Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Genome wide analysis of gene expression in LPS stimulated splenic B cell.

ABSTRACT: Analysis of class switch recombination, maturation or differenciation of B cells at gene expression levels. The hypothesis tested in the present study was that TLR signaling in B cells plays an pivotal role for class switch, maturation and differenciation. Total RNA obtained from cultured splenic B cells. Gene expression compared between control and cKO B cells.

ORGANISM(S): Mus musculus

SUBMITTER: Takashi MaruYama

PROVIDER: E-GEOD-57837 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Control of Toll-like receptor-mediated T cell-independent type 1 antibody responses by the inducible nuclear protein IκB-ζ.

Hanihara-Tatsuzawa Fumito F Miura Hanae H Kobayashi Shuhei S Isagawa Takayuki T Okuma Atsushi A Manabe Ichiro I MaruYama Takashi T

The Journal of biological chemistry 20140814 45

Antibody responses have been classified as being either T cell-dependent or T cell-independent (TI). TI antibody responses are further classified as being either type 1 (TI-1) or type 2 (TI-2), depending on their requirement for B cell-mediated antigen receptor signaling. Although the mechanistic basis of antibody responses has been studied extensively, it remains unclear whether different antibody responses share similarities in their transcriptional regulation. Here, we show that mice deficien ...[more]

PMID: 25124037

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Project description:Environmental conditions are quite eﬀective during propagation and industrial application of Baker’s yeast (Saccharomyces cerevisiae). The change of temperature is one of the most important conditions which aﬀects the dough-leaving capacity of yeast cells. Accordingly, heat changes play an essential role in the commercial and economic impact of the yeast. Recent technologies in genomics have been used for analysis of global gene expression proﬁles such as microarray and RNA sequencing to solve the problems related with industrial application of yeast. Hereby, the aim of this study is to explore the eﬀects of heat stresses on global gene expression proﬁles and to identify the candidate genes for the heat stress response in commercial baker’s yeast by using microarray technology and comparative statistical data analyses. Data from all hybridizations and array normalization were analyzed using the GeneSpringGX 12.1 (Agilent) and the R 2.15.2 program language. In the analysis of this dataset, all required statistical methods are performed comparatively in each step and the best performed ones are used in further computations. Hence, as the ﬁrst step of the analyses, diﬀerent background normalization algorithms such as MAS5.0, RMA, MBEI and GC-RMA were applied and the algorithm which gives the most accurate ﬁndings was chosen for the normalization procedure. As a result, expression values, computed from CEL ﬁles, were processed by Robust Multiarray Analysis (RMA) which is the selected procedure for the normalization of the systematic diﬀerences between samples. In order to determine diﬀerentially expressed genes under heat stress treatments, two diﬀerent methods, namely, the fold-change and the hypothesis testing approaches are executed. In the fold-change method, various cut-oﬀ values are implemented while diﬀerent multiple testing procedures are performed for the hypothesis testing. Under the heat shock and temperature-shift stress conditions, up/down regulated diﬀerentially expressed probes were functionally categorized into the diﬀerent groups via the cluster analyses. Transcriptome changes under the heat shock and temperature-shift stress treatments show that the number of diﬀerentially up-regulated genes among the heat shock proteins (HSPs) and transcription factors (TFs) changed signiﬁcantly. Consequently, the identiﬁcation of thousands of genes related with heat stress treatments via microarray technology and comparative statistical analysis resulted in the creation of big picture which provides the understanding of the importance for the baker’s yeast industrial applications.

Dataset Information

Genome wide analysis of gene expression in LPS stimulated splenic B cell.

Publications

Control of Toll-like receptor-mediated T cell-independent type 1 antibody responses by the inducible nuclear protein IκB-ζ.

Similar Datasets

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