SW837 Input 2
Homo sapiens
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-FIRST-PUBLIC
2019-07-08T17:04:29Z
ENA-LAST-UPDATE
2019-03-15T16:43:15Z
External Id
SAMEA5425117
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
Submitter Id
E-MTAB-7786:SW837 Input 2
broker name
ArrayExpress
cell line
SW837
common name
human
disease
rectal adenocarcinoma
organism part
rectum
replicate
2
sample name
E-MTAB-7786:SW837 Input 2
scientific_name
Homo sapiens