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| Status |
Public on Feb 26, 2021 |
| Title |
ES_2W_1_Muscle_ATAC |
| Sample type |
SRA |
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| Source name |
Muscle
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| Organism |
Sus scrofa |
| Characteristics |
breed: Enshi Black
tissue: muscle
age: 2 weeks
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Approximately 5 mg of tissue samples was crushed into a fine powder in liquid nitrogen.The pulverized tissues were suspended in 1mL ice-cold PBS and were gently spun down. The cell pellet was re-suspended in 1 mL lysis buffer (50 mM HEPES with pH 7.5, 140 mM NaCl, 1mM EDTA with pH 8.0, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100), followed by isolation of 50,000 nuclei using previously published protocol with minor modifications (Buenrostro et al., 2015). Then the transposition reaction mix (12.5 μL TD buffer, 10 μL ddH2O, and 2.5 μL TDE) was added to the isolated nuclei. The reaction system was incubated at 37 °C for 1 hour followed immediately by purification with the Qiagen MinElute PCR Purification Kit.
The transposed DNA fragments were amplified with the appropriate number of cycles as determined by qPCR. The amplified PCR products were quantified and sequenced using an Illumina Hiseq X ten PE150 platform.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Description |
individual 1
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| Data processing |
The clean data was obtained after removing reads with adapter contamination or low quality.
After checking and trimming the adapter with Cutadapt (version 1.14), the ATAC-Seq reads were mapped to pig susScr11.1 genome using Bowtie2 (version 2.3.4.1).
Low MAPQ reads (less than 25) and duplicated reads of mapped BAM files were removed with SAMTools v1.2 and Picard v1.126.
The narrow peaks and the bedgraph files of -log10(p-value) signal tracks for each replicate were called individually with MACS2 v2.1.0 (-g genome.size -p 0.01 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits) following the guide of ENCODE project ATAC-seq pipeline. It was download at https://github.com/kundajelab/atac_dnase_pipelines.
The narrow peaks were filtered with the cutoff for P<1E-05. The bigwig files of -log10(p-value) signal tracks were generated with MACS2 v2.1.0 and bedGraphToBigWig command based on bedgraph files from the previous step.
Genome_build: susScr11.1
Supplementary_files_format_and_content: Bigwig files of signal tracks and bed files of narrow peaks for each sample.
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| Submission date |
Jan 08, 2020 |
| Last update date |
Feb 27, 2021 |
| Contact name |
Shuhong Zhao |
| E-mail(s) |
shzhao@mail.hzau.edu.cn
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| Organization name |
Huazhong Agricultural University
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| Street address |
No.1,Shizishan Street, Hongshan District
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| City |
Wuhan |
| ZIP/Postal code |
430070 |
| Country |
China |
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| Platform ID |
GPL22918 |
| Series (1) |
| GSE143288 |
A compendium map of Cis-Regulatory Elements in the Pig Genome and epigenetic comparison with the human Genome |
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| Relations |
| SRA |
SRX7438571 |
| BioSample |
SAMN13676565 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4256388_ES_2W_1_Muscle_ATAC.bigwig |
1.1 Gb |
(ftp)(http) |
BIGWIG |
| GSM4256388_ES_2W_1_Muscle_ATAC.narrowPeak.gz |
4.7 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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