Comment[ArrayExpressAccession]	E-MTAB-2204
MAGE-TAB Version	1.1
Investigation Title	FOXK2 ChIP-seq Illumina
Comment[Submitted Name]	FOXK2 ChIP-seq Illumina
Experiment Description	Chromatin immunoprecipitation of FOXK2 (tagged with Flag and His tags) in U2OS cells detected by Illumina sequencing
Experimental Design	binding_site_identification_design
Comment[AEExperimentType]	ChIP-seq
Comment[AEExperimentDisplayName]	ChIP-seq of FOXK2 tagged with Flag and His tags in U2OS cells detected by Illumina sequencing
Experimental Factor Name	immunoprecipitate
Experimental Factor Type	immunoprecipitate
Quality Control Type	biological replicate
Quality Control Term Source REF	EFO
Public Release Date	2014-07-23
Person Last Name	Donaldson
Person First Name	Ian
Person Mid Initials	J
Person Email	ian.donaldson@manchester.ac.uk
Person Phone
Person Address	University of Manchester, Manchester, UK
Person Affiliation	University of Manchester
Person Roles	submitter
Protocol Name	P-MTAB-36934	P-MTAB-36935	P-MTAB-36936	P-MTAB-36937
Protocol Type	growth protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	high throughput sequence alignment protocol
Protocol Description	U2OS cells, were grown in DMEM supplemented with 10% foetal bovine serum.	ChIP was performed as previously described (Marais et al., 2010) using ~8-10 x 10+7 U2OS-FOXK2-HF cells stably expressing FOXK2 tagged with Flag and His tags (~4M-^W150 mm plates) . Marais A, Ji Z, Child ES, Krause E, Mann DJ, Sharrocks AD. 2010. Cell cycle-dependent regulation of the Forkhead transcription factor FOXK2 by CDK-cyclin complexes. J Biol Chem. 285: 35728-35739. Anti-Flag (Sigma-Aldrich, F3165)	~10-20 ng of immunoprecipitated DNA from U2OS was sent for sequencing using the Illumina platform according to the manufacturers protocols.	ELAND software (Illumina) was used to align reads against the hg18 reference genome. All 36 bp were aligned and filtered using default parameters.
Protocol Term Source REF	EFO	EFO	EFO	EFO
Protocol Hardware			Illumina Genome Analyzer IIx
Term Source Name	EFO
Term Source File	http://www.ebi.ac.uk/efo
SDRF File	E-MTAB-2204.sdrf.txt
PubMed ID	24748658
Publication Author List	Ji Z, Mohammed H, Webber A, Ridsdale J, Han N, Carroll JS, Sharrocks AD
Publication Title	The forkhead transcription factor FOXK2 acts as a chromatin targeting factor for the BAP1-containing histone deubiquitinase complex.
Publication DOI	10.1093/nar/gku27