dna methylation array platform  (INFINIUM Inc)

Journal: Schizophrenia research

Article Title: DNA hypermethylation of serotonin transporter gene promoter in drug naïve patients with schizophrenia

doi: 10.1016/j.schres.2013.12.007

Figure Lengend Snippet: The upper lines show original DNA sequence and the lower lines bisulfite modified DNA sequence assuming that all of cytosines (C) followed by guanine (G) are methylated. The candidate CpGs for methylation are in bold and gray. DNA sequences flanking the MSP and qMSP primer sites amplifying methylated (M) and unmethylated (U) products are underlined. The site corresponding to the Probe # CG26741280 of the Illumina DNA methylation array is underlined and bolded in original DNA sequence. There are two SP1 binding sites in 5-HTT promoter region which are marked with yellow color (GGGCGG and CCGCCC).

Article Snippet: Methods: Whole genome DNA methylation profiling was performed for a total of 24 samples (including two saliva samples) using the Illumina 450K DNA methylation array platform, followed by bisulfite sequencing to identify candidate CpGs for further analysis.

Techniques: Sequencing, Modification, Methylation, DNA Methylation Assay, Binding Assay

Journal: Schizophrenia research

Article Title: DNA hypermethylation of serotonin transporter gene promoter in drug naïve patients with schizophrenia

doi: 10.1016/j.schres.2013.12.007

Figure Lengend Snippet: A. Bisulfite sequencing of 5-HTT promoter region in representative samples for identification overall methylation pattern and partially methylated sites (indicated by arrows) for subsequent MSP and qMSP analysis. The original DNA sequence (top line) and bisulfite modified DNA sequence (bottom line) are placed at the top of sequence traces. The red segment of the bottom line shows a representative differentially methylated site. B. MSP analysis of a representative control (1), SCZ (2) and BD (3) using post-mortem brain samples. Placental DNA (P) was used as a negative control for methylation. C. MSP analysis of saliva DNA of a representative control subject (1) and a SCZ patient (2) using F1R1 qMSP primers. The β-Actin promoter amplified with primers designed from a CpG free region was used for the normalization of unmethylated (U) and methylated (M) products during qMSP analysis. L indicates a 100bp DNA ladder. D. Serial dilution of standard samples to optimize conditions for qMSP analysis in the test trials.

Article Snippet: Methods: Whole genome DNA methylation profiling was performed for a total of 24 samples (including two saliva samples) using the Illumina 450K DNA methylation array platform, followed by bisulfite sequencing to identify candidate CpGs for further analysis.

Techniques: Methylation Sequencing, Methylation, Sequencing, Modification, Control, Negative Control, Amplification, Serial Dilution

Journal: Schizophrenia research

Article Title: DNA hypermethylation of serotonin transporter gene promoter in drug naïve patients with schizophrenia

doi: 10.1016/j.schres.2013.12.007

Figure Lengend Snippet: A. There was higher promoter DNA methylation in SCZ patients compared to the controls and first degree relatives of SCZ patients (SCZ FM) at site A. Notably, SCZ patients and drug naïve SCZ patients (DN SCZ) exhibit higher degree of DNA methylation. Drug use in SCZ patients (DU SCZ) reduced 5-HTT promoter DNA hypermethylation. B. Similar to site A, the 5-HTT promoter DNA methylation in SCZ was higher than controls at site B, particularly in drug naïve patients.

Article Snippet: Methods: Whole genome DNA methylation profiling was performed for a total of 24 samples (including two saliva samples) using the Illumina 450K DNA methylation array platform, followed by bisulfite sequencing to identify candidate CpGs for further analysis.

Techniques: DNA Methylation Assay

Journal: Schizophrenia research

Article Title: DNA hypermethylation of serotonin transporter gene promoter in drug naïve patients with schizophrenia

doi: 10.1016/j.schres.2013.12.007

Figure Lengend Snippet: A: The Y axis indicates promoter DNA methylation of 5-HTT (site B) normalized with the PCR product of β-Actin promoter in SCZ and BD versus controls. B: The Y axis indicates relative expression of 5-HTT normalized with β-Actin expression. As shown, in SCZ the expression of 5-HTT is significantly less than controls as well as BD patients.

Article Snippet: Methods: Whole genome DNA methylation profiling was performed for a total of 24 samples (including two saliva samples) using the Illumina 450K DNA methylation array platform, followed by bisulfite sequencing to identify candidate CpGs for further analysis.

Techniques: DNA Methylation Assay, Expressing