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Sample GSM4819885 Query DataSets for GSM4819885
Status Public on Dec 08, 2020
Title Ctrl H3K27ac Rep 2
Sample type SRA
 
Source name Skeletal muscle
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: Muscle stem cells
genotype: control
chip antibody: H3K27ac
Treatment protocol Cultured satellite cells were treated with siRNA targeting LncMyod for 48h before harvest
Growth protocol Satellite cells were isolated from mouse hindlimb and cultured in F10 supplemented with 10% HS and P/S
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Library was constructed using ChIPmentation protocol from Schmidl et al., (2015). Briefly, antibody-bound DNA was tagmented using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) and amplified to construct ChIP-seq library. Library was then sequenced using DNBSEQ-G400 sequencer (BGI) (2 x 100).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model DNBSEQ-G400
 
Data processing Reads were mapped to mm10 using bowtie2 v2.3.2 (Langmead et al., 2009) with default parameters.
Duplicates reads were marked using the MarkDuplicates module of Picard v2.9.2 with default settings. Unmapped and duplicate reads as well as read alignments with a mapping quality below 10 were removed using samtools v1.3 (Li et al., 2009) with parameters ‘-F 1540 -q 10 -b’.
Reads from sample replicates were pooled together into a single file using samtools v1.3 (Li et al., 2009).
For each individual sample replicate as well as pooled replicates, the predominant fragment length was estimated for use during peak calling using phantompeakqualtools v1.2 (Kharchenko, Tolstorukov & Park, 2008).
Relaxed narrow and broad peak calling to determine enriched regions was performed on individual sample replicates as well as pooled replicates using MACS2 v2.1.1 (Zhang et al., 2008) with treatment and control as input files and parameters ‘-g mm -p 1e-2 --nomodel --shift 0 --extsize {estimated fragment length from last step} -B --SPMR’.
Peaks called in the pooled replicates were kept and considered a consensus peak if they had at least a 50% overlap with peaks called in the individual replicates. This was done using intersect in bedtools v2.26.0 (Quinlan, Hall, 2010).
Fold-change signals were generated with the bdgcmp command in MACS2 v2.1.1 (Zhang et al., 2008) and then converted to BigWig format using the UCSC bedGraphToBigWig v332 tool.
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak files containing consensus peak calls of pooled samples; BigWig treatment over control fold change tracks
 
Submission date Oct 06, 2020
Last update date Dec 09, 2020
Contact name Tom Cheung
Organization name Hong Kong University of Science and Technology
Department Division of Life Science
Street address Clear Water Bay, Kowloon
City Hong Kong
ZIP/Postal code N/A
Country Hong Kong
 
Platform ID GPL28457
Series (1)
GSE159131 Histone modifications in LncMyoD-KD mouse muscle stem cells by ChIP-seq
Relations
BioSample SAMN16382359
SRA SRX9251424

Supplementary file Size Download File type/resource
GSM4819885_H3K27ac_ChIP_Ctrl2.bw 416.7 Mb (ftp)(http) BW
GSM4819885_H3K27ac_ChIP_Ctrl2_peaks.narrowPeak.gz 912.9 Kb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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