Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
KLF4

Cell type

Cell type Class
Pancreas
Cell type
PDAC
NA
NA

Attributes by original data submitter

Sample

source_name
Pancreatic Ductal Adenocarcinoma (PDAC) cell line
cell type
original PDAC cell line
genotype/variation
wild type
antibody
Anti-KLF4
chip antibody vendor
RnD

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP lysates were generated from 2-5x10^6 cells for histone marks or 20-40x10^6 cells for transcription factors. 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 Genome Analyzer II

hg19

Number of total reads
19332623
Reads aligned (%)
79.0
Duplicates removed (%)
17.8
Number of peaks
14662 (qval < 1E-05)

hg38

Number of total reads
19332623
Reads aligned (%)
81.0
Duplicates removed (%)
16.4
Number of peaks
14658 (qval < 1E-05)

Base call quality data from DBCLS SRA