|
| Status |
Public on Nov 13, 2020 |
| Title |
ChIP_Input_WT_mESC |
| Sample type |
SRA |
| |
|
| Source name |
ESC
|
| Organism |
Mus musculus |
| Characteristics |
cell type: ESC
genotype/variation: wild type
antibody: none
|
| Growth protocol |
ES cells were cultured on gelatin-coated dishes in ES cell media containing 1.5 µM CHIR9901 (GSK3 inhibitor) for several passages to remove feeder cells. ES cells were passed by washing with PBS, and dissociating with trypsin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked with formaldehyde and subsequently sonicated. Sonicated cell extracts were used for ChIP assays.
ChIP-enriched DNA was end-repaired using the End-It DNA End-Repair kit (Epicentre), followed by addition of a single A nucleotide, and ligation of PE adapters (Illumina) or custom indexed adapters. PCR was performed using Phusion High Fidelity PCR master mix
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Direct sequencing following sonication of x-linked chromatin
|
| Data processing |
Sequence reads were obtained and mapped to the mouse (mm9) genomes with Bowtie2.
The RBPM measure (reads per base per million reads) was used to generate graph files.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph
|
| |
|
| Submission date |
May 05, 2019 |
| Last update date |
Nov 13, 2020 |
| Contact name |
Benjamin L Kidder |
| E-mail(s) |
[email protected]
|
| Organization name |
Wayne State University
|
| Department |
Oncology
|
| Lab |
Laboratory of Epigenomics
|
| Street address |
4100 John R St
|
| City |
Detroit |
| State/province |
MI |
| ZIP/Postal code |
48201 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE130721 |
H4K20me3 methyltransferase SUV420H2 regulates pluripotent embryonic stem cells [ChIP-seq] |
| GSE130725 |
H4K20me3 methyltransferase SUV420H2 shapes the three-dimensional chromatin landscape of pluripotent embryonic stem cells |
|
| Relations |
| BioSample |
SAMN11578666 |
| SRA |
SRX5793973 |
