Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
HNF1A

Cell type

Cell type Class
Digestive tract
Cell type
Caco-2
Primary Tissue
Colon
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
Colorectal adenocarcinoma cells
cell line
Caco2
antibody
HNF1 (Santa-Cruz sc-6554)
style parameter used for peak calling
factor
input used for peak calling
Caco2 Input Replicate 2

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were lysed in lysis buffer (5mM PIPES pH 8.0, 85mM KCL, 0.5% NP-40, 1x Protese Inhibitor Cocktail (Roche)). Nuclei were isolated by centrifugation, lysed in RIPA buffer (1x PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, Protease Inhibitor Cocktail), and sonicated. Protein-DNA complexes were isolated with the FOXA2 antibody. DNA ends were blunted using T4 DNA polymerase, Klenow DNA polymerase, and T4 polynucleotide kinase. Next, DNA was incubated with Klenow exo- to add 5’ adenine overhangs. Multiplex adaptors were then ligated to the ends and converted to dsDNA using 5 cycles of PCR. DNA was size-selected to contain fragments between 200 and 300bp and PCR amplified for 5 cycles. DNA was purified with 1.2x AMPsureXP beads. Sequencing was preformed on an Illumina Hi-Seq.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
22292715
Reads aligned (%)
88.7
Duplicates removed (%)
4.8
Number of peaks
2093 (qval < 1E-05)

hg38

Number of total reads
22292715
Reads aligned (%)
90.6
Duplicates removed (%)
3.5
Number of peaks
2271 (qval < 1E-05)

Base call quality data from DBCLS SRA