Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
FOXM1

Cell type

Cell type Class
Kidney
Cell type
293
Primary Tissue
Kidney
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
HEK293 Flp-In cells
cell type
293 Flp
antibody
anti-FOXM1 (GTX-1000276 and GTX102170)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
IP was carried out as described in Schmidt et al. (2009) (PMID 19275939). In brief, cells were cross-linked using 1% formaldehyde for 10 min at RT, reaction was quenched with 1/20th volume 2.5M Glycine and cell pellets were collected after scraping plates. Nuclear lysates were prepared by lysing with LB1 (50mM Hepes-KOH, pH 7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton-X plus PI) 10 min at 4°C and LB2 (10mM Tris-HCl, pH8.0, 200mM NaCl, 1mM EDTA, 0.5M EGTA plus PI) 5 min at 4°C, followed by sonication in LB3 (10mM Tris-HCl, pH8.0, 100mM NaCl, 1mM EDTA, 0.5M EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine plus PI) using a diagnode sonicator to give a fragment size of ~200-300bp. Sonicated lysate was combined with 100ul protein-A magnetic beads preloaded with either 10 ug anti-FOXM1 antibody (GeneTex (USA); cat no. GTX-1000276 and GTX102170) or 10 μl anti-GFP antibody (Abcam, Cambridge, UK; ab290) O/N at 4°C. Beads were washed X6 in RIPA buffer (50mM HEPES pH7.6, 1mM EDTA, 0.7% Na deoxycholate, 1% NP-40, 0.5M LiCl) and DNA was eluted for 16 hr at 65°C in elution buffer (50mM Tris-HCl, pH8.0, 10mM EDTA, 1% SDS). Extracted DNA was treated with RNase A for 30 min at 37°C, followed by Proteinase K for 1 hr at 55°C, and DNA was purified by phenol-chloroform extraction and quntified by bioanalyzer and quibit. Illumina ChIP-seq kit sample prep kit was used to prepare duplicate/triplicate samples

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
36209008
Reads aligned (%)
92.8
Duplicates removed (%)
4.9
Number of peaks
1127 (qval < 1E-05)

hg38

Number of total reads
36209008
Reads aligned (%)
94.3
Duplicates removed (%)
3.9
Number of peaks
928 (qval < 1E-05)

Base call quality data from DBCLS SRA