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Sample GSM1827581 Query DataSets for GSM1827581
Status Public on May 04, 2017
Title TL myometrial epigenome
Sample type genomic
 
Channel 1
Source name 5mC MeDIP myometrium of women with term laboring (TL); London
Organism Homo sapiens
Characteristics pregnancy: term laboring (TL)
tissue: myometrium
term length: full-term
with or without labor: laboring
antibody: 5-methylcytosine (5mC) mAb (Eurogentec)
Extracted molecule genomic DNA
Extraction protocol Myometrial tissue was collected from the upper margin of a lower segment uterine incision at cesarean section as we have previously described. Any decidua and serosa were removed, and the remaining myometrium was flash frozen in liquid nitrogen and stored at -80°C before analysis. Labor was defined as the presence of regular uterine contractions (every 3–4 min), resulting in cervical effacement and dilation. The myometrial epigenome was compared in six groups of women: term laboring (TL, n = 11); term no labor consisting of two sets of tissues, one collected in San Antonio (TNL-san, n = 10) and one collected in London (TNL-lon, n = 9); preterm no labor (PTNL, n = 10); idiopathic preterm laboring (iPTL, n = 6); and twin gestations with preterm laboring (tPTL, n = 7). Genomic DNA was isolated from each myometrial tissue sample using DNeasy spin columns (Qiagen). Following isolation, DNA quality and quantity of all the isolations were measured using NanoDrop 2000 (Thermo Fisher Scientific) and each DNA sample was routinely examined by agarose gel electrophoresis with ethidium bromide staining to verify the absence of contaminating RNA and to determine the extent of genomic DNA degradation. Genomic DNA samples in each of the six groups were combined, resulting in six pools of DNA that were then subjected to methylated DNA immunoprecipitation (MeDIP) analysis.
Label Cy5
Label protocol Fragmented genomic DNA (10 ug) was denatured and immunoprecipitated using the mouse monoclonal antibody against 5-methylcytosine (clone 33D3, Eurogentec). A portion of the fragmented DNA (20%) was left untreated to serve as input control. Immunoprecipitated and input DNA were amplified using GenomePlex Complete Whole Genome Amplification (WGA2) Kit (Sigma-Aldrich). After cleanup with QIAquick PCR Purification columns (Qiagen), immunoprecipitated and input DNA were denatured and differentially labeled with fluorescent Cy5 and Cy3 dyes, respectively, using Dual-Color DNA Labeling Kit (Roche NimbleGen).
 
Channel 2
Source name Input myometrium of women with term laboring (TL); London
Organism Homo sapiens
Characteristics pregnancy: term laboring (TL)
tissue: myometrium
term length: full-term
with or without labor: laboring
antibody: none
Extracted molecule genomic DNA
Extraction protocol Myometrial tissue was collected from the upper margin of a lower segment uterine incision at cesarean section as we have previously described. Any decidua and serosa were removed, and the remaining myometrium was flash frozen in liquid nitrogen and stored at -80°C before analysis. Labor was defined as the presence of regular uterine contractions (every 3–4 min), resulting in cervical effacement and dilation. The myometrial epigenome was compared in six groups of women: term laboring (TL, n = 11); term no labor consisting of two sets of tissues, one collected in San Antonio (TNL-san, n = 10) and one collected in London (TNL-lon, n = 9); preterm no labor (PTNL, n = 10); idiopathic preterm laboring (iPTL, n = 6); and twin gestations with preterm laboring (tPTL, n = 7). Genomic DNA was isolated from each myometrial tissue sample using DNeasy spin columns (Qiagen). Following isolation, DNA quality and quantity of all the isolations were measured using NanoDrop 2000 (Thermo Fisher Scientific) and each DNA sample was routinely examined by agarose gel electrophoresis with ethidium bromide staining to verify the absence of contaminating RNA and to determine the extent of genomic DNA degradation. Genomic DNA samples in each of the six groups were combined, resulting in six pools of DNA that were then subjected to methylated DNA immunoprecipitation (MeDIP) analysis.
Label Cy3
Label protocol Fragmented genomic DNA (10 ug) was denatured and immunoprecipitated using the mouse monoclonal antibody against 5-methylcytosine (clone 33D3, Eurogentec). A portion of the fragmented DNA (20%) was left untreated to serve as input control. Immunoprecipitated and input DNA were amplified using GenomePlex Complete Whole Genome Amplification (WGA2) Kit (Sigma-Aldrich). After cleanup with QIAquick PCR Purification columns (Qiagen), immunoprecipitated and input DNA were denatured and differentially labeled with fluorescent Cy5 and Cy3 dyes, respectively, using Dual-Color DNA Labeling Kit (Roche NimbleGen).
 
 
Hybridization protocol Equal amounts (34 ug) of Cy5- and Cy3-labeled samples were combined and hybridized to each Human DNA Methylation 2.1M v2 genome tilling array (Roche NimbleGen) for 16-20 h at 42˚C using NimbleGen hybridization System 4. After washing, the hybridized arrays were dried using ArrayIt high-speed microarray centrifuge.
Scan protocol Arrays were scanned on NimbleGen MS 200 microarray scanner using NimbleGen Data Collection software.
Description 5mC MeDIP myometrium of women with term laboring (TL); London
Data processing Arrays were processed using the standard protocol (NimbleGen Arrays User’s Guide for DNA methylation analysis v1.0.
log2 (MeDIP/input) ratio in gff files.
 
Submission date Jul 20, 2015
Last update date May 04, 2017
Contact name Kohzoh Mitsuya
E-mail(s) mitsuya@uthscsa.edu
Phone 210-567-7064
Organization name University of Texas Health Science Center San Antonio
Department Center for Pregnancy and Newborn Research
Lab Leslie Myatt
Street address 7703 Floyd Curl Drive
City San Antonio
State/province Texas
ZIP/Postal code 78229-3900
Country USA
 
Platform ID GPL16284
Series (1)
GSE71123 MeDIP assay using human myometrium of women with preterm labor of different phenotypes vs. normal term labor

Supplementary file Size Download File type/resource
GSM1827581_TL_myometrial_epigenome.gff.gz 29.1 Mb (ftp)(http) GFF
GSM1827581_TL_myometrial_epigenome_Cy3.pair.gz 41.3 Mb (ftp)(http) PAIR
GSM1827581_TL_myometrial_epigenome_Cy5.pair.gz 41.2 Mb (ftp)(http) PAIR
Processed data provided as supplementary file

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