Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K36me3

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
H3K36me3 (Abcam 9050)

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
57952736
Reads aligned (%)
62.0
Duplicates removed (%)
10.1
Number of peaks
5655 (qval < 1E-05)

mm9

Number of total reads
57952736
Reads aligned (%)
61.8
Duplicates removed (%)
10.0
Number of peaks
5697 (qval < 1E-05)

Base call quality data from DBCLS SRA