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Sample GSM5966777 Query DataSets for GSM5966777
Status Public on Mar 23, 2023
Title Estradiol teatment [CT-E2]
Sample type genomic
 
Channel 1
Source name UTERUS
Organism Mus musculus
Characteristics agent: Estradiol teatment
strain: CD-1
fraction: experimental (IP)
Treatment protocol Pregnant CD-1 mice were then housed individually and continuously treated with vehicle control (DMSO) via a mini-osmotic pump (Alzet model # 1002) beginning on Day 9 of gestation.At the age of 6 weeks of offspring, the female offspring (N=12 per group) were ovariectomized; after 2 weeks they were treatedwith a single intraperitoneal injection of 300ng of estradiol (E2).
Growth protocol Eight-week-old CD-1 female mice were bred to male mice of the same strain and examined every 12 hours until the presence of a vaginal plug was detected. Detection of a vaginal plug was considered day 0.5 of pregnancy.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted using the Qiagen DNeasy Kit, following the manufacturer’s protocol including the RNase A treatment.The DNA was then sonicated on ice to a chromatin size range of 100 to 2,000 bp, with 700 bp average. Sonication efficiency was optimized and tested on agarose gel before performing Methylated DNA immunoprecipitation (MeDIP).Genomic DNA was extracted using the Qiagen DNeasy Kit, following the manufacturer’s protocol including the RNase A treatment.The DNA was then sonicated on ice to a chromatin size range of 100 to 2,000 bp, with 700 bp average. Sonication efficiency was optimized and tested on agarose gel before performing Methylated DNA immunoprecipitation (MeDIP).For MeDIP, DNA was incubated with 5 μg of a 5-methylcytosine antibody (Eurogentec, BI-MECY-0100) to immunoprecipitate methylated DNA fragments overnight, with agitation at 4 °C.
Label Cy5
Label protocol Samles labeled in parallel using the NimbleGen Dual-Color Labeling Kits. Cy3 Random and Cy5 Random Nonamers fromCy5-labeled experimental (IP) sample and Cy3-labeled control (input) sample.
 
Channel 2
Source name UTERUS
Organism Mus musculus
Characteristics fraction: control, input
agent: Estradiol teatment
strain: CD-1
Treatment protocol Pregnant CD-1 mice were then housed individually and continuously treated with vehicle control (DMSO) via a mini-osmotic pump (Alzet model # 1002) beginning on Day 9 of gestation.At the age of 6 weeks of offspring, the female offspring (N=12 per group) were ovariectomized; after 2 weeks they were treatedwith a single intraperitoneal injection of 300ng of estradiol (E2).
Growth protocol Eight-week-old CD-1 female mice were bred to male mice of the same strain and examined every 12 hours until the presence of a vaginal plug was detected. Detection of a vaginal plug was considered day 0.5 of pregnancy.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted using the Qiagen DNeasy Kit, following the manufacturer’s protocol including the RNase A treatment.The DNA was then sonicated on ice to a chromatin size range of 100 to 2,000 bp, with 700 bp average. Sonication efficiency was optimized and tested on agarose gel before performing Methylated DNA immunoprecipitation (MeDIP).Genomic DNA was extracted using the Qiagen DNeasy Kit, following the manufacturer’s protocol including the RNase A treatment.The DNA was then sonicated on ice to a chromatin size range of 100 to 2,000 bp, with 700 bp average. Sonication efficiency was optimized and tested on agarose gel before performing Methylated DNA immunoprecipitation (MeDIP).For MeDIP, DNA was incubated with 5 μg of a 5-methylcytosine antibody (Eurogentec, BI-MECY-0100) to immunoprecipitate methylated DNA fragments overnight, with agitation at 4 °C.
Label Cy3
Label protocol Samles labeled in parallel using the NimbleGen Dual-Color Labeling Kits. Cy3 Random and Cy5 Random Nonamers fromCy5-labeled experimental (IP) sample and Cy3-labeled control (input) sample.
 
 
Hybridization protocol Samles hybridization using NimbleGen Hybridization Kit, brifely adding solution to each sample Incubate at +95°C for 5 minutes, protected from light. Then place tubes at 42°C for at least 5 minutes.
Scan protocol NimbleGen MS 200 Microarray Scanner
Data processing Data were analyzed by using Roche NimbleGen Software DEVA
normalized_ratio, ks_test, Genes presenting a peak score greater than 3 were identified
 
Submission date Mar 23, 2022
Last update date Mar 24, 2023
Contact name Yuping Zhou
E-mail(s) joezhouyp@gmail.com
Organization name Yale
Department OB/GYN
Lab Taylor Lab
Street address 310 cedar street
City new haven
State/province CT
ZIP/Postal code 06511
Country USA
 
Platform ID GPL18163
Series (2)
GSE199213 The steroid hormone estriol (E3) regulates epigenetic programming of fetal mouse brain and reproductive tract [NimbleGen]
GSE199214 The steroid hormone estriol (E3) regulates epigenetic programming of fetal mouse brain and reproductive tract

Supplementary file Size Download File type/resource
GSM5966777_529665A03_2012-03-07_CT-E2_2012-03-08T135936_ks_test.gff.gz 5.9 Mb (ftp)(http) GFF
Processed data provided as supplementary file
Processed data are available on Series record

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