NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4256388 Query DataSets for GSM4256388
Status Public on Feb 26, 2021
Title ES_2W_1_Muscle_ATAC
Sample type SRA
 
Source name Muscle
Organism Sus scrofa
Characteristics breed: Enshi Black
tissue: muscle
age: 2 weeks
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.
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model HiSeq X Ten
 
Description individual 1
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.
 
Submission date Jan 08, 2020
Last update date Feb 27, 2021
Contact name Shuhong Zhao
E-mail(s) shzhao@mail.hzau.edu.cn
Organization name Huazhong Agricultural University
Street address No.1,Shizishan Street, Hongshan District
City Wuhan
ZIP/Postal code 430070
Country China
 
Platform ID GPL22918
Series (1)
GSE143288 A compendium map of Cis-Regulatory Elements in the Pig Genome and epigenetic comparison with the human Genome
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap