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E-GEOD-55438 - Banking Placental Tissue: An Optimized Collection Procedure for Genome-Wide Analysis of Nucleic Acids [methylation]

Status
Released on 9 June 2014, last updated on 14 June 2014
Organism
Homo sapiens
Samples (48)
Array (1)
Protocols (5)
Description
Banking of high-quality placental tissue specimens will enable biomarker discovery and molecular studies on diseases involving placental dysfunction. Systematic studies aimed at developing feasible standardized methodology for placental collection for genomic analyses are lacking. To determine the acceptable timeframe for placental collection, we collected multiple samples from first and third trimester placentas at serial time points 0-120 minutes after delivery, simultaneously comparing the traditional snap-freeze technique to collection in commercial solutions designed to preserve RNA (RNAlaterTM, Ambion), and DNA (DNAgard®, Biomatrica). The performance of RNAlater for preserving DNA was also tested. Nucleic acid quality was assessed by determining the RNA integrity number (RIN) and genome-wide expression and DNA methylation microarray profiling. We found that samples collected in RNAlater had higher and more consistent RINs compared to snap frozen tissue, with similar RINs obtained for tissue collected in RNAlater as large (1 cm3) and small (~0.1 cm3) tissue pieces. RNAlater appeared to better stabilize the time zero gene expression pattern compared to snap freezing for first trimester placenta. Microarray DNA methylation analysis showed that overall the DNA methylation profiles remained quite stable over a two hour time period after removal of the placenta from the uterus, with the DNAgard condition being superior to both snap freezing and RNAlater. The collection of placental samples in RNAlater and DNAgard is simple, and eliminates the need for liquid nitrogen or a freezer on-site. Moreover, the quality of the nucleic acids and the resulting data from samples collected in these preservation solutions is actually higher than that from samples collected using the traditional snap-freeze method. Thus, this new approach to placental sample collection is both easier to implement in busy clinical environments and yields higher quality data. 48 samples In this study, our objective was to identify the optimal timing and mode of collection for nucleic acids of sufficient quality to perform genome-wide RNA gene expression and DNA methylation studies for downstream molecular and functional enrichment analysis. To do this, we evaluated three different placenta collection methods: snap freezing in liquid nitrogen, RNAlaterTM, and DNAgard, over a two-hour window upon removal from the uterus, to determine: 1) the optimal collection method(s) for evaluation of mRNA expression and DNA methylation; and 2) the time period after delivery during which such optimal samples should be collected.
Experiment type
methylation profiling by array 
Contacts
Rathi D Thiagarajan <rthiagarajan@ucsd.edu>, Francesca Boscolo, Jeanne F Loring, Jessica Kim, Louise C Laurent, Lynlee M Wolfe, Mana Parast, Rathi D Thagarajan, Ron Coleman, Veronique Tache, Wai K Kwan
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-55438.idf.txt
Sample and data relationshipE-GEOD-55438.sdrf.txt
Processed data (2)E-GEOD-55438.processed.1.zip, E-GEOD-55438.processed.2.zip
Additional data (1)E-GEOD-55438.additional.1.zip
Array designA-GEOD-13534.adf.txt
Links