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| Status |
Public on May 29, 2024 |
| Title |
ATAC_Ctrl_rep2 |
| Sample type |
SRA |
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| Source name |
neuron
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: cortex
age: 4 months
Sex: male
treatment: Corn oil
mouse id: 767
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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 were homogenized in the lysis buffer (0.32 M sucrose, 5 mM CaCl2, 3 mM MgAce2, 0.1 mM EDTA, 10 mM Tris-HCl, pH = 8, 0.1% NP-40), and neuronal (NeuN+) nuclei were enriched by FACS sorting using MoFlo Astrios EQ cell sorter (Beckman Counter).
Chramotin were digested with 5 μl of Tn5 enzyme in 50 μl of digestion buffer (TD501-02, TruePrep DNA Library Preparation Kit V2, Vazyme, China) at 37 ◦C for 30 min. MinElute gel extraction kit (Qiagen, 28604) was used for DNA purification. Then, DNA was eluted in 24 μl of EB buffer and subjected to the PCR amplification with the reaction set as follows:24 μl of DNA,5 μl of PPM, 10 μl of 5 × TAB, 5 μl of N7 primer, 5 μl of N5 primer, and 1 μl of TAE buffer, and the PCR programming was: 72 ◦C for 3 min,98 ◦C for 30 s, 11 cycles of amplification: 98 ◦C for 30 s, 60 ◦C for 30 s, 72 ◦C for 30 s. Library DNA was purified using SPRI magnetic beads (Beckman, B23318) with a size between 150 bp and 500 bp was selected. The quality of the library was evaluated by Agilent 4200 TapeStation, and the concentration was measured with Qubit4. The library was then sent for sequencing on Novaseq6000 set paired-end, 150 bp (PE150).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| 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 parameters set as: -X 1000.
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) |
| GSE249015 |
Epigenetic profiling in adult brain after prenatal BPA exposure [ATAC-seq] |
| GSE249016 |
Epigenetic profiling in adult brain after prenatal BPA exposure |
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| Relations |
| BioSample |
SAMN38510686 |
| SRA |
SRX22686684 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7925195_ATAC_Ctrl_rep2.bw |
169.7 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
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