Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Liver
Cell type
Liver
MeSH Description
A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.

Attributes by original data submitter

Sample

source_name
Liver
background strain
C3H
tissue
liver
developmental stage
adult
antibody
Upstate 12-370
replicate
2

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Mice were anesthetized in a chamber with isoflurane (Butler Animal Health Supply). When the mouse was completely under anesthetic, it was transferred to a surgical surface and its head was inserted into a nosecone containing isoflurane. Mouse livers were perfused with 10 ml of 50 ng/ml heparin in PBS, followed by 5 ml 1% formaldehyde in PBS (Chaya et al, 2001). Perfused livers sat for 10 min of formaldehyde perfusion time at room temperature. The mouse was then sacrificed by cervical dislocation. The livers were removed and placed in 6 ml buffer A (15 mM Hepes [pH 7.6], 60 mM KCl, 15 mM NaCl, 0.2 mM EDTA, 0.5 mM EGTA, 0.34 M sucrose, 0.15 mM 2-mercaptoethanol, 125 mM glycine) on ice, and minced with scalpels. The liver was homogenized with a Teflon pestle in a glass homogenizer and a portion was observed under a microscope to confirm nuclear isolation. The nuclear suspension was filtered through a 100 μm cell strainer, layered onto a 1.5 ml cushion of 1:1 of buffer A: buffer B (15 mM Hepes [pH 7.6], 60 mM KCl, 15 mM NaCl, 0.1 mM EDTA, 0.1 mM EGTA, 2.1 M sucrose, 0.15 mM 2-mercaptoethanol) in 15 ml Corex tubes, centrifuged in a fixed angle rotor at 10K rpm for 10 min at 4°C, and the supernatant was removed. The pellets were suspended in 5 ml solution A and layered again onto 1:1 of buffer A:B, and centrifuged in a fixed angle rotor at 5K rpm for 10 min at 4°C, and the supernatant was removed. The pellet was suspended into 4 ml sonication buffer (50 mM Tris [pH8], 2 mM EDTA, 0.5 % N-Lauroylsarcosine, complete EDTA-free protease inhibitor cocktail (Roche)) and incubated for 5 min at room temperature, then 5 min on ice. The nuclear lysate was transferred to two 15 ml polystyrene conical tubes and sonicated for 45 min to 55 min (30 sec ON/ 30 sec OFF setting) with cool down intervals every 5 min using Bioruptor Sonicator UCD-200 equipped with the blue lid adaptor unit. RNase A was added to 25 ng/ul and incubated at room temperature for 10 min. Debris was removed by centrifugation at 14K rpm for 10 min at 4°C. The supernatant was dialyzed in TE (10 mM Tris [pH8], 1 mM EDTA) using 3500 MWCO Slide-A Lyzer Dialysis cassette (Thermo Scientific) at 4°C overnight. ChIP-exo experiments were carried out essentially as described with minor alterations (Rhee and Pugh, 2012). With prepared sonicated chromatin, chromatin immunoprecipitation (ChIP) was performed on biological duplicates for FoxA2 (Upstate 07-633) and IgG as a control (Upstate 12-370). See Rhee et al, Cell 2011. Libraries were created for two replicates each of FoxA2 chIP and IgG chIP. Sequencing was performed using an Illumina HiSeq 2000.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
7706868
Reads aligned (%)
82.5
Duplicates removed (%)
59.5
Number of peaks
172 (qval < 1E-05)

mm9

Number of total reads
7706868
Reads aligned (%)
82.4
Duplicates removed (%)
59.9
Number of peaks
185 (qval < 1E-05)

Base call quality data from DBCLS SRA