|
| Status |
Public on Dec 19, 2018 |
| Title |
Fibroblast Non_CD sample 28 from patient 15 |
| Sample type |
genomic |
| |
|
| Source name |
patient 15
|
| Organism |
Homo sapiens |
| Characteristics |
gender: F
disease state: Non_Crohn's Disease
disease stage: Non_Crohn's Disease
montreal score: None
age: 57
passage: 1
sampleID: 28
thiopurine usage: No
atnf usage: No
cell type: Ileal fibroblast
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from the fibroblasts using the QIAamp DNA mini kit (Qiagen, Valencia, CA), and bisulfite converted using the EZ DNA Methylation Kit (Zymo Research) according to manufacturer’s protocol. The bisulfite-converted DNA was subsequently analyzed on the Illumina HumanMethylation EPIC BeadChip Array at ServiceXS in Leiden, the Netherlands.
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina protocol
|
| |
|
| Hybridization protocol |
bisulphite converted DNA was hybridised to Illumina Infinium Human Methylation EPIC Beadchip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| Description |
200325570057_R08C01
|
| Data processing |
Minfi (v1.20.0) for reading the data; MethylAid (v1.8.0) for quality control
Unmethylated and methylated signal intensities in Series supplementary file
|
| |
|
| Submission date |
Jun 07, 2017 |
| Last update date |
Dec 19, 2018 |
| Contact name |
Peter Henneman |
| Organization name |
Academic Medical Center Amsterdam
|
| Department |
Clinical Genetics
|
| Lab |
Genome Diagnostics
|
| Street address |
Meibergdreef 9
|
| City |
Amsterdam |
| State/province |
Noord Holland |
| ZIP/Postal code |
1105 AZ |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL21145 |
| Series (1) |
| GSE99788 |
A distinct epigenetic profile distinguishes stenotic from non-inflamed fibroblasts in the ileal mucosa of Crohn's disease patients [methylation] |
|
