Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Blood
Cell type
RAW 264.7
Primary Tissue
Blood
Tissue Diagnosis
Leukemia

Attributes by original data submitter

Sample

source_name
RAW 264.7
cell line
RAW 264.7
cell type
macrophage; Abelson murine leukemia virus transformed
treatment
1 hour LPS
antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Approximately 10x10^6 of untreated or stimulated (1h and 4h with LPS) RAW cells were used for each experiment. Cells were crosslinked with 0.75% formaldehyde for 10 min at RT and chromatin was sonicated as described previously (Soldi et. Al, 2013). Each chromatin input was immunoprecipitated with 10 g of antibody. beads were washed in Buffer A (20 mM Tris-HCl pH 7.6, 2 mM EDTA, 0.1% SDS, 1% Triton-100, 150 mM NaCl), Buffer B (20 mM Tris-HCl pH 7.6, 2 mM EDTA, 0.1% SDS, 1% Triton-100, 300 mM NaCl) and once in TE containing 50 mM NaCl. DNA was eluted in TE containing 2% SDS and de-crosslinked overnight at 65°C. DNA was then purified by Qiaquick columns (QIAGEN) and quantified with Picogreen. Library preparation for Illumina sequencing (HiSeq 2000) was carried out using a described protocol (Garber et al., 2012) with slight modifications (Ostuni et al., 2013). The purified DNA libraries were quantified both with a 2100 Bioanalyzer (Agilent Technologies) and Qubit (LifeTechnologies) and diluted to a working concentration of 10 nM.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
55547241
Reads aligned (%)
95.1
Duplicates removed (%)
13.6
Number of peaks
594 (qval < 1E-05)

mm9

Number of total reads
55547241
Reads aligned (%)
94.9
Duplicates removed (%)
13.6
Number of peaks
661 (qval < 1E-05)

Base call quality data from DBCLS SRA