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
ChIP Sequencing for cMyc in LNCaP cells post 10nM DHT
treatment
10nM DHT 3 hours
cell line
LNCaP

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
20 million cells/replicate were fixed using 1% formaldehyde for 10 minutes at 24C, quenched for 5 minutes with 0.125M glycine, and stored at -80C until use. Pellets were then thawed on ice and lysed using 1% SDS_lysis buffer, sonicated for 27 cycles (30on/30ff) using a temperature controlled bioruptor, and spun down at max speed for 10 minutes. Clarified chromatin was then incubated with primary antibody overnight, and genomic DNA washed and isolated the next morning. ChIP sequencing libraries (20ng DNA/sample) were constructed using the KAPA Hyper Prep Kit (Illuminia- Kapa biosystems Cat # KK8502, NimbleGen SeqCap Adapter Kit A- Roche Cat # 07 141 530 001) according to the manufactures instructions. Libraries were assessed for quality, purity, and size using DNA High Sensitivity Bioanalyzer chips, and those passing QC were quantified using the Library Quantification Kit from Illiumina (Kapa Biosystems KK4854). Libraries were pooled to a final concentration of 10nM and sequenced using the Illumina HiSeq 4000

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
32026006
Reads aligned (%)
52.6
Duplicates removed (%)
29.1
Number of peaks
14449 (qval < 1E-05)

hg38

Number of total reads
32026006
Reads aligned (%)
53.5
Duplicates removed (%)
28.1
Number of peaks
14224 (qval < 1E-05)

Base call quality data from DBCLS SRA