Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
KLF4

Cell type

Cell type Class
Blood
Cell type
HAP1
NA
NA

Attributes by original data submitter

Sample

source_name
KLF4_HAP1+OKS
source
chronic myeloid leukemia
cell type
HAP1
culture media
DMEM+FBS
status
Overexpression in HAP1
chip antibody
R&D Systems RRID:AB_2130224

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were cross-linked for 10 minutes at room temperature by the addition of one-tenth of the volume of 11% formaldehyde solution to the PBS followed by quenching with glycine. Cells were washed twice with PBS, then the supernatant was aspirated and the cell pellet was conserved in -80°C. Pellets were lysed, resuspended in 1mL of LB1 on ice for 10 min (50 mM HEPES-KOH pH 7.4, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10% Glycerol, 0.5% NP40, 0.25% Tx100, protease inhibitors), then after centrifugation resuspend in LB2 on ice for 10 min (10 mM Tris pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA and protease inhibitors). After centrifugation, resuspend in LB3 (10 mM Tris pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% NaDOC, 0.1% SDS and protease inhibitors) for histone marks and SDS shearing buffer (10 mM Tris pH8, EDTA 1mM, SDS 0.15% and protease inhibitors) for transcription factor and sonicated (Covaris settings: 5% duty, 200 cycle, 140 PIP, 20 min), yielding genomic DNA fragments with a bulk size of 100-300bp. Coating of the beads with the specific antibody and carried out during the day at 4°C, then chromatin was added overnight at 4°C for histone marks while antibody for transcription factor is incubated with chromatin first with 1% Triton and 150mM NaCl. Subsequently, washes were performed with 2x Low Salt Wash Buffer (10 mM Tris pH 8, 1 mM EDTA, 150mM NaCl, 0.15% SDS), 1x High Salt Wash Buffer (10 mM Tris pH 8, 1 mM EDTA, 500 mM NaCl, 0.15% SDS), 1x LiCl buffer (10 mM Tris pH 8, 1 mM EDTA, 0.5 mM EGTA, 250 mM LiCl, 1% NP40, 1% NaDOC) and 1 with TE buffer. Final DNA was purified with Qiagen Elute Column. Up to 10 nanograms of ChIPed DNA or input DNA (Input) were prepared for sequencing. Library was quality checked by DNA high sensitivity chip (Agilent). Quality controlled samples were then quantified by picogreen (Qubit® 2.0 Fluorometer, Invitrogen). Cluster amplification and following sequencing steps strictly followed the Illumina standard protocol. Libraries were ligated with Illumina adaptors

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
31170312
Reads aligned (%)
69.8
Duplicates removed (%)
25.3
Number of peaks
4586 (qval < 1E-05)

hg38

Number of total reads
31170312
Reads aligned (%)
70.4
Duplicates removed (%)
24.9
Number of peaks
4664 (qval < 1E-05)

Base call quality data from DBCLS SRA