Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CBX3

Cell type

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

Attributes by original data submitter

Sample

source_name
LNCAP cells
cell line
LNCAP
cell type
human prostate cancer cells
treatment
Veh
antibody
Millipore 05-690 (Lot#3224566)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were cross-linked with 1% formaldehyde at room temperature for 10 min. And then the cross-linking was quenched with 0.125M glycine for 5 min. Chromatin was fragmented using a Bioruptor® Pico (Diagenode) for 10 min at high power, with an interval of 30 s between pulses to get around 200bp fragments and precleared using 20 μl Protein G Dynabeads (Life Technologies, Cat# 10009D). Subsequently, the soluble chromatin was incubated with 2-5 μg antibodies at 4°C overnight. Immunoprecipitated complexes were collected using 30 μl Protein G Dynabeads, which have been saturated with PBS/1% BSA over night at 4°C, per reaction. For all ChIPs, after de-crosslinking overnight at 65°C, final ChIP DNA was extracted and purified using QIAquick spin columns (QIAGEN). The libraries were constructed following Illumina's Chip-Seq Sample prep kit.

Sequencing Platform

instrument_model
Illumina NovaSeq 6000

hg38

Number of total reads
36204539
Reads aligned (%)
67.7
Duplicates removed (%)
12.9
Number of peaks
2070 (qval < 1E-05)

hg19

Number of total reads
36204539
Reads aligned (%)
67.4
Duplicates removed (%)
13.3
Number of peaks
1301 (qval < 1E-05)

Base call quality data from DBCLS SRA