| attributes |
| Alias |
E-MTAB-7786:SW837 H3K79me3 3 |
| Broker name |
ArrayExpress |
| Description |
Protocols: SW837 cells were grown in DMEM/F-12 medium supplemented with 10% fetal bovine serum, 100 units/ml penicillin and 100 μg/ml streptomycin at 37°C and 5% CO2. Upon washing with PBS, cells were crosslinked with 1% formaldehyde for 20 minutes and quenched using 125 mM glycine. Upon scraping, nuclear pellets were prepared in and washed with the nuclear preparation buffer (150mM NaCl, 20 mM EDTA, 50 mM Tris-HCl (pH 7.5), 0.5% v/v NP-40, 1% v/v Triton-X-100, 20 mM NaF). Samples were sonicated in sonication buffer (150mM NaCl, 20 mM EDTA, 50 mM Tris-HCl (pH 8), 1% v/v NP-40, 0.5% v/v Sodium deoxycholate, 20 mM NaF, 0.1% SDS) for 20 cycles (30s on/off). Samples were precleared using 50% Sepharose 4B slurry (GE Healthcare) and incubated with the respective antibodies overnight: H3K27ac (196-050, Diagenode), H3K79me3 (C15310068, Diagenode) and H2Bub1 (55465, Cell Signaling). Sepharose beads with Protein A (for rabbit antibodies) or Protein G (for mouse antibodies) were added to samples and incubated for 2 hours followed by washes, de-crosslinking, and DNA extraction. DNA extraction was performed using Roti(R)-phenol/chloroform/Isoamylalcohol (Roth) followed by precipitation in 100% ethanol and washes with 70% ethanol. Libraries for DNA from ChIP were made using the NEBNext Ultra DNA library preparation kit according to the manufacturer's instructions. |
| ENA checklist |
ERC000011 |
| INSDC center alias |
University Medical Center Gottingen Clinic for General, Visceral and Pediatric Surgery Tumor Epigenetics |
| INSDC center name |
University Medical Center Gottingen Clinic for General, Visceral and Pediatric Surgery Tumor Epigenetics |
| INSDC first public |
2019-07-08T17:04:29Z |
| INSDC last update |
2019-03-15T16:43:15Z |
| INSDC status |
public |
| SRA accession |
ERS3230404 |
| Sample Name |
ERS3230404 |
| Title |
SW837 H3K79me3 3 |
| cell_line |
SW837 |
| disease |
rectal adenocarcinoma |
| organism |
Homo sapiens |
| organism part |
rectum |
| replicate |
3 |
|