|
| Status |
Public on Mar 23, 2023 |
| Title |
Estriol teatment [E3-CT] |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
UTERUS
|
| Organism |
Mus musculus |
| Characteristics |
agent: Estriol teatment
strain: CD-1
fraction: experimental (IP)
|
| Treatment protocol |
Pregnant CD-1 mice were then housed individually and continuously treated with E3 (50µl of 0.46mg/ml in DMSO to approximate human exposure) 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 treated with a single intraperitoneal injection of vehicle control (DMSO).
|
| 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: Estriol teatment
strain: CD-1
|
| Treatment protocol |
Pregnant CD-1 mice were then housed individually and continuously treated with E3 (50µl of 0.46mg/ml in DMSO to approximate human exposure) 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 treated with a single intraperitoneal injection of vehicle control (DMSO).
|
| 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 |
|
