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
CFPAC1.FOXA2KO.ChIP.FOXA2
cell line
CFPAC1 genome-edited clonal cell line
cell type
Pancreatic Ductal Adenocarcinoma (PDAC) cell line
chip antibody
Anti-FOXA2 (Antibody sc-6554 Lot. A1014)
treatment
Isolation of clonal cell line by dilution of CFPAC1 cells electroporated with plasmid pX330A_D10A-1x4 containing Cas9 nickase (Multiplex CRISPR/Cas9 Assembly System Kit; Addgene # 1000000055) and guides targeting FOXA2 gene.

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
33204124
Reads aligned (%)
80.2
Duplicates removed (%)
14.7
Number of peaks
40361 (qval < 1E-05)

hg38

Number of total reads
33204124
Reads aligned (%)
81.7
Duplicates removed (%)
13.5
Number of peaks
40623 (qval < 1E-05)

Base call quality data from DBCLS SRA