|
| Status |
Public on Oct 26, 2020 |
| Title |
Input_CTL |
| Sample type |
SRA |
| |
|
| Source name |
Mouse embryonic fibroblast(MEF)
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Mouse embryonic fibroblast(MEF)
chip antibody: Input
media: Normal
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP experiments, cell lysates were clarified from sonicated nuclei and IP with mePontin antibody.
The sequencing library is prepared by random fragmentation of the DNA, followed by 5' and 3' adapter ligation. Alternatively, "tagmentation" combines the fragmentation and ligation reactions into a single step that greatly increases the efficiency of the library preparation process. Adapter-ligated fragments are then PCR amplified and gel purified.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2.
For peak calling for mePontin, we used Homer (v4.7.2). mePontin upon glucose starvation was compared against control input.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including mePontin peak information
|
| |
|
| Submission date |
Sep 15, 2020 |
| Last update date |
Oct 26, 2020 |
| Contact name |
Young Suk Yu |
| Organization name |
Seoul National University
|
| Street address |
1-Gwanak-ro, Gwanak-gu
|
| City |
Seoul |
| ZIP/Postal code |
08826 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE157952 |
Genome binding/occupancy profiling of methylated Pontin under glucose starvation |
|
| Relations |
| BioSample |
SAMN16133358 |
| SRA |
SRX9124084 |
