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Status |
Public on Nov 06, 2018 |
Title |
PL115_vc |
Sample type |
genomic |
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|
Source name |
genomic DNA from PL115 aCA placenta
|
Organism |
Homo sapiens |
Characteristics |
patient id: PL115 tissue: Chorionic villi pathology group: chorioamnionitis fetal sex: M gestational age: 29 850k plate: WG5121338-msa4 850k sentrix_id: 200889820041 850k sentrix_position: R07C01
|
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
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|
|
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
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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
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|
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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 |
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