Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
E2F1

Cell type

Cell type Class
Breast
Cell type
MCF-7
Primary Tissue
Breast
Site of Extraction
Pleura
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
MCF-7
biomaterial_provider
ATCC
lab
USC
lab description
Farnham - University of Southern California
datatype
ChipSeq
datatype description
Chromatin IP Sequencing
cell
MCF-7
cell organism
human
cell description
mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis
cell karyotype
cancer
cell lineage
ectoderm
cell sex
F
treatment
None
treatment description
No special treatment or protocol applies
antibody
HA-E2F1
antibody antibodydescription
Mouse Monoclonal antibody HA.11 clone 16B12 was raised against the twelve amino acid peptide CYPYDVPDYASL. This second-generation HA antibody is an excellent substitute for the 12CA5 monoclonal antibody. The HA.11 antibody recognizes the influenza hemagglutinin epitope (YPYDVPDYA) which has been used extensively as a general epitope tag in expression vectors. The extreme specificity of the antibody allows unambiguous identification and quantitative analysis of the tagged protein. The HA.11 antibody recognizes HA epitopes located in the middle of protein sequences as well as at the N- or C-terminus. Antibody Target: HA-E2F1
antibody targetdescription
The HA-E2F1 protein is a derivative of E2F1, a member of the E2F family of transcription factors. The E2F family plays a crucial role in the control of cell cycle and action of tumor suppressor proteins and is also a target of the transforming proteins of small DNA tumor viruses. The E2F proteins contain several evolutionary conserved domains found in most members of the family. These domains include a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. This version of E2F1 includes an N terminal HA tag and a modified ER ligand binding domain to allow regulated translocation to the nucleus.
antibody vendorname
Covance
antibody vendorid
MMS-101P
control
UCDavis
control description
Input library was prepared at UC Davis.
control
UCDavis
control description
Input library was prepared at UC Davis.
controlid
wgEncodeEH000762
labversion
MCF-7 cells stably expressed a tagged HA-E2F1 were fragmented using Bioruptor, precipitated with StaphA and an antibody to the HA tag,
replicate
1
softwareversion
PeakSeq1.0 (fdr 0.001)

Sequenced DNA Library

library_name
GSM935477: USC_ChipSeq_MCF-7_HA-E2F1_UCDavis
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg19

Number of total reads
58130579
Reads aligned (%)
57.3
Duplicates removed (%)
9.8
Number of peaks
25804 (qval < 1E-05)

hg38

Number of total reads
58130579
Reads aligned (%)
57.8
Duplicates removed (%)
9.3
Number of peaks
25785 (qval < 1E-05)

Base call quality data from DBCLS SRA