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| Status |
Public on Oct 31, 2022 |
| Title |
ATAC_M6 |
| Sample type |
SRA |
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| Source name |
Mouse prostate tumor cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: Mouse prostate tumor cells
strain: C57BL/6
treatment: treated with tamoxifen for 6 months
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
To reduce the amount of contaminating mitochondrial DNA, we performed an optimized ATAC-seq protocol. In brief, cells were collected and washed once with PBS. The cells were then lysed in ice-cold lysis buffer (10 mM Tris-HCl, pH 7.4; 10 mM NaCl; 3 mM MgCl2; 0.1% NP-40; 0.1% Tween 20; and 0.01% digitonin) for 3 min on ice. Immediately after lysis, nuclei were washed with 1 mL of wash buffer (10 mM Tris-HCl, pH 7.4; 10 mM NaCl; 3 mM MgCl2; and 0.1% Tween 20) and then centrifuged at 500 g for 10 min at 4 °C. To prepare sequencing libraries, a TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501) was utilized for the following steps.
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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 |
In brief, after raw reads were trimmed by TrimGalore-0.5.0, Bowtie2 was used to map the reads to the mm10 genome. Samtools-1.4 was further utilized for bam file sorting and indexing. The “bamCoverage” function of deepTools was utilized to generate .bw files with counts per million (CPM) normalization.
Genome_build: mm10
Supplementary_files_format_and_content: peak and bigWig
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| Submission date |
Dec 17, 2021 |
| Last update date |
Nov 01, 2022 |
| Contact name |
Fei Li |
| E-mail(s) |
lifei6@sibcb.ac.cn
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| Organization name |
Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences
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| Street address |
320 Yue-Yang Road Shanghai
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| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE191181 |
Evaluation of chromatin accessibility during prostate cancer progression |
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| Relations |
| BioSample |
SAMN24175410 |
| SRA |
SRX13445026 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5741227_ATAC-RC-1_L1_807D79.cpm.bw |
165.9 Mb |
(ftp)(http) |
BW |
| GSM5741227_ATAC-RC-1_L1_807D79_peaks.narrowPeak.gz |
559.1 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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