|
| Status |
Public on Dec 11, 2013 |
| Title |
female-NPA1 pool |
| Sample type |
genomic |
| |
|
| Source name |
female-NPA1_pool
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
cell type: T cell (CD3 positive)
state: NPA aggressivity trajectory
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
T cells were isolated from the PBMCs by immunomagnetic positive selection using CD3 dynabeads (Dynal). T cells DNA was extracted with Wizard Genomic DNA Purification kit (Promega) following the manufacturers protocol. Genomic DNA was quantified using Picogreen protocol (Quant-iT PicoGreen dsDNA Products, Invitrogen) and read on SpectraMAX GeminiXS Spectrophotometer. Bisulfite conversion was performed with 500 ng of genomic DNA using the EZ-96 DNA Methylation-Gold Kit (Zymo Research) according to the manufacturer's instructions.
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Infinium Assay Protocol
|
| |
|
| Hybridization protocol |
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol, except that 8ul of bisulfite converted material was used to initiate the amplification step.
|
| Scan protocol |
Arrays were scanned using the Illumina iScan Reader using standard recommended Illumina scanner settings.
|
| Description |
NPA aggressivity trajectory
pool female-NPA1 of T cell (CD3 positive) DNA methylation from NPA females
|
| Data processing |
Data analysis was performed using the Methylation module (version 1.9.0) of the GenomeStudio software (Illumina; version 2011.1). Significant differences in methylation levels between CPA and control groups were obtained using the Illumina custom method with a False Discovery Rate (FDR) < 0.05. Beta-values with detection P-value > 0.001 were removed from the analysis since they are considered to fall below the minimum intensity and threshold. All the probes that contained a SNP within 10 bp of the CpG site were excluded from the analysis to ensure equal annealing efficiency between the samples.
|
| |
|
| Submission date |
Dec 10, 2013 |
| Last update date |
Dec 11, 2013 |
| Contact name |
Moshe Szyf |
| E-mail(s) |
moshe.szyf@mcgill.ca
|
| Organization name |
McGill University
|
| Department |
Pharmacology
|
| Street address |
McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309
|
| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H3G 1Y6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE53191 |
DNA Methylation Signature of Childhood Chronic Physical Aggression in T Cells of Both Men and Women (Illumina) |
| GSE53193 |
DNA Methylation Signature of Childhood Chronic Physical Aggression in T Cells of Both Men and Women |
|
