Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
GFP

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_GFP fusion protein
cell line
K562
cell type
erythromyeloblastoid leukemia cells
genotype/variation
expressing CBX2-GFP fusion protein
chip antibody
Anti-GFP antibody
chip antibody vendor
Abcam

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin immune precipitation (ChIP) was essentially performed as described previously (Frank et al., 2001). Briefly, K562 cells were transduced with the lentiviral GFP-fusion vectors encoding GFP-CBX2, PCGF1-GPF, MEL18/PCGF2-GFP, BMI1/PCGF4-GFP, GFP-RING1A or GFP-RING1B. K562 cells expressing GFP-fusions at relatively low levels were sorted and expanded and subsequently crosslinked. ChIP reactions were performed using the following antibodies: anti-GFP (ab290, Abcam), anti-H3K27me3 (07-449, Millipore), and anti-H2AK119ub (D27C4, Cell Signaling Technology). ChIP efficiencies were determined by qPCR. Sequencing samples were prepared according to the manufacturer's protocol (Illumina). End repair was performed using the precipitated DNA using Klenow and T4 PNK. A 3’ protruding A base was generated using Taq polymerase and adapters were ligated. The DNA was loaded on gel and a band corresponding to ~300 bp (ChIP fragment + adapters) was excised. The DNA was isolated, amplified by PCR and used for cluster generation on the Illumina HiSeq 2000 genome analyze. ChIP seq libraries were preapared according to Illumina's standard protocol.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
37769900
Reads aligned (%)
92.8
Duplicates removed (%)
17.0
Number of peaks
1061 (qval < 1E-05)

hg19

Number of total reads
37769900
Reads aligned (%)
92.3
Duplicates removed (%)
17.8
Number of peaks
1159 (qval < 1E-05)

Base call quality data from DBCLS SRA