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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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RNA-seq of rrp6 delta S. cerevisiae cells during Unfolded Protein Response time course

ABSTRACT: UPR Time course of rrp6 delta cells. ER stress induced by 1ug/mL Tunicamycin treatment. 3 time points: Untreated, Tm 2H , Wash 3H Untreated = no treatment T2 = two-hour Tm treatment (1ug/mL) T3= Wash 3H = wash of the cells after the two-hour Tm treatment and 3-hour recovery in medium without drug

INSTRUMENT(S): Illumina HiSeq 1500

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER:

PROVIDER: E-MTAB-13744 | biostudies-arrayexpress |

SECONDARY ACCESSION(S): E-MTAB-10511

REPOSITORIES: biostudies-arrayexpress

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RNA-seq of WT vs isw1 delta S. cerevisiae cells during Unfolded Protein Response time course

Project description:UPR Time course of WT and isw1delta cells. ER stress induced by 1ug/mL Tunicamycin treatment. 3 time points: Untreated, Tm 2H , Wash 3H Untreated = no treatment T2 = two-hour Tm treatment (1ug/mL) T3= Wash 3H = wash of the cells after the two-hour Tm treatment and 3-hour recovery in medium without drug

2022-10-06 | E-MTAB-10511 | biostudies-arrayexpress

Expression data of ex vivo and stimulated p14 TE (day 8) and p14 TM (day 46)

Project description:The spectrum of pathogen-specific CD8+T cell functionalities, including their chemokine production profiles, remains incompletely defined. Here, we have employed microarray analyses to determine the gene expression profiles of lymphocytic choriomeningits virus- (LCMV-) specific effector (TE) and memory (TM) CD8+T cells in the established p14 chimera model; analyses of p14 TE and TM expression profiles were conducted directly ex vivo and after 3h TCR engagement using aCD3 and aCD28 antibodies (note that the present ex vivo p14 TE and TM data have previously been uploaded in the context of a related study [GSE38462] and are included here due to analyses now conducted together with stimulated p14 TE and TM data).

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RNA-seq of roots of Schrenkiella parvula seedlings treated with 0mM or 175mM NaCl for 0 h, 3 h, 24 h and 48 h.

Project description:The purpose of the experiments is to understand transcriptional reprogramming in roots of halophyte Schrenkiella parvula (S. parvula) that may contribute to its high salt tolerance. Root materials were harvested from S. parvula seedlings grown on agar plates with ½ strength Murashige-Skoog (½MS) medium including vitamins for 4 days and transferred to ½MS medium supplemented with 0mM or 175mM NaCl for 0h, 3h, 24h or 48h.

2023-02-18 | E-MTAB-12424 | biostudies-arrayexpress

Sulfamethoxazole – Trimethoprim represses csgD but 2 maintains virulence genes at 30°C in a clinical 3 Escherichia coli O157:H7 isolate

Project description:The high frequency of prophage insertions in the mlrA gene of clinical serotype O157:H7 isolates renders such strains deficient in csgD-dependent biofilm formation but prophage induction may restore certain mlrA properties. In this study we used transcriptomics to study the effect of high and low sulfamethoxazole–trimethoprim (SMX-TM) concentrations on prophage induction, biofilm regulation, and virulence gene expression in strain PA20 under environmental conditions following five-hour and 12-hour exposures. SMX-TM at a sub-lethal concentration induced strong RecA expression resulting in concentration- and time-dependent major transcriptional shifts with emphasis on up-regulation of genes within horizontally-transferred chromosomal regions (HTR). Neither high or low levels of SMX-TM stimulated csgD expression at either time point, but both levels resulted in slight suppression. Full expression of Ler-dependent genes paralleled expression of group 1 pch homologues in the presence of high glrA. Finally, stx2 expression, which is strongly dependent on prophage induction, was enhanced at 12 hours but suppressed at five hours, in spite of early SOS initiation by the high SMX-TM concentration. Our findings indicate that, similar to host conditions, exposure to environmental conditions increased the expression of virulence genes in a clinical isolate but genes involved in the protective biofilm response were suppressed.

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Sequence database choice significantly affects taxonomic and functional metaproteomic results in gut microbiota studies

Project description:Elucidating the role of gut microbiota in physiological and pathological processes has recently emerged as a key research aim in life sciences. In this respect, metaproteomics (the study of the whole protein complement of a microbial community) can provide a unique contribution by revealing which functions are actually being expressed by specific microbial taxa. However, its wide application to gut microbiota research has been hindered by challenges in data analysis, especially related to the choice of the proper sequence databases for protein identification. Here we present a systematic investigation of variables concerning database construction and annotation, and evaluate their impact on human and mouse gut metaproteomic results. We found that both publicly available and experimental metagenomic databases lead to the identification of unique peptide assortments, suggesting parallel database searches as a mean to gain more complete information. Taxonomic and functional results were revealed to be strongly database-dependent, especially when dealing with mouse samples. As a striking example, in mouse the Firmicutes/Bacteroidetes ratio varied up to 10-fold depending on the database used. Finally, we provide recommendations regarding metagenomic sequence processing aimed at maximizing gut metaproteome characterization, and contribute to identify an optimized pipeline for metaproteomic data analysis.

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2025-04-02 | E-MTAB-14965 | biostudies-arrayexpress

Extracellular matrix remodeling enhancing astrocyte lysosome pathway to reverse memory defected in Alzheimer’s disease

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Transcriptome Analysis of ER Stress-Related Genes in Cyclocarya paliurus

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Acetylation enhances TET2 function in protecting against abnormal DNA methylation during oxidative stress [A2780 damage time points - methylation]

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