Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me1

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, shZMYND8, H3K4me1 ChIP
cell line
DU145
cell type
prostate cancer cell line
tissue derivation
prostate; derived from brain metastatic site
treatment
shZMYND8
chip antibody
H3K4me1 (Abcam, ab8895, lot GR251663-1), Drosophila-specific H2Av (Active Motif, 61686, lot 18815002)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP with reference exogenous genome (ChIP-Rx) was performed to compare H3K4me1 and H3K4me3 levels in shLuciferase, shJARID1D or shZMYND8 DU145 human prostate cancer cells. Drosophila melanogaster chromatin and Drosophila-specific H2Av antibody were spiked-in to each ChIP reaction as a minor fraction. 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
27881394
Reads aligned (%)
94.6
Duplicates removed (%)
6.7
Number of peaks
355 (qval < 1E-05)

hg19

Number of total reads
27881394
Reads aligned (%)
94.0
Duplicates removed (%)
7.7
Number of peaks
386 (qval < 1E-05)

Base call quality data from DBCLS SRA