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Sample GSM5972950 Query DataSets for GSM5972950
Status Public on Mar 28, 2022
Title Zr3002-1
Sample type SRA
 
Source name Brain
Organism Mus musculus
Characteristics strain: CD-1
Sex: Female
treatment: Estriol
age: 8 weeks
tissue: frontal cortexes
genotype: wild type
Treatment protocol Detection of a vaginal plug was considered day 0.5 of pregnancy. Pregnant CD-1 mice were then housed individually and continuously treated with E3 (50µl of 0.46mg/ml in DMSO to approximate human exposure) or vehicle control (DMSO) via a mini-osmotic pump (Alzet model # 1002) beginning on Day 9 of gestation for 7 days.We began each experiment by treating pregnant mice with E3, and ended by analyzing their offspring.
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 Mouse hippocampus and frontal cortexes were removed and DNA was extracted using the Quick-DNA Microprep Kit (Cat#D3020) from Zymo research
Samples were sent to Zymo Research to process and analyze using the Methyl-MiniSeq Full Service library preparation. Briefly, libraries were prepared from 200-500 ng of genomic DNA digested with 60 units of TaqαI and 30 units of MspI (NEB) sequentially and then extracted with Zymo Research (ZR) DNA Clean & Concentrator TM-5 kit (Cat#: D4003). Fragments were ligated to pre-annealed adapters containing 5’-methyl-cytosine instead of cytosine according to Illumina’s specified guidelines (www.illumina.com). Adaptor-ligated fragments of 150–250 bp and 250–350 bp in size were recovered from a 2.5% NuSieve 1:1 agarose gel (ZymocleanTM Gel DNA Recovery Kit, ZR Cat#: D4001). The fragments were then bisulfite-treated using the EZ DNA Methylation-Lightning TM Kit (ZR, Cat#: D5020). Preparative-scale PCR was performed and the resulting products were purified (DNA Clean & ConcentratorTM - ZR, Cat#D4005) for sequencing on an Illumina HiSeq. Sequence alignments and data analysis
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 4000
 
Description FE311
FE311_vs_FCT14_CG_top3000.xlsx
FE311_vs_FCT14_CHH_top3000.xlsx
FE311_vs_FCT14.CG (1).csv
FE311_vs_FCT14.CHG.csv
Data processing Library strategy: Methylation mini-Sequencing
Sequence reads from bisulfite-treated Methyl-MiniSeq® libraries were identified using standard Illumina base calling software and then raw FASTQ files were adapter, filled-in nucleotides, and quality trimmed using TrimGalore0.6.4.FastQC0.11.8 was used to assess the effect of trimming and overall quality distributions of the data. Alignment to the mm10 reference genome was performed using Bismark0.19.0. Methylated and unmethylated read totals for each CpG site were called using MethylDackel0.4.0. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. Fisher’s exact test was performed on each CpG, CHG and CHH site that has at least 5x coverage.10% difference in methylation value between groups and a p-value (unadjusted) of < 0.05 was used to identify significantly differentially methylated cytosines. Promoter, gene body, and CpG island annotations were added for each CpG included in the comparison where available.
Assembly: mm10
Supplementary files format and content: Excel, CSV and gz files for each Sample
 
Submission date Mar 25, 2022
Last update date Mar 28, 2022
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 GPL21103
Series (2)
GSE199214 The steroid hormone estriol (E3) regulates epigenetic programming of fetal mouse brain and reproductive tract
GSE199434 The steroid hormone estriol (E3) regulates epigenetic programming of fetal mouse brain and reproductive tract [methylation]
Relations
BioSample SAMN26976162
SRA SRX14617542

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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