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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Long non-coding RNAs and enhancer RNAs regulate the lipopolysaccharide-induced inflammatory response in human monocytes

ABSTRACT: Investigating the response of long non-coding RNA expression to LPS stimulation in human monocytes. This experiment is related to the microarray study E-MTAB-2408.

INSTRUMENT(S): Illumina Genome Analyzer IIx

ORGANISM(S): Homo sapiens

SUBMITTER: Nicholas Ilott

PROVIDER: E-MTAB-2399 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Long non-coding RNAs and enhancer RNAs regulate the lipopolysaccharide-induced inflammatory response in human monocytes.

IIott Nicholas E NE Heward James A JA Roux Benoit B Tsitsiou Eleni E Fenwick Peter S PS Lenzi Luca L Goodhead Ian I Hertz-Fowler Christiane C Heger Andreas A Hall Neil N Donnelly Louise E LE Sims David D Lindsay Mark A MA

Nature communications 20140609

Early reports indicate that long non-coding RNAs (lncRNAs) are novel regulators of biological responses. However, their role in the human innate immune response, which provides the initial defence against infection, is largely unexplored. To address this issue, here we characterize the long non-coding RNA transcriptome in primary human monocytes using RNA sequencing. We identify 76 enhancer RNAs (eRNAs), 40 canonical lncRNAs, 65 antisense lncRNAs and 35 regions of bidirectional transcription (RB ...[more]

PMID: 24909122

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Long non-coding RNAs and enhancer RNAs regulate the lipopolysaccharide-induced inflammatory response in human monocytes - microarray study

Project description:Investigating the response of long non-coding RNA expression to LPS stimulation in human monocytes. This experiment is related to the RNA-seq study E-MTAB-2399.

2014-04-25 | E-MTAB-2408 | biostudies-arrayexpress

Global mRNA transcriptome analysis of wild type and Hfq mutant strains of Serratia marcescens by RNAseq

Project description:In order to identify changes in the global mRNA transcriptome caused by deletion of the RNA-binding protein Hfq in Serratia marcescens, total mRNA was isolated from wild type Serratia marcescens Db10 and an otherwise isogenic strain carrying an in-frame deletion of the hfq gene (SMDB11_4482) and analysed by RNAseq. Four independent biological replicates were sequenced for each strain using the Illumina HiSeq platform. The data was used to identify the nature and extent of changes in transcript level between the two strains and to inform on the role of Hfq in virulence of Serratia marcescens, an opportunist bacterial pathogen.

2017-08-01 | E-MTAB-4501 | biostudies-arrayexpress

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2015-02-18 | E-GEOD-64349 | biostudies-arrayexpress

RNA-seq to identify the target genes of Pmar1 transcription factor in the Sea Urchin embryo

Project description:The transcriptome of embryos which overexpress Pmar1 is compared to the transcriptomes of embryos which do not express Pmar1. For this purpose, sea urchin embryo RNAs were prepared from 3 experimental conditions: over expression of Pmar, over expression of dominant negative cadherin (dnCad), non injected embryos (NI)

2023-06-16 | E-MTAB-12938 | biostudies-arrayexpress

mouse_F.tularensis

Project description:Eight week old female C57 Black mice were fasted for 24 hours prior to a single intraperitoneal injection of 350mg/kg of acetaminophen in phosphate buffer saline (PBS) (treatment group) or PBS (control group). The mice were euthanized at different time points post exposure (4, 24, or 48 hours after exposure to Francisella tularensis subspecies tularensis SchuS4).

2013-03-29 | E-MTAB-1571 | biostudies-arrayexpress

Combining transcriptome and proteome analysis to identify and characterize the RpoS regulon in Pseudomonas fluorescens

Project description:Background: Microorganisms are the major cause of food spoilage during storage, processing and distribution. Pseudomonas fluorescens is a typical spoilage bacterium that contributes to a large extent to the spoilage process of proteinaceous food. RpoS is considered an important global regulator involved in stress survival and virulence in many pathogens. Our previous work revealed that RpoS contributed to the spoilage activities of P. fluorescens by regulating resistance to different stress conditions, extracellular acylated homoserine lactone (AHL) levels, extracellular protease and total volatile basic nitrogen (TVB-N) production. However, RpoS-dependent genes in P. fluorescens remained undefined. Results: RNA-seq transcriptomics analysis combined with quantitative proteomics analysis basing on multiplexed isobaric tandem mass tag (TMT) labeling was performed for the P. fluorescens wild-type strain UK4 and its derivative carrying a rpoS mutation. A total of 375 differentially expressed genes (DEGs) and 212 differentially expressed proteins (DEPs) were identified in these two backgrounds. The DGEs were further verified by qRT-PCR tests, and the genes directly regulated by RpoS were confirmed by 5’-RACE-PCR sequencing. The combining transcriptome and proteome analysis revealed a role of this regulator in several cellular processes, including polysaccharide metabolism, intracellular secretion and extracellular structures, cell well biogenesis, stress responses, ammonia and biogenic amine production, which may contribute to biofilm formation, stress resistance and spoilage activities of P. fluorescens. Moreover, in this work we indeed observed that RpoS contributed to the production of the macrocolony biofilm’s matrix.

2019-11-12 | PXD010845 | Pride

BCAM0258 overexpression mutant

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2014-05-30 | E-MTAB-2079 | biostudies-arrayexpress

Genome-wide analysis of p53 transcriptional programs in B cells upon exposure to genotoxic stress in vivo [RNA-Seq]

Project description:The tumor suppressor p53 is a transcription factor that coordinates the cellular response to DNA damage. Here we provide an integrated analysis of p53 genomic occupancy and p53-dependent gene regulation in the splenic B and non-B cell compartments of mice exposed to whole-body ionizing radiation, providing insight into general principles of p53 activity in vivo. In unstressed conditions, p53 bound few genomic targets; induction of p53 by ionizing radiation increased the number of p53 bound sites, leading to highly overlapping profiles in the different cell types. Comparison of these profiles with chromatin features in unstressed B cells revealed that, upon activation, p53 localized at active promoters, distal enhancers, and a smaller set of unmarked distal regions. At promoters, recognition of the canonical p53 motif as well as binding strength were associated with p53-dependent transcriptional activation, but not repression, indicating that the latter was most likely indirect. p53-activated targets constituted the core of a cell type-independent response, superimposed onto a cell type-specific program. Core response genes included most of the known p53-regulated genes, as well as many new ones. Our data represent a unique characterization of the p53-regulated response to ionizing radiation in vivo. Total RNA profiling of gene expression in the splenic B and non-B cell compartments of wild-type and Trp53-/-mice exposed to whole-body ionizing radiation by Illumina sequencing

2015-08-24 | E-GEOD-71176 | biostudies-arrayexpress

Single-cell RNA-seq of the human Lineage– cells derived from the adipose stromal vascular fraction across depots

Project description:We used single-cell RNA-seq to characterize the heterogeneity of the human Lin- stromal vascular fraction across five adipose depots. We mollecularly assessed Lin- SVF cells from subcutaneous, omentum, mesocolic, and perirenal fat depots, as well as gallbladder-associated fat using 10x Genomics.

2023-09-30 | E-MTAB-12893 | biostudies-arrayexpress

Identification of expressed and conserved human non-coding RNAs

Project description:Methods: RNA profiles of 12 tissues were generated by deep sequencing using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: This work has focused on identification of non-coding RNAs expressed in human tissues. We have identified a set of non-coding RNAs that are both expressed and conserved, as described in the manuscript accompagnying this work. total RNA profiles of 12 normal human tissues, no replicates.

2013-09-01 | E-GEOD-45326 | biostudies-arrayexpress

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