Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

Cell type Class
Blood
Cell type
K-562
Primary Tissue
Blood
Tissue Diagnosis
Leukemia Chronic Myelogenous

Attributes by original data submitter

Sample

source_name
K562 cell
cell type
Wild type K562 lymphoblast cells

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
K562 cells were sorted and crosslinked with 1% formaldehyde at room temperature (RT) for 10 min, and the reaction was stopped by 0.125M glycine at RT for 5 min. Cross-linked cells were lysed and sonicated to 200-500 bp fragments (Bioruptor, Diagenode). ChIP-qualified antibodies (anti-CTCF) were added to the sonicated chromatin and incubated at 4°C overnight. Following this, 10 μl of protein A magnetic beads (Dynal, Invitrogen) previously washed in RIPA buffer were added and incubated for an additional 2 hours at 4°C. The bead: protein complexes were washed three times with RIPA buffer and twice with TE buffer. Following transfer into new 1.5 ml collection tube, genomic DNA was eluted for 2 hours at 68°C in 100 µl Complete Elution Buffer (20 mM Tris pH 7.5, 5 mM EDTA, 50 mM NaCl, 1% SDS, 50 µg/ml proteinase K), and combined with a second elution of 100 µl Elution Buffer (20 mM Tris pH 7.5, 5 mM EDTA, 50 mM NaCl) for 10 min at 68°C. ChIPed DNA was purified by MinElute Purification Kit (Qiagen) and eluted in 12 µl elution buffer. Chip-Seq libraries was constructed using Rubicon Genomics ThruPLEX® DNA-seq Kit

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
14228932
Reads aligned (%)
97.0
Duplicates removed (%)
31.1
Number of peaks
4921 (qval < 1E-05)

hg19

Number of total reads
14228932
Reads aligned (%)
96.2
Duplicates removed (%)
31.5
Number of peaks
4815 (qval < 1E-05)

Base call quality data from DBCLS SRA