Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CUX1

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_Control shRNA
cell line
K562
cell type
myeloid leukemia cell line
shRNA
control shRNA
chip-antibody
CUX1 sc-6327 Santa Cruz

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
RNA was isolated using Trizol. Genomic DNA was isolated follwing the Myers Lab ChIP-seq Protocol v042211.2 (www.encodeproject.org), Barcoded RNA-seq libraries were generated using the standard Illumina TruSEQ kit. Barcoded ChIP-seq libraries were made with Ovation Ultralow Library kit (NuGEN).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
29875805
Reads aligned (%)
73.2
Duplicates removed (%)
24.2
Number of peaks
1421 (qval < 1E-05)

hg38

Number of total reads
29875805
Reads aligned (%)
74.6
Duplicates removed (%)
23.3
Number of peaks
1418 (qval < 1E-05)

Base call quality data from DBCLS SRA