Tailored Escherichia coli K12 strain MC4100 reference genome MYMC4100
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REPOSITORIES: ENA
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Project description:All metazoan eukaryotes express microRNAs (miRNAs), ~22 nt long regulatory RNAs that can repress the expression of mRNAs bearing complementary sequences. Several DNA viruses also express miRNAs in infected cells, suggesting a role in viral replication and pathogenesis. While specific viral miRNAs have been shown to autoregulate viral mRNAs or downregulate cellular mRNAs via novel target sites, the function of the majority of viral miRNAs remains unknown. Here, we report that the miR-K12-11 miRNA encoded by Kaposi’s Sarcoma Associated Herpesvirus (KSHV) shows significant homology to cellular miR-155, including the entire miRNA “seed” region. Using a range of assays, we demonstrate that expression of physiological levels of miRK12- 11 or miR-155 results in the downregulation of an extensive set of common mRNA targets, including genes with known roles in cell growth regulation. Our findings indicate that viral miR-K12-11 functions as an ortholog of cellular miR-155 and has likely evolved to exploit a pre-existing gene regulatory pathway in B-cells. Moreover, the known etiological role of miR-155 in B-cell transformation suggests the possibility that miR-K12-11 may contribute to the induction of KSHV positive B-cell tumors in infected patients. BJAB cells were infected and sorted 48 hours after infection. 12 to 16 days after transduction, gene expression analysis of 10 independent BJAB cell pools, expressing AcGFP only or AcGPF and miR-K12-11, was performed using Human Operon v3.0.2 arrays. Each ample was run against Universal Human Reference RNA, Stratagene. # of Arrays: BJAB = 3 AcGFP only = 10 AcGFP miR-K12-11 = 11
2007-12-18 | E-GEOD-8867 | biostudies-arrayexpress
Project description:Transcriptional profiling of BJAB cells expressing miR-K12-9 and BCBL cells treated with miR-K12-9 inhibitor. To identify host RNA targets of KSHV miRNAs, we took advantage of the observation that RNAs targeted by miRNAs often display small reductions in their steady-state levels, perhaps as a result of their impaired translation. Accordingly, we examined cellular transcript accumulation by array-based expression profiling under four sets of conditions in which KSHV miRNAs were expressed or inhibited.
2012-11-01 | GSE40093 | GEO
Project description:Transcriptional profiling of BJAB cells expressing miR-K12-9 and BCBL cells treated with miR-K12-9 inhibitor. To identify host RNA targets of KSHV miRNAs, we took advantage of the observation that RNAs targeted by miRNAs often display small reductions in their steady-state levels, perhaps as a result of their impaired translation. Accordingly, we examined cellular transcript accumulation by array-based expression profiling under four sets of conditions in which KSHV miRNAs were expressed or inhibited. Cells transfected with negative control miRNA compared to miR-K12-9 or negative miRNA inhibitor compared to miR-K12-9 inhibitor.
2012-11-01 | E-GEOD-40093 | biostudies-arrayexpress
Project description:Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.
2009-06-03 | E-MEXP-1872 | biostudies-arrayexpress
Project description:Sequencing of E. coli K-12 MC4100 mutant derivatives
| PRJNA320059 | ENA
Project description:Proteomics analysis in Escherichia coli K12 (E. coli K12) at DMP concentrations of 0 mg·kg-1 (CK) and 80 mg·kg-1 (DMP) revealed the toxicity of DMP
2022-01-02 | PXD030690 |
Project description:DNA microarrays were conducted on E. coli K12 cells stressed with 10 μM in N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine (TPEN). Overall, 260 genes varied in expression, 114 up-regulated and 146 down-regulated by Zn deprivation Keywords: TPEN stress
2008-12-31 | GSE11303 | GEO
Project description:All metazoan eukaryotes express microRNAs (miRNAs), ~22 nt long regulatory RNAs that can repress the expression of mRNAs bearing complementary sequences. Several DNA viruses also express miRNAs in infected cells, suggesting a role in viral replication and pathogenesis. While specific viral miRNAs have been shown to autoregulate viral mRNAs or downregulate cellular mRNAs via novel target sites, the function of the majority of viral miRNAs remains unknown. Here, we report that the miR-K12-11 miRNA encoded by Kaposi’s Sarcoma Associated Herpesvirus (KSHV) shows significant homology to cellular miR-155, including the entire miRNA “seed” region. Using a range of assays, we demonstrate that expression of physiological levels of miRK12- 11 or miR-155 results in the downregulation of an extensive set of common mRNA targets, including genes with known roles in cell growth regulation. Our findings indicate that viral miR-K12-11 functions as an ortholog of cellular miR-155 and has likely evolved to exploit a pre-existing gene regulatory pathway in B-cells. Moreover, the known etiological role of miR-155 in B-cell transformation suggests the possibility that miR-K12-11 may contribute to the induction of KSHV positive B-cell tumors in infected patients. Keywords: miRNA stable expression comparisons
2007-12-19 | GSE8867 | GEO
Project description:Brief description of the data submitted: Three LC-MS/MS files acquired using Data Dependent Acquisition (DDA) for
(1) NIST 1950 Frozen Human Plasma standard reference material subjected to reversed-phase chromatographic (RPC) metabolomic assay tailored for complex lipid separation;
(2) plasma Long-Term Reference (LTR) sample, routinely integrated in profiling studies at the National Phenome Centre for study-independent monitoring of precision, analysed by hydrophilic interaction liquid chromatography (HILIC) metabolomic assay tailored for small molecule polar metabolites;
(3) pooled Long-Term Reference (LTR) urine sample, routinely integrated in profiling studies at the National Phenome Centre for study-independent monitoring of precision, analysed by reversed-phase chromatographic (RPC) metabolomic assay tailored for small molecule metabolites.
Paper title: MS2Query: Reliable and Scalable MS2 Mass Spectral-based Analogue Search
Author list: Niek F. de Jonge, Joris R. Louwen, Elena Chekmeneva, Stephane Camuzeaux, Femke J. Vermeir, Robert S. Jansen, Florian Huber, Justin J.J. van der Hooft
Citation: bioRxiv 2022.07.22.501125; doi: https://doi.org/10.1101/2022.07.22.501125
2022-11-04 | MSV000090642 | MassIVE
Project description:Transcriptome sequencing of E.coli K12 in LB media in early exponential phase and transition to stationary phase
2010-10-20 | E-MTAB-387 | biostudies-arrayexpress