Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Epitope tags

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
Cultured K562 cells_dCas9_HS2_CR4_FLAG
cell line
K562
transduced gene
dCas9
grna target
globin HS2 enhancer
chip antibody
anti-FLAG
chip antibody vendor
Sigma-Aldrich

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For each replicate, 2 ×10^7 nuclei were re-suspended in 1 mL of RIPA buffer (1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS in PBS at pH 7.4). Samples were sonicated using a Diagenode Bioruptor XL sonicator at 4°C to fragment chromatin to 200-500 bp segments. Insoluble components were removed by centrifugation for 15 min at 15000 rpm. We conjugated 5 µg of anti-FLAG (Sigma-Aldrich, F1804), or anti-H3K9me3 (Abcam, ab8898) to 200 µl of either sheep anti-rabbit or sheep anti-mouse IgG magnetic beads (Life Technologies 11203D/11201D). Sheared chromatin in RIPA was then added to the antibody-conjugated beads and incubated on a rotator overnight at 4°C. After incubation, beads were washed five times with a LiCl wash buffer (100 mM Tris at pH 7.5, 500 mM LiCl, 1% NP-40, 1% sodium deoxycholate), and remaining ions were removed with a single wash with 1 mL of TE (10 mM Tris-HCl at pH 7.5, 0.1 mM Na2EDTA) at 4°C. Chromatin and antibodies were eluted from beads by incubating for 1 h at 65°C in IP elution buffer (1% SDS, 0.1 M NaHCO3), followed by incubating overnight at 65°C to reverse formaldehyde cross-links. DNA was purified using MinElute DNA purification columns (Qiagen). Illumina TruSeq adapted libraries were constructed using an Apollo 324 NGS Library Prep System with a PrepX Complete ILMN DNA Library Kit (WaferGen Biosystems Inc). ChIP products were amplified with 15 cycles of PCR, and fragments 150-700 bp in length were selected using an AxyPrep MAG PCR Clean-Up Kit (Axygen MAG-PCRCL-50). Libraries were sequenced using single end 50 bp reads on an Illumina HiSeq.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
27344744
Reads aligned (%)
97.6
Duplicates removed (%)
2.1
Number of peaks
986 (qval < 1E-05)

hg19

Number of total reads
27344744
Reads aligned (%)
96.8
Duplicates removed (%)
3.4
Number of peaks
976 (qval < 1E-05)

Base call quality data from DBCLS SRA