Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
FOXM1

Cell type

Cell type Class
Uterus
Cell type
HeLa
Primary Tissue
Cervix
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
HeLa S3_FOXM1 ChIP
cell line
HeLa S3
cell type
epithelial
chip antibody
FOXM1 Antibody (C-20)
chip antibody vendor
Santa Cruz

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
HeLa cells were fixed with 1% formaldehyde before the DNA was sonicated to a fragment length of 200-600bp with a Bioruptor® (Diagenode, Sparta, NJ). Antibodies were bound to a mix of Protein A and Protein G Dynabeads® (Life Technologies, Grand Island, NY) before an 18 hour incubation at 4°C with the fragmented DNA. DNA was washed and crosslinks reversed before purification with a QIAquick™ PCR purification kit (QIAGEN, Valencia, CA). DNA concentrations were measured using Quant-iT™ PicoGreen® (Life Technologies, Grand Island, NY). A library was constructed from the bound fragments per manufacturer's protocols and the DNA fragments from each independent ChIP were sequenced independently at the UNC High Throughput Sequencing Facility using an Illumina Genome Analyzer II.

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

hg19

Number of total reads
16956667
Reads aligned (%)
44.2
Duplicates removed (%)
3.7
Number of peaks
674 (qval < 1E-05)

hg38

Number of total reads
16956667
Reads aligned (%)
45.0
Duplicates removed (%)
2.9
Number of peaks
640 (qval < 1E-05)

Base call quality data from DBCLS SRA