Computational protocol: Decreased Brain pH as a Shared Endophenotype of Psychiatric Disorders

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Protocol publication

[…] We used the following mouse brain transcriptome data: frontal cortex and hippocampal dentate gyrus (DG) of Shn2 KO mice (microarray) (), hippocampal DG of Camk2a HKO mice (microarray) (), and whole brains of Chd8 HKO mice (RNA-sequencing) (). Gene expression patterns in the frontal cortex of Camk2a HKO mice (n=6, 6) and hippocampal DG of Cn KO mice (n=6, 6) were analyzed via microarray (Mouse Genome 430 2.0 Array; Affymetrix, Santa Clara, CA), as previously described (). Gene expression patterns in the frontal cortex and hippocampal DG of Nrgn KO mice (n=5, 5) were analyzed via RNA-sequencing using the HiSeq platform in accordance with the manufacturer’s instructions (Illumina, San Diego, CA). A total of eight transcriptome data sets were used in the present study. Genes with an absolute fold change >1.2 and a t-test P-value <0.05 (mutants vs controls; without correction for multiple testing) were imported into the bioinformatics tool BaseSpace (Illumina), with which the gene expression data obtained from different platforms were matched (). Genes meeting the above criteria are included in . Genes with altered expression in at least four of the eight data sets (yielding 80 features; ) were selected based on the criteria of the BaseSpace tool and assessed for enrichment in biological themes using the DAVID functional annotation clustering tool, ADGO, and GOToolBox, in which the default feature listings and algorithm settings were used. […]

Pipeline specifications

Software tools BaseSpace, GOToolBox
Application RNA-seq analysis
Organisms Homo sapiens, Mus musculus
Chemicals Lactic Acid