Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Blood
Cell type
RAJI
Primary Tissue
Blood
Tissue Diagnosis
Malignant Lymphoma - Burkitts Type

Attributes by original data submitter

Sample

source_name
Raji cells
cell type
Raji cells
chip antibody
H3K4me3 (Millipore, 07-473)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
10 ng of Raji H3K4me3 ChIP DNA was processed into a sequencing library using teh Bioo Scientific NEXTflex ChIP-seq kit (Cat# 5143-01) according to the manufacturers instructions. Chromatin immunoprecipitation (ChIP) assay was performed as previously described (Scharer et al. Cancer Research, 69:709-717). Briefly, the indicated cells were fixed in 1% formaldehyde for 10 minutes, nuclei isolated, and sonicated to an average chromatin fragment size of 200-600 bp. 30 mg chromatin was immunoprecipitated with 5 μg anti-CIITA, anti-H3K27ac or anti-H3K4me3 antibody over night at 4 degrees. Antibody-chromatin complexes were captured with Protein A magnetic beads (Invitrogen), cross-links reversed, and DNA purified. Input fraction was isolated after sonication and prior to the IP. See each sample for speicific extract protocols

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
12968143
Reads aligned (%)
65.8
Duplicates removed (%)
45.0
Number of peaks
8928 (qval < 1E-05)

hg19

Number of total reads
12968143
Reads aligned (%)
65.2
Duplicates removed (%)
45.4
Number of peaks
8932 (qval < 1E-05)

Base call quality data from DBCLS SRA