Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
FOXA2

Cell type

Cell type Class
Pancreas
Cell type
CFPAC-1
Primary Tissue
Pancreas
Tissue Diagnosis
Adenocarcinoma Ductal

Attributes by original data submitter

Sample

source_name
Chromatin IP against FOXA2
cell line background
CFPAC1
cell type
Pancreatic Ductal Adenocarcinoma (PDAC) cell line
genotype/variation
Empty vector overexpressing CFPAC1 cell line
chip antibody
Anti-FOXA2 (Antibody sc-6554 Lot. A0715)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP lysates were generated from 50x10^6 cells. Cells were fixed in 1% formaldehyde for 10min. Lysate was immunoprecipitated with 10ug of antibody. Antibodies were pre-bound overnight to 100ul of G protein-coupled paramagnetic beads in PBS/BSA 0.5%. Beads were then added to lysates (the preclearing step was omitted) and incubation was let to proceed overnight. Beads were washed 6 times in a modified RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and once in TE containing 50mM NaCl. DNA was eluted in TE containing 2% SDS and crosslinks reversed by incubation overnight at 65ºC. DNA was then purified by AMPure XP SPRI (Beckman Coulter) and quantified using Quantifluor (Promega). ChIP DNA was prepared for HiSeq2000 or NextSeq500 Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, PCR with index primers and purification. A mixture of T4 DNA polymerase, DNA polymerase I and T4 kinase was used according to manufacturer's instruction. Library preparation is carried out on SPRIworks Fragment Library System.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
42119191
Reads aligned (%)
88.1
Duplicates removed (%)
9.9
Number of peaks
46156 (qval < 1E-05)

hg38

Number of total reads
42119191
Reads aligned (%)
89.6
Duplicates removed (%)
8.7
Number of peaks
46393 (qval < 1E-05)

Base call quality data from DBCLS SRA