Antigen

Antigen Class

TFs and others

Antigen

CTCF

Cell type

Cell type Class

Prostate

Cell type

LNCAP

Primary Tissue

Prostate

Tissue Diagnosis

Carcinoma

Sample

source_name

androgen-sensitive human prostate adenocarcinoma cell line LNCaP

cell line

androgen-sensitive human prostate adenocarcinoma cell line LNCaP

chip antibody

CTCF

input dna level

NA

library preparation protocol

Bioo (now PerkinElmer) NEXTflex

geo_loc_name

missing

collection_date

missing

Sequenced DNA Library

library_name

GSM5880326

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Lysates were prepared from sonicated nuclei and histone-DNA complexes were isolated with antibody. Bioo ChIP libraries were prepared using the NEXTflex ChIP-Seq Kit (Bioo Scientific, now PerkinElmer) following the manufacturer's protocol. "Diagenode" ChIP libraries were prepared using the Diagenode MicroPlex Library Preparation Kit v2 (Diagenode) following the manufacturer's protocol. "KAPA" ChIP libraries were prepared using the KAPA HyperPrep Kit (Roche) following the manufacturer's protocol. "NEB" ChIP-Seq libraries were prepared using the NEBNext® Ultra II™ DNA Library Prep Kit for Illumina® (New England BioLabs, Inc., Ipswich, MA) following the manufacturer's protocol.

Sequencing Platform

instrument_model

Illumina HiSeq 3000

hg38

Number of total reads

37891742

Reads aligned (%)

90.8

Duplicates removed (%)

85.9

Number of peaks

4161 (qval < 1E-05)

hg19

Number of total reads

37891742

Reads aligned (%)

90.0

Duplicates removed (%)

87.3

Number of peaks

3898 (qval < 1E-05)