Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
FOXM1

Cell type

Cell type Class
Pluripotent stem cell
Cell type
hESC VAL-3
NA
NA

Attributes by original data submitter

Sample

source_name
human embryonic stem cell
cell type
ES cells
passage
73
cell line
VAL-3
chip-antibody
Santa Cruz FOXM1-C20 (sc-502)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
VAL-3 cells were treated with 1% paraformaldehyde for chromatin cross-linking before cell lysis and sonication to generate DNA fragments. Fragmented chromatin mixed with Dynabeads protein G was incubated with either FOXM1 antibody or rabbit IgG at 4°C overnight. Successive rounds of magnetic clearance were performed, followed by crosslink reversal with NaCl incubation and protein digestion with proteinase K. DNA was purified using the Wizard® PCR clean-up system (Promega) Libraries were prepared according to Illumina's instructions. Briefly, DNA-end was repaired to overhang a 3'-dA, then adapters were ligated to the end DNA fragments. DNA fragments with proper size (usually 100-300bp, including adaptor sequence) were selected after PCR amplification, followed by library construction.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
21721942
Reads aligned (%)
59.1
Duplicates removed (%)
35.1
Number of peaks
1236 (qval < 1E-05)

hg38

Number of total reads
21721942
Reads aligned (%)
60.3
Duplicates removed (%)
34.1
Number of peaks
1179 (qval < 1E-05)

Base call quality data from DBCLS SRA