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
LNCaP95
cell line
LNCaP95
transfection
shGFP
treatment
ETOH
antibody
HOXB13

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Approximately 10^7 cells were cross-linked with 1% formaldehyde for 10min. Lysed cells were sonicated in a Covaris E210 sonicator. Sheared chromatin was incubated with antibodies over night and immunoprecipitated using Dynabeads Protein A (Life Technologies). Chromatin was treated with RNaseA and Protease K and purified using phenol-chloroform extraction. Sequencing libraries were generated according to manufacturer's instructions (ThruPLEX DNA-seq Kit, Rubicon Genomics) and then sequenced on the Illumina NextSeq 500 platform

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
44529829
Reads aligned (%)
89.3
Duplicates removed (%)
7.7
Number of peaks
10654 (qval < 1E-05)

hg38

Number of total reads
44529829
Reads aligned (%)
91.6
Duplicates removed (%)
6.1
Number of peaks
10913 (qval < 1E-05)

Base call quality data from DBCLS SRA