|
| Status |
Public on Mar 14, 2013 |
| Title |
PB_3_r |
| Sample type |
genomic |
| |
|
| Source name |
Peripheral blood
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
slide: 6929689021
array: R03C01
array_name: 6929689021_R03C01
sample_group: MS
smoking_evernever: E
smoking_5years: W5Y
ms_case_control: case
sample_year: 2009
age_sampling: 48
py: 17
smoke_free_years: 0
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted with the Sigma Gene Elute Mammalian Genomic DNA miniprep Kit, according to standard instructions.
|
| Label |
Cy3 and Cy5
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol
|
| Scan protocol |
Beachips were scanned using an iScan
|
| Description |
SAMPLE_3
Peripheral blood
|
| Data processing |
Raw intesities exported from GenomeStudio software were imported into R and analyzed with the Bioconductor lumi package. Probes on chromosomes X and Y were removed. Probes with a detection P-value > 0.01 exceeding 5% of the samples were also filtered out. Color-bias adjustment and quantile normalization were performed as implemented in lumi. BMIQ correction was applied to beta values to correct for probe type bias.
|
| |
|
| Submission date |
Feb 01, 2013 |
| Last update date |
Jun 27, 2017 |
| Contact name |
Francesco Marabita |
| E-mail(s) |
francesco.marabita@ki.se
|
| Organization name |
Karolinska Institutet
|
| Street address |
Karolinska University Hospital
|
| City |
Stockholm |
| ZIP/Postal code |
17176 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL13534 |
| Series (1) |
| GSE43976 |
An evaluation of analysis pipelines for DNA methylation profiling using the Illumina Human Methylation 450k platform |
|
