Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Prostate
Cell type
DU 145
Primary Tissue
Prostate
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
DU145 cells, untreated, H3K4me3 ChIP
cell line
DU145
cell type
prostate cancer cell line
tissue derivation
prostate; derived from brain metastatic site
treatment
None
chip antibody
H3K4me3 (Millipore, 07-473, lot 2664283)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
DU145 prostate cells were cross-linked with 1% formaldehyde at room temperature for 10 min and then lysed and sonicated to fragment genomic DNA sizes to 200-500 bp. Chromatin samples were incubated with specific antibodies overnight at 4℃. The protein-DNA complexes were immobilized on protein A/G beads. The bound fractions were washed with low salt, high salt, LiCI wash buffer and TE buffer. Reverse-crosslinking of the eluted DNA were carried out at 67℃ for 8 hours. After RNase A and protease K digestion, DNA fraction was purified using PCR purification kit. ChIP DNA libraries were prepared for sequencing using standard Illumina protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
40052963
Reads aligned (%)
95.5
Duplicates removed (%)
30.8
Number of peaks
34312 (qval < 1E-05)

hg19

Number of total reads
40052963
Reads aligned (%)
95.3
Duplicates removed (%)
30.9
Number of peaks
34154 (qval < 1E-05)

Base call quality data from DBCLS SRA