|
| Status |
Public on Nov 06, 2018 |
| Title |
PL107_vc |
| Sample type |
genomic |
| |
|
| Source name |
genomic DNA from PL107 aCA placenta
|
| Organism |
Homo sapiens |
| Characteristics |
patient id: PL107
tissue: Chorionic villi
pathology group: non_chorioamnionitis
fetal sex: F
gestational age: 30
850k plate: WG5121338-msa4
850k sentrix_id: 200925700012
850k sentrix_position: R01C01
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA was extracted by standard salt method and purified using Qiagen DNeasy Kit according to standard instructions
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| Data processing |
Using R version 3.4.1. One amnion sample was removed from the analysis as it was a poor quality sample (sample not included in these GEO records). Array probes targeting sex chromosomes, with evidence of cross-hybridization, 59 rs probes, polymorphic probes, poor quality probes (detection p value >0.01 in >20 % of samples or <3 bead replicates in >20 % of samples) were eliminated.
Processed data matrices include: average beta (normalized by functional normalization and combat corrected for batch variables)
Signal intensities file includes: Methylated (signal A) and unmethylated (signal B) signal intensities
|
| |
|
| Submission date |
Jun 08, 2018 |
| Last update date |
Nov 06, 2018 |
| Contact name |
Wendy Robinson |
| E-mail(s) |
wprobinsonlab@gmail.com
|
| Organization name |
University of British Columbia
|
| Department |
Medical Genetics
|
| Lab |
Robinosn
|
| Street address |
950 W 28th Ave
|
| City |
Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V5Z 4H4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL21145 |
| Series (1) |
| GSE115508 |
DNA methylation profiling of acute chorioamnionitis-associated placentas and fetal membranes : insights into epigenetic variation in spontaneous preterm births |
|
