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P52 transgenic expression with or without LPS in mouse lungs

ABSTRACT: To understand the mechanism by which p52 expression augments tumorigenesis, gene expression microarray analysis was performed using mRNA isolated from lungs of CCSP-p52 and WT mice on dox for 1 week to identify genes with altered expression in CCSP-p52 mice. The microarray dataset includes eight samples, with two replicates for each combination of two factors (p52 and LPS).Since samples with and without LPS stimulation were processed and microarray profiled at the same time, we assumed the random data variations were similar across all samples and built a linear model across the eight samples accounting for both p52 and LPS experimental factors. The coefficient (estimated log fold change) and p-value associated with the p52 factor were retrieved for the selection of differentially expressed genes. When selecting top-ranking p52-induced genes, only probe sets mapping to known genes and having positive expression changes were considered. While the used microarrays were Affymetrix Mouse Gene 1.0 ST arrays, in the later step of probe set annotation we used annotation table associated with Mouse Gene 1.1 ST (GPL11533 table). The Robust Multichip Average method implemented in R package “oligo” (v1.28.3) was employed to normalize imported raw data. Probe sets interrogating control, unmapped, or intron sequences were ignored, leaving 79% of probe sets for a differential expression analysis. Linear models and empirical Bayes methods implemented in R package “limma” (v3.20.8) were applied to estimate log fold changes and p-values for the p52-vs-WT effect.

ORGANISM(S): Mus musculus

PROVIDER: GSE71648 | GEO | 2017/11/22

SECONDARY ACCESSION(S): PRJNA291700

REPOSITORIES: GEO

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Project description:This series represent several subgroups of experiments designed to investigate the role of basal immunoglobulin signaling in immature B cell development. The first subgroup of arrays (Ctrl Mhi, Cre Mhi, Cre Mlo) was done to identify the changes in gene expression in immature B cells as a consequence of inducible deletion of surface IgM expression via Cre-LoxP mediated excision of Ig heavy chain. The second subgroup of arrays (GFPneg, GFPpos, FxE Ctrl, FxE HA) was done to identify the changes in gene expression in immature B cells as a consequence of blockade of tyrosine kinase signaling with herbimycin A treatment. The third subgroup of arrays (FxD, FxE, B6 Mneg, HEL Mhi) was done to establish gene expression profiles of immature B, pre B and pro B cells as reference platforms for the other two subgroups. (Tze etal. Public Library of Science Biology, 2005) The appended supplementary tables are described as follows: TABLE 1: Transformed array signal intensities used for statistical analysis. Listed are all probe sets excluding masked probe sets and Affymetrix hybridization control probe sets. Results are based on the following definitions: - Values with detection p values <0.1 were considered present. - Signal intensities with detection = "A" or with values < 20 were set to "20". TABLE 2: Genes differentially expressed between Ctrl Mhi and Cre Mlo cell populations and associated signal values. Results are based on the following definitions: - 2-fold or greater difference in means - difference in mean expression values > 200 - P < 0.01 (by Student's T test) TABLE 3: Probesets used for clustering in Figures 2 and 3 of publication TABLE 4: Probesets used for clustering in Figure 7 of publication TABLE 5: Correlation coefficients between all cell populations. Correlation coefficients were calculated as an additional method to demonstrate the relationship of the various cell populations to each other. Shown are the correlation coefficients generated using the mean expression values for each of the 101 transcripts from Figure 7 of publication. Keywords = bone marrow B cells

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P52 transgenic expression with or without LPS in mouse lungs

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