|
| Status |
Public on May 29, 2020 |
| Title |
GlcNAc_ChipSeq_3 |
| Sample type |
SRA |
| |
|
| Source name |
GlcNAc_ChipSeq
|
| Organism |
Mus musculus |
| Characteristics |
cell line: AinV15
cell type: Embryonic Stem (ES) Cells
chip antibody: O-linked N-acetylglucosamine (O-GlcNAc) Monoclonal antibody HGAC85 (Thermo, MA1-076, lot UD288370)
|
| Growth protocol |
Mouse ES cells were cultured in N2B27 medium supplemented with (PD0325901 (0.2 μM) and CHIR99021 (3 μM; both Sigma), 1% ES grade fetal bovine serum and leukemia inhibitory factor. ES cells were maintained on gelatin-coated (Sigma) plates at 37 °C in a 6% CO2 humidified chamber.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was carried out as previously described (Boulard et al., 2015) with a slight modification: chromatin was sonicated using a Covaris S220 Sonicator with peak power 150, duty factor 25, cycles/burst 200.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Illumina RTA and bcl2fastq2 (version 2.17) were used for basecalling and conversion to fastq files.
Reads were mapped to the mouse genome (mm10) using bowtie2 (v2.2.2) and default parameters. Duplicate reads were removed using samtools rmdups (v1.3.1). Bedgraph files were created using macs2 (v2.0.10) using -g 1.87e9, --SPMR, and -B flags. Bedgraph files were converted to bigWig using the UCSC genome browser toolkit.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files of normalized read counts (counts per million)
|
| |
|
| Submission date |
Apr 15, 2020 |
| Last update date |
May 29, 2020 |
| Contact name |
John R. Edwards |
| E-mail(s) |
[email protected]
|
| Organization name |
Washington University School of Medicine
|
| Department |
Center for Pharmacogenomics
|
| Street address |
660 S. Euclid Ave, Campus Box 8220
|
| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE93539 |
Protein O-GlcNAcylation Silences Methylated Promoters in Mammalian Genomes |
|
| Relations |
| BioSample |
SAMN14602531 |
| SRA |
SRX8120165 |
