|
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
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|
|
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
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|
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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 |