Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
HOXB13

Cell type

Cell type Class
Prostate
Cell type
Prostate cancer cells
NA
NA

Attributes by original data submitter

Sample

source_name
Localized tumor HOXB13
tissue
localized prostate tumor tissue
chip antibody
HOXB13
chip antibody vendor
Santa Cruz Biotechnology
chromosome
AR enhancer location

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
One (histone ChIP) or three (transcription factor ChIP) 2 mm2 frozen cores were pulverized using the Covaris CryoPrep system. Tissue was fixed using 1% formaldehyde and chromatin sheared to 300-500 bp in size using the Covaris E220 ultrasonicator. Resulting chromatin was incubated overnight with indicated antibodies. Purified immunoprecipitates were isolated and quantified by Qubit fluorometer. DNA sequencing libraries were prepared using the ThruPLEX-FD Prep kit (Rubicon Genomics). Libraries were sequenced using 75-bp reads on the Illumina platform at the Dana-Farber Cancer Institute.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
1561008
Reads aligned (%)
97.6
Duplicates removed (%)
0.0
Number of peaks
494 (qval < 1E-05)

hg38

Number of total reads
1561008
Reads aligned (%)
97.7
Duplicates removed (%)
0.0
Number of peaks
489 (qval < 1E-05)

Base call quality data from DBCLS SRA