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| Status |
Public on May 29, 2024 |
| Title |
H3K9me3_BPA_rep1 |
| Sample type |
SRA |
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| Source name |
cortex
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: cortex
age: 4 months
Sex: male
treatment: BPA (40 ug/kg bw/day)
mouse id: 800
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| 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.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cortex homogenate was used for H3K27me3 ChIP. As for H3K9me3, Nuclei was extracted from the cortex of male offspring and neuronal (NeuN+) nuclei were enriched by FACS sorting using MoFlo Astrios EQ cell sorter (Beckman Counter). nuclei were suspended in the MNase digestion buffer (10 mm Tris, pH 7.5, 4 mm MgCl2, and 1 mM Ca2+) and chromatin was digested with MNase at 28 ℃ for 10 min to obtain mononucleosomes and incubated with H3K9me3 (Abcam AB8898) and H3K27me3 (Millipore, 07-449) antibody at 4 ℃ overnight. The immunoprecipitated complexes were captured by Protein AG Magnetic Beads (Thermo Scientific 88803) and washed with 1 mL low-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris, 150 mM NaCl), 1 mL high-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris, 500 mM NaCl), 500 uL Lithium Cloride buffer (1% IGEPAL-CA 630, 1% Deoxycholic acid, 1 mM EDTA, 10 mM Tris, 0.25 M LiCl), 1 mL TE buffer (1 mM EDTA, 10 mM Tris). ChIP DNA was eluted in 60 uL Elution buffer (0.1M NaHCO3, 1% SDS) and incubated with RNase A, followed by proteinase K incubation. Finally, ChIP DNA was purified using SPRI magnetic beads (Beckman, B23318).
End-repairing (Lucigen Corporation, ER0720) and A-tailing (Lucigen Corporation, KL11101K) was performed and then ChIP DNA was ligated (Lucigen Corporation, LK0750H) with Y-adaptor (Vazyme, N802) and subjected to PCR amplification (Vazyme, N618-01).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Raw data were first analyzed by FastQC for quality control and then filtered out adaptor and low-quality reads by Trim-galore (--quality 20 --phred33 --stringency 1 --length 20) to obtain clean data.
clean data were mapped to the reference genome (UCSC, mm10) using Bowtie2 v2.4.1 with default settings.
SAMtools v1.6 were used to convert SAM files to BAM files, sort and build the alignment file index.
Bigwig files were generated using bamCoverage with parameters set as: --binSize 10 --normalizeUsing RPKM --effectiveGenomeSize 2652783500 --ignoreForNormalization chrX chrM
Assembly: mm10
Supplementary files format and content: Tab-delimited bigwig text files for each sample
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| Submission date |
Nov 30, 2023 |
| Last update date |
May 29, 2024 |
| Contact name |
Yan Jiang |
| E-mail(s) |
yan_jiang@fudan.edu.cn
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| Organization name |
Fudan University
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| Department |
Institutes of Brain Science
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| Street address |
131 Dongan rd
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| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE249014 |
Epigenetic profiling in adult brain after prenatal BPA exposure [ChIP-seq] |
| GSE249016 |
Epigenetic profiling in adult brain after prenatal BPA exposure |
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| Relations |
| BioSample |
SAMN38514894 |
| SRA |
SRX22690506 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7925189_H3K9me3_BPA_rep1.bw |
241.6 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
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