Curated Sample Data


Genome
hg19
Antigen Class
Histone
Antigen
macroH2A2
Cell type Class
Liver
Cell type
Hep G2

Cell type information


Primary Tissue
Liver
Tissue Diagnosis
Carcinoma Hepatocellular

Attributes by Original Data Submitter


source_name
Hepatocellular carcinoma
cell line
HepG2
chip antibody
anti-macroH2A2 (Buschbeck et al., 2009, PMID:19734898)

Metadata from Sequence Read Archive

Library Description


library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Formaldehyde was added to the culture medium to a final concentration of 1%. Cross-linking was allowed to proceed for 10 min at room temperature and stopped by addition of glycine at a final concentration of 0.125 M, followed by an additional incubation for 5 min. Fixed cells were washed twice with TBS (20 mM Tris at pH 7.4, 150 mM NaCl) and harvested in SDS Buffer (50 mM Tris at pH 8.1, 0.5% SDS, 100 mM NaCl, 5 mM EDTA, and protease inhibitors). Cells were pelleted by centrifugation, and suspended in 4 mL of IP Buffer (100 mM Tris at pH 8.6, 0.3% SDS, 1.7% Triton X-100, and 5 mM EDTA). Cells were disrupted by sonication. The lysate was then diluted with IP buffer to a final volume of 9 mL. For each immunoprecipitation, diluted lysate was precleared by addition of blocked protein A beads. Samples were immunoprecipitated overnight at 4°C with polyclonal antibodies specific for either macroH2A1 (3 μg), macroH2A2 (3 μg), IgG (3μg, ab46540, Abcam). Immune complexes were recovered by adding 30 μL of blocked protein A beads and incubated for 2 h at 4°C. Beads were washed and eluted, and cross links were reversed as described by Aparicio (1999). This included successive washes in 1 mL of Mixed Micelle Buffer (20 mM Tris at pH 8.1, 150 mM NaCl, 5 mM EDTA, 5% w/v sucrose, 1% Triton X-100, and 0.2% SDS), Buffer 500 (50 mM HEPES at pH 7.5, 0.1% w/v deoxycholic acid, 1% Triton X-100, 500 mM NaCl, and 1 mM EDTA), LiCl Detergent Wash Buffer (10 mM Tris at pH 8.0, 0.5% deoxycholic acid, 0.5% NP-40, 250 mM LiCl, and 1 mM EDTA), and TE (pH 7.5). The eluted material was phenol/chloroform-extracted and ethanol-precipitated. DNA was resuspended in 50 μL of waternand quantified with PicoGreen. Libraries were prepared for sequencing using standard Illumina protocols

Platform Information


instrument_model
Illumina HiSeq 2000

External Database Query

Logs in read processing pipeline


Number of total reads
180858570
Reads aligned (%)
98.0
Duplicates removed (%)
73.5
Number of peaks
25250 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA