Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMAD2

Cell type

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

Attributes by original data submitter

Sample

source_name
PANC-1 cells
tissue
Pancreatic ductal adenocarcinoma
tissue
pancreatic carcinoma
treatment
TGFb
duration of treatment
1 hour
chip antibody
SMAD2/3 (R&D, AF3797)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and SMAD2/3--DNA complexes were isolated with antibody. Libraries were prepared according to NEB DNA UltraKit's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 12 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated using Ampure SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the H-Seq2000 following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
54212051
Reads aligned (%)
72.3
Duplicates removed (%)
26.7
Number of peaks
1138 (qval < 1E-05)

hg38

Number of total reads
54212051
Reads aligned (%)
74.1
Duplicates removed (%)
25.3
Number of peaks
958 (qval < 1E-05)

Base call quality data from DBCLS SRA