GSM2339536: Total input Hepa 1.6 cells; Mus musculus; ChIP-Seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
Input control
Antigen
Input control
Cell type
Cell type Class
Liver
Cell type
Hepa 1-6
Primary Tissue
Liver
Tissue Diagnosis
Carcinoma Hepatocellular
Attributes by original data submitter
Sample
source_name
Total input Hepa 1.6 cells
strain background
C57L
genotype/variation
WT
developmental stage/age
hepatoma
cell line
Hepa 1-6 (ECACC 92110305)
tissue/cell type
Liver hepatoma (Derived from BW7756 tumour in a C57L mouse)
Sequenced DNA Library
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were washed with PBS, fixed for 10 minutes at 1% formaldehyde, and quenched with glycine (at 125 mM final) for 5 minutes at room temperature. Cells were washed three times with ice-cold PBS, and harvested. The pellet was lysed, resuspended in 1 mL of sonication buffer (10 mM Tris at pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% NaDOC, 0.5% NLS, and protease inhibitors), transferred to TC 12x12 tubes (Covaris), and sonicated (Covaris settings: 30 minutes, 5% duty cycle, 140W, 200 cycles). Chromatin was decrosslinked (RNAse A at 1μg/μL, 65°C overnight), purified and quantified by Nanodrop. Fragment size was assessed on a Bioanalyzer High Sensitivity chip (Agilent 2100). Immunoprecipitations were performed with 40 ug of chromatin (for KAP1 and SETDB1), or 20 ug of chromatin (for histone modifications), with antibody-coupled magnetic beads (Dynabeads, ThermoFisher) in IP buffer (10 mM Tris at pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 2% Triton X-100, and protease inhibitors) overnight. Chromatin was decrosslinked (Proteinase K at 400ng/μL, 65°C overnight) and DNA purified for analysis. Illuminal ChIP-seq protocol