Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TBP

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
TBP ChIP-seq (Human K562 cells) Rep 1
cell line
K562 cells
chip antibody
anti-TBP rabbit polyclonal, Santa Cruz Technology, catalog # sc-204X (ChIP-grade), lot # C-0513
multiplex barcode
GTGGCC

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
cells were cross-linked in 1.0% formaldehyde. Cells were then dounced to bread down cells and extract nuclei. Chromatin was sonicated by bioruptor to an average size of 300~500 bp. 300 ul soluble chromatin from ~ 10 million cells was used DNA-protein-complexes were isolated with specific antibodies. Sequencing libraries were prepared following Illumina's instructions: DNA was end repaired using T4 DNA polymerase, DNA polymerase I large fragment (Klenow polymerase) and T4 polynucleotide kinase. A single 3'-A overhang was added to the blunted ends using Klenow 3'-5' exo- polymerase. Adapters with single 3'-T overhangs were ligated to the adenylated fragments, and after a size-selection step using AmPure beads (200-250 bp) the adapter modified DNA was PCR-amplified. Following cluster generation on the flowcell surface, the sequencing libraries were sequenced following Illumina's protocol.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
23901621
Reads aligned (%)
36.6
Duplicates removed (%)
61.8
Number of peaks
13412 (qval < 1E-05)

hg38

Number of total reads
23901621
Reads aligned (%)
37.2
Duplicates removed (%)
61.4
Number of peaks
13596 (qval < 1E-05)

Base call quality data from DBCLS SRA