GSM3428231: 12 OGG1-APseq 6Gy 30min rep3 input; Homo sapiens; ChIP-Seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
Unclassified
Antigen
Unclassified
Cell type
Cell type Class
Liver
Cell type
Hep G2
Primary Tissue
Liver
Tissue Diagnosis
Carcinoma Hepatocellular
Attributes by original data submitter
Sample
source_name
HepG2
cell type
hepatocellular carcinoma cell line
treatment
X-rays, 6Gy, 30min
processing
OGG1 digest/ aldehyde reactive probe
enrichment
input
Sequenced DNA Library
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Total genomic DNA was extracted using a Blood and Tissue Kit (Qiagen, catalogue number 69506) and genomic DNA was kept on ice during the process. Antioxidants were not applied in this experiment to avoid artefacts through sequence specific effects. Since treated samples and the untreated control are exposed to the same technical artefacts from sample processing, these should be accounted for in the data analysis. 5.7mg of genomic DNA was tagged with biotin using 5mM Aldehyde Reactive Probe (ARP; Life Technologies, catalogue number A10550) in phosphate buffered saline (PBS) for 2h at 37°C. Genomic DNA was then purified using AMPure beads (Agencourt, catalogue number A63882) with 1.8x bead solution, 2x 70% ethanol washing; beads were not allowed to dry to prevent DNA from sticking. Both the damage-enriched and input DNA were in vitro repaired using PreCR (NEB catalogue number M0309L). The input DNA and supernatant of the pull-down were purified using AMPure beads. The purified pull-down was recombined with the beads and library preparation was performed on the re-pooled sample containing the supernatant and the beads. A 125bp paired-end ChIP-Seq library preparation kit (KAPA Biosystems catalogue number KK8504) was used and sequencing performed using an Illumina HiSeq 2000 on first a rapid and then a high-output run (catalogue number FC-401-4002). The resulting data were subsequently combined.