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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 08, 2020 |
| Title |
LncMyoD-KD MyoD Rep 1 |
| Sample type |
SRA |
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| Source name |
Skeletal muscle
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: Muscle stem cells
genotype: LncMyoD-KD
chip antibody: MyoD-ChIP
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| Treatment protocol |
Cultured satellite cells were treated with siRNA targeting LncMyod for 48h before harvest
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| Growth protocol |
Satellite cells were isolated from mouse hindlimb and cultured in F10 supplemented with 10% HS and P/S
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| 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).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
DNBSEQ-G400 |
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| 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
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| Submission date |
Oct 06, 2020 |
| Last update date |
Dec 09, 2020 |
| Contact name |
Tom Cheung |
| Organization name |
Hong Kong University of Science and Technology
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| Department |
Division of Life Science
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| Street address |
Clear Water Bay, Kowloon
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| City |
Hong Kong |
| ZIP/Postal code |
N/A |
| Country |
Hong Kong |
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| Platform ID |
GPL28457 |
| Series (1) |
| GSE159131 |
Histone modifications in LncMyoD-KD mouse muscle stem cells by ChIP-seq |
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| Relations |
| BioSample |
SAMN16382348 |
| SRA |
SRX9251434 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4819895_MyoD_ChIP_KD1.bw |
296.9 Mb |
(ftp)(http) |
BW |
| GSM4819895_MyoD_ChIP_KD1_peaks.narrowPeak.gz |
289.0 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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