Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Pancreas
Cell type
PANC-1
Tissue
Pancreas/Duct
Disease
Epithelioid Carcinoma

Attributes by original data submitter

Sample

source_name
PANC1 Cancer Cell line
cell line
PANC1
antibody
anti-CTCF

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq library preparation is described in O’Geen et al (Methods Mol Biol. 2011;791:265-286) using protein A/G beads to collect the immunoprecipitates. Approximately 5 x 10^7 MCF7 and PANC1 cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature, crosslinking was quenched with 0.125 M glycine for 5 minutes at room temperature and cell pellets were collected and stored at -80°C. Nuclei were digested with 2000U HindIII prior to dilute solid-surface ligation reactions. For the ChIP-Seq, the anti-CTCF antibody was from Cell Signaling Technology CTCF (D31H2) XP® Lot 1, 3418S.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
25860409
Reads aligned (%)
177.6
Duplicates removed (%)
9.4
Number of peaks
34639 (qval < 1E-05)

hg38

Number of total reads
25860409
Reads aligned (%)
179.3
Duplicates removed (%)
9.2
Number of peaks
35340 (qval < 1E-05)

Base call quality data from DBCLS SRA