Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
FOXA2

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

Alias
E-MTAB-805:Human-Foxa2-Hep
Broker name
ArrayExpress
Description
Protocols: Briefly, 14-15 day old mice were injected with DEN (20 mg/kg body weight) (Sigma) to initiate tumor growth. Beginning at 28 days, mice were injected with TCPOBOP (3 mg/kg bodyweight) (Sigma) once every two weeks for a total of eight times to promote tumor growth.DEN-induced liver injury experiments were carried out as described previously (Naugler etal., 2007), except that 50 mg/kg body weight Faslodex or estrogen were intraperitoneally injected daily for seven days before DEN treatment. The human samples were not treated. Chromatin was extracted from mouse livers following the protocol described in Li et al. NSMB 2011 [PMID 21623366]. ChIP was performed on the liver chromatin samples. ChIP-DNA was prepared for sequencing with the Illumina GAII sequencer at the Functional Genomics Center at the Institute for Diabetes, Obesity and Metabolismat the University of Pennsylvania.
INSDC center alias
UNIVERSITY OF PENNSYLVANIA
INSDC center name
University of Pennsylvania, USA
INSDC first public
2012-06-25T20:05:40Z
INSDC last update
2018-03-08T15:33:19Z
INSDC status
public
OrganismPart
liver
SRA accession
ERS074989
Sample Name
ERS074989
Sex
female
StrainOrLine
Caucasian
Title
Human-Foxa2-Hep

Sequenced DNA Library

library_name
Hu_Liver_Hep_FoxA2
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Briefly, 14-15 day old mice were injected with DEN (20 mg/kg body weight) (Sigma) to initiate tumor growth. Beginning at 28 days, mice were injected with TCPOBOP (3 mg/kg bodyweight) (Sigma) once every two weeks for a total of eight times to promote tumor growth.DEN-induced liver injury experiments were carried out as described previously (Naugler etal., 2007), except that 50 mg/kg body weight Faslodex or estrogen were intraperitoneally injected daily for seven days before DEN treatment. The human samples were not treated. Chromatin was extracted from mouse livers following the protocol described in Li et al. NSMB 2011 [PMID 21623366]. ChIP was performed on the liver chromatin samples. ChIP-DNA was prepared for sequencing with the Illumina GAII sequencer at the Functional Genomics Center at the Institute for Diabetes, Obesity and Metabolismat the University of Pennsylvania.

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

hg19

Number of total reads
8301762
Reads aligned (%)
75.5
Duplicates removed (%)
18.1
Number of peaks
662 (qval < 1E-05)

hg38

Number of total reads
8301762
Reads aligned (%)
77.5
Duplicates removed (%)
16.8
Number of peaks
533 (qval < 1E-05)

Base call quality data from DBCLS SRA