Comment[ArrayExpressAccession]	E-GEOD-46070
MAGE-TAB Version	1.1									
Public Release Date	2013-10-10
Investigation Title	Gene regulation and priming by Topoisomerase IIα in embryonic stem cells									
Comment[Submitted Name]	Gene regulation and priming by Topoisomerase IIα in embryonic stem cells
Experiment Description	This SuperSeries is composed of the SubSeries listed below. Refer to individual Series									
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl								
Person Last Name	Thakurela									
Person First Name	Sudhir									
Person Email	geo@ncbi.nlm.nih.gov									
Person Affiliation	IMB									
Person Address	IMB, Ackermaanweg4, Mainz, Germany									
Person Roles	submitter									
Protocol Name	P-GSE46070-1	P-GSE46070-4	P-GSE46070-5	P-GSE46070-7	P-GSE46070-10	P-GSE46070-9	P-GSE46070-3	P-GSE46070-2	P-GSE46070-8	P-GSE46070-6
Protocol Description	Nimblegen array intensity files were read and log2 enrichments (log2 bound/input ratios) for each individual probe were calculated using the R package Ringo (version 1.14.0, R version 2.12.1). To remove dye artifacts , both arrays were loess-normalized and scale normalized using the normalizeWithinArrays and normalizeBetweenArrays function from the limma package (version 3.6.9) ID_REF =  VALUE = loess-normalized, scale-normalized log2 (ChIP/Input) ratio	According to Nimblegen guidelines	Hybridization was performed according to standard Nimblegen procedure	Feeder-free ESCs were seeded at a density of 3.3 *10^6 cells in 10 cm dishes, medium was changed after 24 h and cells were treated after 32 h for 16 h with 500nM ICRF-193 (Sigma) or DMSO as a control.	FAIRESeq libraries were prepared by using standard ChIP library protocol for sequencing using standard Illumina protocols	RNA was extracted using Rneasy kit (Qiagen) RNA libraries were prepared for sequencing using standard Illumina protocols	ChIP experiments were performed as described before (F. Mohn et al., Mol Cell 30, 755 (Jun 20, 2008)), starting with 70 µg of chromatin and 5 µg of the Top2α antibody and the material was amplified using whole genome amplification kit (Sigma) before labeling for hybridization.	ES cells were grown as dercribed previously (Bibel 2007)	Wild type cells were grown as previously described (Bibel et al. 2004; Plachta et al. 2004; Bibel et al. 2007)	Scanning was performed with NimbleScan.
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	nucleic acid library construction protocol	nucleic acid library construction protocol	nucleic acid library construction protocol	growth protocol	growth protocol	array scanning protocol
Experimental Factor Name	STRAIN OR LINE	CHIP ANTIBODY	CELL TYPE	COMPOUND						
Experimental Factor Type	strain or line	chip antibody	cell type	compound						
PubMed ID	24072229									
Comment[SecondaryAccession]	GSE46070									
Comment[GEOReleaseDate]	2013-10-10									
Comment[ArrayExpressSubmissionDate]	2013-04-15									
Comment[GEOLastUpdateDate]	2013-10-17									
Comment[AEExperimentType]	ChIP-chip by tiling array									
Comment[AEExperimentType]	RNA-seq of coding RNA									
Comment[AEExperimentType]	ChIP-seq									
SDRF File	E-GEOD-46070.hyb.sdrf.txt	E-GEOD-46070.seq.sdrf.txt