Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
HOXB13

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
tissue
LNCaP cells
chip antibody
HOXB13 (Cell Signaling, 90944)
treatment
EtOH

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were collected and crosslinked with 1% methanol-free formaldehyde for 10 minutes and fixation was quenched using 125 mM glycine for 8 minutes. The cell pellets were centrifuged and washed twice in cold PBS. Each pellet was resuspended in 1 ml of lysis buffer (50 mM Tris HCl pH 8, 0.5% SDS, 10 mM EDTA with protease and phosphatase inhibitors (Thermo Scientific)) and lysed for 20 minutes at 4°C. The nuclei were collected by centrifugation and resuspended in a second lysis buffer (10 mM Tris HCl pH 7.5, 150 mM NaCl, 0.1% SDS, 1 mM EDTA, 1% NP-40, 1% sodium deoxycholate, with protease and phosphatase inhibitors (Thermo Scientific)). The protein-bound chromatin was sheared by sonication (Diagenode, Bioruptor Pico). Input sheared chromatin was reserved as a control for downstream ChIP-seq analysis. Equal volumes of sheared chromatin were immunoprecipitated with specified antibodies. Libraries were generated using the Hyper Prep Kit (Kapa Biosystems) following the manufacturer's recommended protocol.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
39485212
Reads aligned (%)
91.6
Duplicates removed (%)
3.2
Number of peaks
16133 (qval < 1E-05)

hg38

Number of total reads
39485212
Reads aligned (%)
92.8
Duplicates removed (%)
3.0
Number of peaks
15504 (qval < 1E-05)

Base call quality data from DBCLS SRA