Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
HBZ

Cell type

Cell type Class
Blood
Cell type
KK1
NA
NA

Attributes by original data submitter

Sample

source_name
KK1 BirA HBZ
cell line
KK1
disease state
Adult T-cell Leukemia/Lymphoma (ATLL)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Streptavidin DynaBeads Other: 20 million exponentially growing cells were collected per sample and cross-linked with 1% formaldehyde for 10 min at room temperature. The cross-linked cells were resuspended in ice-cold RIPA buffer (10mM Tris-HCl pH8, 140 mM NaCl, 1mM EDTA pH 8, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS and 0.1% sodium deoxycholate) to a final concentration of 4 million cells/ml. DNA was sheared with a Misonix XL sonicator. Chromatin was incubated with MyOne Streptavidin T1 Dynabeads (Thermo Fisher Scientific), washed 3 times with RIPA Buffer, once with LiCl Buffer (10 mM Tris-HCl pH8, 250 mM LiCl, 0.5% NP40, 0.5% Sodium Deoxycholate, 1 mM EDTA), once with TE pH 8.0 and finally resuspended in 100 ul TE pH8 containing RNase A (0.2 ug/ul). Reverse crosslinking was performed overnight at 65 C, followed by treatment with 20 ug Proteinase K (Invitrogen) for 2 h at 50 C. Final DNA purification was performed with QIAquick PCR Purification columns (QIAGEN). ChIP DNA was used to generate ChIP-seq libraries with the NEXTflex Illumina ChIP-seq Library Prep Kit (Bio Scientific) according to manufacturer's instructions.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
47203449
Reads aligned (%)
2.0
Duplicates removed (%)
98.0
Number of peaks
1729 (qval < 1E-05)

hg38

Number of total reads
47203449
Reads aligned (%)
2.4
Duplicates removed (%)
97.5
Number of peaks
1699 (qval < 1E-05)

Base call quality data from DBCLS SRA