 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 29, 2024 |
| Title |
RRBS_Ctrl_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
cortex
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: cortex
age: 4 months
Sex: male
treatment: Corn oil
mouse id: 701
|
| Treatment protocol |
Timed-pregnant C57BL/6Slac mice were randomly assigned into two groups, receiving either corn oil (Ctrl) or BPA (40 ug/kg bw/day) administered by oral gavage from gestational day 0.5 to 13.5.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei was extracted from cortex homogenates and incubated with 5 ul of 10 mg/mL RNaseA (Sigma R6513) in 500 ul PK lysis buffer (1 M Tris pH8, 50 mM EDTA, 2% SDS, 2 M NaCl) at 37 ℃ for 15 minutes, followed by 10 μl of 20 mg/mL proteinase K (Sigma P2308) incubation at 52 ℃ overnight. The samples were then added with phenol/chloroform (1:1) (Solarbio P1021), mixed with vortex, and centrifugated with 15000 g at RT for 10 minutes. The supernatant was taken and precipitated with isopropanol. The precipitated genomic DNA (gDNA) was washed in 70% ethanol, air dried and dissolved in buffer EB (Qiagen 19086). A total of 1 ug DNA was used for for RRBS library preparation.
gDNA was spiked in with unmethylated lambda DNA and incubated with MspI enzyme to obtain 200 to 1000 bp fragments. The DNA fragments were then subjected to bisulfite conversion for converting any unmethylated cytosine to Uracil by EZ DNA Methylation-Gold Kit (Zymo Research, United States). The Accel-NGS® Methyl-Seq DNA Library Kit (Swift, MI) was used for library preparation and 200-400 bp DNA fragments were purified for further sequencing.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
MspI
|
| Data processing |
Sequenced reads were filtered and trimmed with “fastp” () (version 0.23.4, -q 20 -u 50 -n 5)
Clean data were aligned to the mouse genome mm10 and lambda phage genome with Bowtie2 () (version 2.2.3) in default settings
Aligned reads were deduplicated with “deduplicate_bismark” function of Bismark (version 0.22.1).
The “bismark_methylation_extractor” function of Bismark (--no_overlap --ignore_r2 2 --comprehensive) were used to extract methylation information, and the bisulfite conversion rate was calculated according to the methylation level of spiked-in lambda DNA
Assembly: mm10
Supplementary files format and content: Tab-delimited coverage text files for each sample
|
| |
|
| Submission date |
Nov 30, 2023 |
| Last update date |
May 29, 2024 |
| Contact name |
Yan Jiang |
| E-mail(s) |
yan_jiang@fudan.edu.cn
|
| Organization name |
Fudan University
|
| Department |
Institutes of Brain Science
|
| Street address |
131 Dongan rd
|
| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE249013 |
Epigenetic profiling in adult brain after prenatal BPA exposure [RRBS] |
| GSE249016 |
Epigenetic profiling in adult brain after prenatal BPA exposure |
|
| Relations |
| BioSample |
SAMN38512511 |
| SRA |
SRX22687965 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7925171_RRBS_Ctrl_rep1.bismark.cov.gz |
10.3 Mb |
(ftp)(http) |
COV |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
