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| Status |
Public on Mar 01, 2021 |
| Title |
Dataset for Placental Genomic and Epigenomic Signatures in Infants Borns at Extremely Low Gestational Age [DNA methylation] |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by array
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| Summary |
These analyses set out to evaluate placental genomic and epigenomic signatures in newborns from the Extremely Low Gestational Age Newborns (ELGAN) cohort. Genome-wide mRNA, microRNA, and DNA methylation profiles were obtained from placenta samples collected at birth. Analyses were conducted to better understand placental molecular signatures and relate these to placental, maternal, infant, and later-in-life health indices.
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| Overall design |
This study involves the evaluation of patients from the ELGAN cohort, comprised of pregnancies that ended in livebirths prior to completing 28 weeks of gestation. Subjects were recruited from 2002 to 2004, and consisted of pregnant women scheduled to give birth at one of 14 participating institutions. Study procedures were approved by the Institutional Review Board at each of the 14 participating ELGAN sites, and consent was provided prior to hospital admission or soon after delivery. At or prior to delivery, maternal and demographic and clinical assessments were completed. A trained research nurse measured demographic and pregnancy variables after delivery using a structured questionnaire. Each infant’s anthropometric measures were recorded throughout hospitalization and at follow-up. Women participating in the ELGAN study also agreed to the collection of placenta samples. Immediately after delivery, placental tissue samples were collected and flash frozen in liquid nitrogen and stored at -80°C until processed. Placental tissue (~0.2g) was cut from the frozen biopsy sample and rinsed with sterile 1 X PBS to remove residual blood. Samples were then homogenized in Buffer RLT with β-mercaptoethanol (Qiagen, Valencia CA). An AllPrep DNA/RNA/miRNA Universal Kit (Qiagen, Valencia CA) was used to extract DNA and RNA. Illumina HiSeq 2500 was used to determine genome-wide mRNA expression profiles. The HTG EdgeSeq miRNA Whole Transcriptome Assay (HTG Molecular Diagnostics, Tucson, AZ) was used to evaluate genome-wide microRNA expression profiles. Extracted DNA samples were bisulfate-converted using the EZ DNA methylation kit (Zymo Research, Irvine, CA) and associated methylation levels quantification using the Infinium MethylationEPIC BeadChip (Illumina, San Diego, CA).
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| Contributor(s) |
Fry RC, Rager JE, Santos H, Roell K |
| Citation(s) |
35121757 |
| Submission date |
Feb 28, 2021 |
| Last update date |
Feb 25, 2022 |
| 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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| Platforms (1) |
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| Samples (411)
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| Relations |
| BioProject |
PRJNA705466 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE167885_DNAm_beta_values.csv.gz |
2.7 Gb |
(ftp)(http) |
CSV |
| GSE167885_RAW.tar |
5.8 Gb |
(http)(custom) |
TAR (of IDAT) |
| Processed data are available on Series record |
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