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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of Arabidopsis wild type (Col) and stomata mutant

ABSTRACT: As the gate for gas exchange and water vapor, stomata play an essential role in plant development. It has been a long time that many research focus on how the opening and closing of stomata is controlled. Until recently, studies on how stomata are formed in Arabidopsis just emerge. With a cluster of guard cells in one stomate in flp-1/myb88 mutant, it will be great interest to understand how FLP/MYB88 control stomata development. By taking advantaging of microarray technology, we intend to study a set of genes regulated by FLP/MYB88, which will facilitate us to better explore the biological functions of FLP/MYB88 in stomata development, even in the biotic or abiotic stresses. Experiment Overall Design: By comparing the gene expression differences between the wild type and stomata mutant--flp-1/myb88, we are trying to see which genes' transcripts are affected in flp-1/myb88 mutant.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Zidian Xie

PROVIDER: E-GEOD-12911 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Gene expression comparison between Arabidopsis wild type (Col) and stomata mutant

Project description:As the gate for gas exchange and water vapor, stomata play an essential role in plant development. It has been a long time that many research focus on how the opening and closing of stomata is controlled. Until recently, studies on how stomata are formed in Arabidopsis just emerge. With a cluster of guard cells in one stomate in flp-1/myb88 mutant, it will be great interest to understand how FLP/MYB88 control stomata development. By taking advantaging of microarray technology, we intend to study a set of genes regulated by FLP/MYB88, which will facilitate us to better explore the biological functions of FLP/MYB88 in stomata development, even in the biotic or abiotic stresses.

2009-09-01 | GSE12911 | GEO

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

Transcription profiling of Arabidopsis wild type and gl3 egl3 trichomeless mutant green seedling tissues

Project description:The development of trichomes (leaf hairs) from pluripotent epidermal cells in Arabidopsis provides a powerful system to investigate the regulatory motifs involved in plant cell differentiation. Genetic studies have revealed that a bHLH transcription factor, GL3, activates downstream genes required for trichome initiation by interacting with a R2R3-MYB protein, GL1. We have taken advantage of several mutants in the trichome developmental pathway and gene expression analyses to identify a set of genes expressed predominantly in Arabidopsis trichomes. Experiment Overall Design: We compared the gene expression between the wild type and trichome mutant, gl3 egl3 using green tissue (not include root).

2009-03-07 | E-GEOD-12522 | biostudies-arrayexpress

Transcription profiling of Arabidopsis wild type and trichomeless mutants

Project description:Trichomes are found on the leaf surface of many plant species. They can be classified into either glandular or non-glandular types. Glandular trichomes are usually multicelluar structures and have long been known to participate in defense against pathogens through the production of specialized chemical products. Non-glandular trichomes, such as those in Arabidopsis thaliana, have been hypothesized to have roles in physical defense against insects, UV protection, detoxification, and heat dispersal. However, it has been difficult to separate a physical role from other possible functions for non-glandular trichomes. We have taken advantage of several mutants in the trichome developmental pathway and gene expression analyses to identify a set of genes expressed predominantly in Arabidopsis trichomes. Experiment Overall Design: We compared the gene expression between the wild type and three trichomeless mutants: gl1, ttg1 and gl3egl1 to see which genes' transcripts are enriched in trichomes.

2008-06-16 | E-GEOD-9597 | biostudies-arrayexpress

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

Transcription profiling of human oral lesions treated with bioadhesive black rasberry gel to determine the effect on gene expression and proinflammatory proteins

Project description:This portion of the study evaluated the effects of topical 10% black raspberry gel application on gene expression profiles of premalignant oral lesions. Topical application of the bioadhesive black rasberry gel was observed to modulate gene expression and reduce proinflammatory proteins in human premalignant oral lesions. Experiment Overall Design: Each patient served as their own internal control. A pretreatment specimen of the premalignant lesion was obtained for baseline parameters. Following six weeks of treatment, the treated lesional tissue was removed. All tissue samples were immediately placed in RNA later and placed in a -80 degree freezer until sample preparation.

2008-06-18 | E-GEOD-10174 | biostudies-arrayexpress

Transcription profiling of human HDAC-42 SEG-1 esophageal adenocarcinoma cells

Project description:The role of acid and bile salts in the pathogenesis of esophageal carcinoma arising from Barrett's metaplasia has been well established. Cell proliferation of Barrett's epithelium in response to pulsatile acid exposure has since been confirmed in vivo using endoscopy specimens. Histone deactylases (HDACs) modulate nucleosomal packaging of DNA, thereby influencing gene transcription and multiple cancer-associated processes. Thus, we conducted microarray analysis to assess the ability of HDAC-42 to modulate key acid-induced changes as well as to impact other genes altered as the normal esophageal epithelium progresses along the metaplasia-dysplasia-esophageal adenocarcinoma continuum. Experiment Overall Design: SEG-1 cells were pretreated for 24 hours with vehicle or HDAC-42, pulsed with media or acidified media (pH 3.5; 20 mins at 37C), replenished with media or HDAC-42, and harvested 6 hours later. Global gene expression analysis was conducted using the human genome chip U133 2.0 Plus.

2008-06-15 | E-GEOD-7964 | biostudies-arrayexpress

Changes in polysome loading as a consequence of RHA downregulation

Project description:RNA helicase A (RHA) binds its target transcripts at the post-transcriptional control element (PCE) located in the 5â?? untranslated region (UTR). This interaction represents an â??RNA switchâ?? that regulates protein synthesis. Down regulation of RHA by siRNAs was used to identify transcripts with RHA-dependent translation. Reduced accumulation of RNA in polysomes was monitored with microarrays. Changes in cytoplasmic RNA steady state abundance was monitored as well. Sixty nine genes exhibit decreased transcript polysome association when subjected to RHA downregulation. A majority of the transcripts that experienced a reduction in the polysome fraction had no significant change in their cytoplasmic abundance (45 genes). Keywords: gene expression array-based Cytoplasmic lysates of cells treated with RHA targeted or non-silencing control siRNAs were separated by sucrose density gradient centrifugation. Ribosomal RNA profiles were generated, fractions containing polysomes were collected, and RNA was extracted.

2010-05-15 | E-GEOD-14055 | biostudies-arrayexpress

Transcription profiling of human SEG1 esophageal cell line treated with OSU-HDAC42, time series

Project description:Title: In vitro and in vivo effects of the orally bioavailable phenylbutyrate-derived histone deacetylase inhibitor OSU-HDAC42 on gene expression in esophageal tissues and in esophageal adenocarcinoma cells; Histone deacetylases (HDACs) modulate nucleosomal packaging of DNA, thereby influencing gene transcription and multiple cancer-associated processes. Thus, we conducted microarray analysis at multiple time-points to assess the ability of OSU-HDAC42, the S enantiomer of the previously published compound HDAC-42, to modulate key acid-induced changes as well as to impact other genes altered as the normal esophageal epithelium progresses along the metaplasia-dysplasia-esophageal adenocarcinoma continuum. Experiment Overall Design: SEG-1 cells were pretreated for 24 hours with vehicle or OSU-HDAC42, pulsed with acidified media (pH 3.5; 20 mins at 37C), replenished with media or OSU-HDAC42, and harvested 3, 6 and 24 hours later. Global gene expression analysis was conducted using the human genome chip U133 2.0 Plus.

2008-04-05 | E-GEOD-9974 | biostudies-arrayexpress

Transcription profiling of human

Project description:This SuperSeries is composed of the following subset Series:; GSE9974: The effect of the HDAC inhibitor OSU-HDAC42 on gene expression in esophageal tissues and adenocarcinoma cells I; GSE9976: The effect of the HDAC inhibitor OSU-HDAC42 on gene expression in esophageal tissues and adenocarcinoma cells II Experiment Overall Design: Refer to individual Series

2008-04-05 | E-GEOD-9987 | biostudies-arrayexpress

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