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Sample GSM5776726 Query DataSets for GSM5776726
Status Public on Jun 23, 2022
Title WT, control, ATAC-seq, rep1
Sample type SRA
Source name Mouse Embryonic Fibroblast (MEF)
Organism Mus musculus
Characteristics cell type: Mouse Embryonic Fibroblast (MEF)
genotype: WT
treatment: control
assay: ATAC-seq
Treatment protocol For glucose starvation samples, cells were treated with Glucose-free DMEM supplemented with dialyzed FBS for 24hrs
Growth protocol WT and Phf20-/- MEF cells were cultured at 37 ℃ in Dulbecco’s modified Eagle medium (DMEM)supplemented with 10 % fetal bovine serum (FBS) and ZellShield in a humidified incubator with 5 % CO2.
Extracted molecule genomic DNA
Extraction protocol For RNA-seq, RNA were harvested using Trizol and purified using Qiagen RNeasy Kit. For ATAC-seq, DNA was fragmented with Mnase. For ChIP-seq, crosslinked DNA was fragmented with sonication and IP with H3K4me1 or H3K4me2 antibody.
All of the libraries (RNA-seq, ATAC-seq and ChIP-seq) were constructed following standard Illumina library preparation protocol
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina HiSeq 4000
Description ATACseq_WT-CTL.merged.dedup.bigwig
Data processing ATAC-seq reads were mapped to mm10 reference using Burrows-Wheeler Aligner (BWA) MEM algorithm (version 0.7.12)
Peak-calling was performed using MACS2 (version 2.1.2) callpeak command with --nomodal --extensive 200 shift -100 -q 0.01 parameters
All Peaks are merged and read counts of each peaks are calculated using bedtools (v2.25.0)
The read counts were processed using DESeq2 (v1.26.0) to identity differentially opening peaks
Genome_build: mm10
Supplementary_files_format_and_content: bigwig format for genome coverage
Submission date Jan 07, 2022
Last update date Jun 23, 2022
Contact name Se Won Park
Organization name Seoul national university
Street address Gwanak-ro 1, Gwanak-gu, Seoul, Seoul Nat'l Univ Bldg504 Rm607
City Seoul
State/province Gwanak-Gu
ZIP/Postal code 08826
Country South Korea
Platform ID GPL21103
Series (2)
GSE193215 PHF20 Activates Autophagy Genes through Enhancer Activation via H3K36me2 Binding Activity [ATAC-seq]
GSE193393 PHF20 Activates Autophagy Genes through Enhancer Activation via H3K36me2 Binding Activity
BioSample SAMN24720871
SRA SRX13654174

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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