Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
GFI1B

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 Cells
cell line
K562 Cells
gender
female
tissue
Bone Marrow
disease
Chronic Myelogenous Leukemia
antibody
Gfi1b
agent
Wnt3a

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed with 1% formaldehyde. Cell lysis was performed using the following buffers: total cell lysis - 5mM PIPES pH 8, 85mM KCl, 0.5% NP-40, 1X protease inhibitor cocktail, 1mM PMSF, and nuclear lysis – 50mM Tris, 10mM EDTA, 1% SDS, 1X protease inhibitor cocktail, 1mM PMSF. After sonication (Covaris E220 sonicator), immunoprecipitation was performed using Protein A/G Dynabeads (Life Technologies) For ChIP-Seq experiments, sequencing libraries were prepared from immunoprecipitated chromatin using the TruSeq DNA kit from Illumina according to the manufacturer's instructions and sequenced using the TruSeq PE Clusterkit v3-cBot-HS. For RNA-Seq, libraries were prepared from RNA extracts using the TruSeq Stranded mRNA kit from Illumina according to the manufacturer's instructions and sequenced using using the TruSeq PE Clusterkit v3-cBot-HS

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
107273404
Reads aligned (%)
174.5
Duplicates removed (%)
8.9
Number of peaks
6190 (qval < 1E-05)

hg38

Number of total reads
107273404
Reads aligned (%)
177.1
Duplicates removed (%)
8.3
Number of peaks
7296 (qval < 1E-05)

Base call quality data from DBCLS SRA