GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM5776754 Query DataSets for GSM5776754
Status Public on Jun 23, 2022
Title WT, GlcStarv, ChIP-seq, H3K4me2
Sample type SRA
Source name Mouse Embryonic Fibroblast (MEF)
Organism Mus musculus
Characteristics cell type: Mouse Embryonic Fibroblast (MEF)
genotype: WT
treatment: Glucose starvation 24hr
assay: ChIP-seq
chip antibody: H3K4me2
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 ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
Data processing ChIP-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 --extensive 200 shift -100 parameters and control as corresponding input data.
The peaks were filtered by q-value < 0.01 and signal value > 5 and merged using bedtools (v2.25.0)
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 GPL24247
Series (2)
GSE193217 PHF20 Activates Autophagy Genes through Enhancer Activation via H3K36me2 Binding Activity [ChIP-seq]
GSE193393 PHF20 Activates Autophagy Genes through Enhancer Activation via H3K36me2 Binding Activity
BioSample SAMN24720767
SRA SRX13654028

Supplementary file Size Download File type/resource
GSM5776754_ChIPseq_WT-GS-H3K4me1.bigwig 117.5 Mb (ftp)(http) BIGWIG
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