Unknown,Transcriptomics,Genomics,Proteomics

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Expression data from patients with global developmental delay and autistic features and normal controls

ABSTRACT: We analyzed the whole-genome mRNA expression profiling of cultured lymphoblastoid cell lines (LCLs) from patients (n=2), carriers (n=2), and unrelated normal controls (n=3), all performed in duplicates using Affymetrix GeneChip Human Exon 1.0 ST arrays, to identify genes and pathways that are significantly dysregulated in affected individuals. Moreover, we have performed global transcriptional profiling in whole blood from patients (n=2) and healthy controls (n=13) using Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays. Global transcriptional profiling of affected individuals and controls revealed significant alterations of genes and pathways in a pattern consistent with previous microarray studies of autism spectrum disorder patients. Whole-genome mRNA expression profiles of samples from whole blood from patients with global developmental delay and autistic features (n=2) and healthy controls (n=13) using Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays.

ORGANISM(S): Homo sapiens

SUBMITTER: Dilek Colak

PROVIDER: E-GEOD-29691 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Recent studies have suggested that deregulated AKT1 signaling is associated with schizophrenia. We hypothesized that if this is indeed the case, we should observe both decreased AKT1 expression as well as deregulation of AKT1 regulated pathways in Peripheral Blood Mononuclear Cells (PBMCs) of schizophrenia patients. We therefore examined PBMC expression levels of AKT1 in schizophrenia patients versus controls, and examined whether functional biological processes in which AKT1 plays an important role are deregulated in schizophrenia patients. We performed a case-control study, investigating whole-genome PBMC gene expression in male, recent onset (<5 years) schizophrenia patients (N=43) as compared to controls (N=29). Genes, differentially expressed between patients and controls were identified using ANOVA with Benjamini-Hochberg correction (false discovery rate (FDR)= 0.05). Functional aspects of the deregulated set of genes were investigated with the Ingenuity Pathway Analysis (IPA) Software Tool. From each participant 30 ml of blood was drawn into heparinized tubes. All blood samples were obtained between 10.00 and 11.00 am to minimize diurnal variation. PBMC‚Äôs were isolated by Ficoll gradient separation, started within 20 minutes after the drawing of blood and performed with minimum time variation. Cells were subsequently disrupted (Qiashredder kit; Qiagen), and RNA was isolated (RNeasy minikit; Qiagen) with an additional DNAse digestion step (RNase-free DNase set; Qiagen), all according to the manufacturer‚Äôs protocol, diluted in nuclease free water, and frozen at ‚Äì80 C before use. Before freezing, RNA purity and quantity was assessed with the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). After thawing the isolated RNA was biotinylated into cRNA using the One-Cycle Target Labeling and Control Reagents Kit (Affymetric Co) according to the manufacturer‚Äôs protocol. Before hybridisation RNA quality and integrity was assessed using the Agilent 2100 BioAnalyzer (Agilent). Biotinylated cRNA was hybridized to the Affymetrix Human Genome U133 plus 2.0 GeneChip¬© microarray containing 54,675 probe sets (Affymetrix Co). Each sample was individually biotinylated and hybridized to an individual microarray. Biotinylation was performed in batches with randomisation of patients and controls according to their ratios across the batches. The arrays were scanned and analyzed using Affymetrix Microarray Suite 4.2 software. Scanning was performed in three batches with randomization of patients and controls according to their ratios across the batches. A case-control study, investigating whole-genome PBMC gene expression in male, recent onset (<5 years) schizophrenia patients (N=43) as compared to controls (N=29). Patients consisted of two subgroups: acutely admitted, severely psychotic (N=22), and remitted patients (N=21). Genes, differentially expressed between patients and controls were identified using ANOVA with Benjamini-Hochberg correction (false discovery rate (FDR)= 0.05).

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Expression data from patients with global developmental delay and autistic features and normal controls

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