GSM2481427: Calu3 H3K9me3 ChIP-seq; Homo sapiens; ChIP-Seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
Histone
Antigen
H3K9me3
Cell type
Cell type Class
Lung
Cell type
Calu-3
Primary Tissue
Lung
Tissue Diagnosis
Adenocarcinoma
Attributes by original data submitter
Sample
source_name
Lung adenocarcinoma cells
cell type
Calu3
antibody
H3K9me3 (Abcam 8898)
Sequenced DNA Library
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
DNase-seq: genomic DNA was digested with different concentrations of DNaseI (NEB) and purified for library construction (Boyle et al. Cell, 2008). ChIP-seq: Cells were lysed in lysis buffer (5mM PIPES pH 8.0, 85mM KCL, 0.5% NP-40, 1x Protese Inhibitor Cocktail (Roche)). Nuclei were isolated by centrifugation, lysed in RIPA buffer (1x PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, Protease Inhibitor Cocktail), and sonicated. Protein-DNA complexes were isolated with the histone antibodies. DNase-seq: libraries were prepared by Drs A. Safa and G. Crawford. ChIP-seq: DNA ends were blunted using T4 DNA polymerase, Klenow DNA polymerase, and T4 polynucleotide kinase. Next, DNA was incubated with Klenow exo- to add 5’ adenine overhangs. Multiplex adaptors were then ligated to the ends and converted to dsDNA using 5 cycles of PCR. DNA was size-selected to contain fragments between 200 and 300bp and PCR amplified for 5 cycles. DNA was purified with 1.2x AMPsureXP beads. Sequencing was preformed on an Illumina Hi-Seq.