Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

Cell type

Cell type Class
Others
Cell type
Epithelial cells
NA
NA

Attributes by original data submitter

Sample

ENA first public
2015-07-24
ENA last update
2018-03-08
ENA-CHECKLIST
ERC000011
External Id
SAMEA3157842
INSDC center alias
Pfizer Neusentis
INSDC center name
Pfizer Neusentis
INSDC first public
2015-07-24T17:01:24Z
INSDC last update
2018-03-08T21:49:23Z
INSDC status
public
Submitter Id
E-MTAB-3137:FOXM1 1
broker name
ArrayExpress
cell type
epithelial cell
common name
human
sample name
E-MTAB-3137:FOXM1 1

Sequenced DNA Library

library_name
FOXM1 1
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
RPE were generated from the hESC cell line SHEF1.3 or iPSC reprogrammed from erythroblasts using the spontaneous differentiation method described previously (Vugler et al., 2008). Pluripotent cells were cultured as feeder-free colonies on hESC-qualified Matrigel (BD) in mTesR1 (StemCell Technologies) media. RPE foci were excised with a scalpel and dissociated into a single cell suspension using Accutase (Gibco) and plated onto CellStart (Invitrogen) coated surfaces. ChIP was performed essentially as described before (Sanders et al., 2013). Briefly, 1 million cells were crosslinked with 1% Formaldehyde for 10 minutes and the reaction was quenched with 125mM glycine. Sonication was performed on isolated nuclei using the Bioruptor Plus with cooling system for 35 cycles of each 30 seconds on and 30 seconds off at the maximum setting leading to a fragment size between 200-300bp. For each IP, 50 ul of Protein A Dynabeads were incubated with 5 ug of the appropriate antibody (anti-FOXM1 [Santa Cruz Biotechnology, SC-502] or Rabbit IgG REF) overnight at 4oC. Chromatin immunoprecipitation was performed by adding the 100 ul of preblocked antibody-bead complexes per sample and incubating overnight at 4oC on a rotator. Elution and crosslink reversal of both sample and input was performed by incubating the samples for 6 hours at 65oC in a waterbath. The DNA was purified using the Zymo ChIP DNA Clean & Concentrator kit (Zymo Research) according to the manufacturer's instructions. The sequencing library was generated using the MicroPlex Library Preparation kit (Diagenode) and size selected using Agencourt AMPure XP. The libraries were quantified using the qPCR based Illumina library quantification kit (Kappa Biosystems) .

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
38667125
Reads aligned (%)
93.7
Duplicates removed (%)
45.4
Number of peaks
1600 (qval < 1E-05)

hg19

Number of total reads
38667125
Reads aligned (%)
92.8
Duplicates removed (%)
47.3
Number of peaks
1384 (qval < 1E-05)

Base call quality data from DBCLS SRA