day old seedlings were chosen as the experimental material because they are highly responsive to BBM GR activation and provide sufficient RNA for the microarray experiments. The biological reproducibility of the data was monitored using two independent single locus 35S:BBM GR lines. The technical reproducibility of the data was monitored using two independently DEX + CHX-treated samples from each transgenic line. Dye effects were monitored in a dye-swap experiment using one of the four RNA samples from the two biological replicates
2010-06-25 | E-GEOD-3399 | biostudies-arrayexpress
Project description:Identification of AP2-O targets
| PRJNA252935 | ENA
Project description:Drosophila eye specification an development relies on a collection of transcription factors termed the retinal determination gene network (RDGN). Two members of this network, Eyes absent (EYA) and Sine oculis (SO), form a transcriptional complex in which EYA provides the transactivation function while SO provides the DNA binding activity. EYA also function as a protein tyrosine phosphatase, raising the question of whether transcriptional output is dependent or independent of phosphatase activity. To explore this, we used microarrays together with binding site analysis, quantitative real-time PCR, chromatin immunoprecipitation, genetics, and in vivo expression analysis to identify new EYA-SO targets. In parallel, we examined the expression profiles of tissue expressing phosphatase mutant eya and found that reducing phosphatase activity did not globally impair transcriptional output. Among the targets identified by our analysis was the cell cycle regulatory gene, string (stg), suggesting that EYA and SO may influence cell proliferation through transcriptional regulation of stg. Future investigation into the regulation of stg and other EYA-SO targets identified in this study will help elucidate the transcriptional circuitries whereby output from the RDGN integrates with other signaling inputs to coordinate retinal development. Keywords: gain of function, expression comparison
2007-11-07 | GSE9538 | GEO
Project description:This study identifies the transcriptomic effects of YBX3 depletion after 2 days of siRNA knockdown. Unspecific siRNA and untreated cells were used as controls. The cells were grown in SILAC media and the effects on protein levels were measured by mass spectrometry. Also an eCLIP (E-MTAB-5888) experiment was performed to identify RNA targets of YBX3.
2019-05-10 | E-MTAB-7455 | biostudies-arrayexpress