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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Genome-wide study of the MSL1 effect on gene expression and mRNA capping efficiency

ABSTRACT: Measurement of capping efficiency (by 5'CAP and 5'noCAP sequencing) in male (S2) and female (Kc) Drosophila melanogaster cells upon depletion of MSL1 by dsRNA compared to the eGFP RNAi control. The measurement of capping efficiency was combined with gene expression measurement by strand specific RNA-Seq in female (Kc) Drosophila melanogaster cells

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Charles Girardot

PROVIDER: E-MTAB-2235 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-wide study of the MSL1 effect on gene expression in Drosophila melanogaster

Project description:Measurement of gene expression by strand specific RNA-Seq in male (S2) Drosophila melanogaster cells upon depletion of MSL1 by dsRNA compared to the eGFP RNAi control.

2016-05-05 | E-MTAB-3434 | 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

H2S regulation the metabolism of cucumber in response to salt-stress through transcriptome and proteome analysis

Project description:In a previous study, we found that H2S alleviates salinity stress in cucumber by maintaining the Na+/K+ balance and by regulating H2S metabolism and the oxidative stress response. However, little is known about the molecular mechanisms behind H2S-regulated salt-stress tolerance in cucumber. Here, an integrated transcriptomic and proteomic analysis based on RNA-seq and 2-DE was used to investigate the global mechanism underlying H2S-regulated salt-stress tolerance. In total, 11 761 differentially expressed genes (DEGs) and 61 differentially expressed proteins (DEPs) were identified. Analysis of the pathways associated with the DEGs showed that salt stress enriched expression of genes in primary and energy metabolism, such as photosynthesis, carbon metabolism and biosynthesis of amino acids. Application of H2S significantly decreased these DEGs but enriched DEGs related to plant-pathogen interaction, sulfur-containing metabolism, cell defense and signal transduction pathways. Notably, changes related to sulfur-containing metabolism and cell defense were also observed through proteome analysis, such as Cysteine synthase 1, Glutathione S-transferase U25-like, Protein disulfide-isomerase and Peroxidase 2. We present the first global analysis of the mechanism underlying H2S regulation of salt-stress tolerance in cucumber through tracking changes in the expression of specific proteins and genes.

2021-09-09 | PXD020642 | Pride

Distribution of histone modificiation H3K27me3 in Drosophila Kc cells, comparison with dCTCF knockdown

Project description:Here we map the localization of H3K27me3 in Drosophila Kc cells, as well as in Drosophila Kc cells wherein dCTCF is knock down. examination of genomic occupancy for H3K27me3, control samples used for Drosophila Kc were previously described (Wood, Van Bortle et al., 2011 GSE30740)

2012-06-18 | E-GEOD-37444 | biostudies-arrayexpress

Kc cells from Drosophila melanogaster during ecdysone treatment and CP190 knockdown

Project description:This SuperSeries is composed of the following subset Series: GSE30686: Gene expression analysis of Kc cells from Drosophila melanogaster during ecdysone treatment and CP190 knockdown GSE30740: Distribution of Drosophila insulator proteins after ecdysone treatment in Kc cells Refer to individual Series

2011-10-13 | E-GEOD-30741 | biostudies-arrayexpress

Distribution of Drosophila insulator proteins DREF in Drosophila Kc167 cells

Project description:Here we map the localization of DREF Drosophila replication related element binding factor in Drosophila Kc cells. Examination of genomic occupancy for DREF, control samples used for Drosophila Kc were previously described (Wood, Van Bortle et al., 2011 GSE30740 and GSE32584). The GSM number for the input for Total Chip_seq data is GSM762849.

2013-05-01 | E-GEOD-39664 | biostudies-arrayexpress

Distribution of Drosophila insulator proteins Mod(mdg4) and L(3)mbt in Kc cells

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2012-06-18 | E-GEOD-36393 | biostudies-arrayexpress

Large-scale multi-species survey of metabolome and lipidome

Project description:This dataset was generated with the goal of comparative study of gene expression in three brain regions and two non-neural tissues of humans, chimpanzees, macaque monkeys and mice. Using this dataset, we performed studies of gene expression and gene splicing evolution across species and search of tissue-specific gene expression and splicing patterns. We also used the gene expression information of genes encoding metabolic enzymes in this dataset to support a larger comparative study of metabolome evolution in the same set of tissues and species. 120 tissue samples of prefrontal cortex (PFC), primary visual cortex (VC), cerebellar cortex (CBC), kidney and skeletal muscle of humans, chimpanzees, macaques and mice. The data accompanies a large set of metabolite measurements of the same tissue samples. Enzyme expression was used to validate metabolite measurement variation among species.

2014-05-30 | E-GEOD-49379 | biostudies-arrayexpress

Distribution of Drosophila insulator proteins after ecdysone treatment in Kc cells

Project description:Here we examine changes in the distribution of Drosophila insulator proteins during the ecdysone response. We performed ChIP-seq analysis in Kc cells at 0, 3, and 48 hours of ecdysone treatment with antibodies against CP190, Su(Hw), dCTCF, and BEAF-32B. Examination of 4 different insulator proteins at 3 time points of ecdysone treatment.

2011-10-13 | E-GEOD-30740 | biostudies-arrayexpress

Distribution of Drosophila insulator proteins during interphase and mitosis

Project description:Here we compare the distribution of insulator proteins during interphase and mitosis. We performed ChIP-seq analysis on purified populations of interphase and mitotic Kc cells, using antibodies against CP190, dCTCF, BEAF, and Su(Hw). Examination of 4 different insulator proteins during interphase and mitosis

2013-01-21 | E-GEOD-32584 | biostudies-arrayexpress

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