Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RING1

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 prostate cancer cells
cell line
DU145 prostate cancer cells
genotype/variation
EED knockdown
chip antibody
Anti-RING1A [rabbit, Cell Signaling, cat# 2820, lot# 1]

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. ChIP was performed using HighCell ChIP kit following manufacturers protocol (Diagenode) ChIP-Seq libraries were prepared using standard Illumina protocol. ChIP-enriched DNA samples (10-20 ng) were converted to blunt-ended fragments using a combination of T4 DNA polymerase, E.coli DNA polymerase I large fragment (Klenow polymerase) and T4 polynuleotide kinase (New England BioLabs, NEB). A single A-base was added to fragment ends by Klenow fragment (3' to 5' exo minus; NEB) followed by ligation of Illumina adaptors (Quick ligase, NEB). The adaptor-modified DNA fragments were enriched by PCR using the Illumina PE1.0/PE2.0 primers and Phusion DNA polymerase (NEB). PCR products were size selected using 3% NuSieve agarose gels (Lonza) followed by gel extraction using QIAEX II reagents (QIAGEN). Libraries were quantified using the Bioanalyzer 2100 (Agilent) and each sample was sequenced in a single lane on the Illumina HiSeq 2000 (40 nucleotide read length).

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

hg19

Number of total reads
35569989
Reads aligned (%)
127.0
Duplicates removed (%)
33.2
Number of peaks
2512 (qval < 1E-05)

hg38

Number of total reads
35569989
Reads aligned (%)
127.6
Duplicates removed (%)
33.1
Number of peaks
2304 (qval < 1E-05)

Base call quality data from DBCLS SRA