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| Status |
Public on Mar 01, 2021 |
| Title |
DNAm_Subject_3100381 |
| Sample type |
genomic |
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| Source name |
Placenta of infants born at low gestational age
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| Organism |
Homo sapiens |
| Characteristics |
tissue: placenta
birthweight (grams): 710
infant sex: Female
mage (age of mother) (years): 36.8
bmi (body mass index): 24.8
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Recruited patients from the ELGAN cohort that were scheduled to give birth at participating institutions between 2002 to 2004. Patients involved in the study comprised of pregnancies that ended in livebirths prior to completing 28 weeks of gestation. Maternal, demographic, and clinical assessments were taken before and after delivery. Each infant's anthropometric measures were recorded throughout hospitalization and at follow-up. Placenta samples were collected immediately after surgery and stored at -80 degrees C until further analysis. DNA molecules with 18 nucleotides or greater were extraced with the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen). and extracted DNA was bisulphate-converted using the EZ DNA methylation kit (Zymo Research, Irvine, CA), followed by quantification using the Infinium MethylationEPIC BeadChip (Illumina, San Diego, CA)
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| Label |
Cy3,Cy5
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| Label protocol |
Extracted DNA was bisulphate-converted using the EZ DNA methylation kit (Zymo Research, Irvine, CA), followed by quantification using the Infinium MethylationEPIC BeadChip (Illumina, San Diego, CA).
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| Hybridization protocol |
not provided
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| Scan protocol |
not provided
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| Data processing |
Raw idat files were loaded into R using the R package minfi
Samples were evaluated for potential sex mismatch, and probes were removed if they had detection p-values < .1 in more than 10% of samples
Raw data were normalized using functional normalization and normal-exponential out-of-band background correction using the R package minfi
Normalized data were corrected for batch effects using ComBat from the R package sva
Beta values are provided as a .csv, post normalization and QC
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| Submission date |
Feb 28, 2021 |
| Last update date |
Mar 01, 2021 |
| Contact name |
Julia Rager |
| E-mail(s) |
jrager@unc.edu
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| Phone |
9199662488
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| Organization name |
UNC
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| Street address |
135 Dauer Drive, CB 7431
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| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
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| Platform ID |
GPL21145 |
| Series (1) |
| GSE167885 |
Dataset for Placental Genomic and Epigenomic Signatures in Infants Borns at Extremely Low Gestational Age [DNA methylation] |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM5114877_202253620007_R01C01_Grn.idat.gz |
6.9 Mb |
(ftp)(http) |
IDAT |
| GSM5114877_202253620007_R01C01_Red.idat.gz |
7.1 Mb |
(ftp)(http) |
IDAT |
| Processed data are available on Series record |
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