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| Status |
Public on Dec 31, 2022 |
| Title |
ATAC-seq_ST2 |
| Sample type |
SRA |
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| Source name |
microglia from whole brain (cerebellum and olfactory bulb removed)
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6Slac
gender: male
age: 5 month
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei was extracted from isolated microglia in 5 ml of lysis buffer (0.32M sucrose, 5 mM CaCl2, MgAce2, EDTA, Tris-HCl pH=8, w/o 0.1% NP-40) and collected by centrifugation.
ATAC-seq library was generated using reagents from TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501-02) according to the manuscript’s instruction with modifications.
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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 |
ATAC-seq: Raw data was first processed by FastQC for quality control, and cleaned using Trim-galore. Clean data were then aligned to the Mouse (mm10) reference genome using default settings of Bowtie2 v2.3.4.3. After removing duplications, Samtools v1.9 was used to sort and build the alignment file index. MACS2 was used for peak calling. Parameters were used as follows: --keep-dup 1 --shift -100 --extsize 200 –nomodel.
RNA-seq: Raw data was first processed by FastQC for quality control, and cleaned using Trim-galore. Clean data were then aligned to the Mouse (mm10) reference genome using default settings of Tophat2 v2.1.1. Then, samtools v1.9 was used to sort and build the alignment file index. Gene expression counts were generated using FeatureCounts v1.6.3. Differential analysis was conducted using DESeq2 and significant genes were selected with padj < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: ATAC-seq: ATAC_peak text files
Supplementary_files_format_and_content: RNA-seq: raw gene counts text files
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| Submission date |
Oct 28, 2021 |
| Last update date |
Dec 31, 2022 |
| 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 (1) |
| GSE186760 |
Epigenetic profiling of microglia-specific gene transcription and chromatin accessibility in mouse forebrain after chronic mild stress |
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| Relations |
| BioSample |
SAMN22645422 |
| SRA |
SRX12813375 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5660680_ATAC_ST2_peaks.narrowPeak.gz |
1.6 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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