Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MYC

Cell type

Cell type Class
Prostate
Cell type
LNCAP
Primary Tissue
Prostate
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
LNCaP
tissue
prostate cancer
cell line
LNCaP
antibody
anti-MYC AF3696 (R&D systems)
treatment
DMSO

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin immunoprecipitation (ChIP) was performed from ~20x106 cells by first cross-linking cells with 1% para-formaldehyde (pFa) in room temperature for 10 minutes. PFa was quenched by addition of 125mM glycine for 10 minutes and cells were washed twice in ice-cold PBS. Next, cells were solubilized into ChIP lysis buffer (0.1% SDS, 1% Triton X-100, 0.15M NaCl, 1mM EDTA, 20mM Tris pH8.0), and samples were sonicated using Bioruptor (Diagenode) to obtain DNA fragments of 200-500 based pairs in length (this was confirmed for every experiment). After sonication, samples were centrifuged and supernatant was used for ChIP. Antibodies for ChIP: RL2 #ab2739 (Abcam) and MYC AF3696 (R&D systems). ChIP was performed over-night in +4˚C, and beads were washed as follows: 2x in wash buffer 1 (0.1% SDS, 0.1% Na-deoxycholate, 1% Triton X-100, 0.15M NaCl, 1mM EDTA, 20mM HEPES pH8.0), 1x in wash buffer 2 (0.1% SDS, 0.1% Na-deoxycholate, 1% Triton X-100, 0.5M NaCl, 1mM EDTA, 20mM HEPES pH8.0), 1x in wash buffer 3 (0.25M LiCl, 0.5% Na-deoxycholate, 0.5% NP-40, 1mM EDTA, 20mM HEPES pH8.0) and 2x in wash buffer 4 (10mM EDTA, 20mM HEPES). After this, DNA was extracted using phenol-chloroform extraction and used for sequencing. Libraries were prepared according Illumina's instructions accompanying the TruSeq library preparation kit.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
26031776
Reads aligned (%)
69.7
Duplicates removed (%)
7.1
Number of peaks
671 (qval < 1E-05)

hg38

Number of total reads
26031776
Reads aligned (%)
70.7
Duplicates removed (%)
6.3
Number of peaks
906 (qval < 1E-05)

Base call quality data from DBCLS SRA