Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Others
Cell type
RT-112
Primary Tissue
Urinary Bladder
Tissue Diagnosis
Carcinoma Transitional Cell

Attributes by original data submitter

Sample

source_name
RT112 CTCF
cell line
RT112
chip antibody
CTCF

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Fixation in 10% Formaldehyde. ChIP using Active Motif High sensitivity ChIP kit ChIP-seq libraries were prepared using NEXTflex ChIP-Seq Kit (#5143-02, Bioo Scientific) following the manufacturer's protocol (V12.10) with some modifications. Briefly, 10 ng of ChIP enriched DNA were end repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK, then size selected and cleaned-up using Agencourt AMPure XP beads (#A63881,Beckman). A single 'A' nucleotide was added to the 3' ends of the blunt DNA fragments with a Klenow fragment (3' to 5'exo minus). The ends of the DNA fragments were ligated to double stranded barcoded DNA adapters (NEXTflex ChIP-Seq Barcodes - 6, #514120, Bioo Scientific) using T4 DNA Ligase. The ligated products were enriched by PCR (2 min at 98°C; [30 sec at 98°C, 30 sec at 65°C, 60 sec at 72°C] x 14 cycles; 4 min at 72°C) and cleaned-up using Agencourt AMPure XP beads. Prior to analyses DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer (Agilent). The libraries were loaded in the flowcell at 8pM concentration and clusters were generated using the Cbot and sequenced on the Illumina Hiseq2500 as single-end 50 base reads following Illumina's instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
44202336
Reads aligned (%)
99.2
Duplicates removed (%)
18.0
Number of peaks
31826 (qval < 1E-05)

hg19

Number of total reads
44202336
Reads aligned (%)
98.3
Duplicates removed (%)
20.2
Number of peaks
31599 (qval < 1E-05)

Base call quality data from DBCLS SRA