Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ZEB1

Cell type

Cell type Class
Pancreas
Cell type
MIA Paca-2
Primary Tissue
Pancreas
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
Pancreatic Ductal Adenocarcinoma (PDAC) cell line
cell line
original PDAC cell line (MiaPaCa2)
antibody
Anti-ZEB1 (Antibody SC-25388 Lot. H1513)
treatment
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP lysates were generated from 20-40x10^6 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 QIAquick columns (Qiagen) and quantified using PicoGreen (Invitrogen). ChIP DNA was prepared for HiSeq 2000 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
Illumina HiSeq 2000

hg19

Number of total reads
38116991
Reads aligned (%)
55.0
Duplicates removed (%)
42.1
Number of peaks
2369 (qval < 1E-05)

hg38

Number of total reads
38116991
Reads aligned (%)
57.0
Duplicates removed (%)
40.6
Number of peaks
2419 (qval < 1E-05)

Base call quality data from DBCLS SRA