|
| 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 |
| E-mail(s) |
pswpjk0909@gmail.com
|
| 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 |
|
| Relations |
| BioSample |
SAMN24720871 |
| SRA |
SRX13654174 |
