Comment[ArrayExpressAccession]	E-GEOD-48930
MAGE-TAB Version	1.1					
Public Release Date	2013-07-17
Investigation Title	Genome-wide mapping of SPDEF and ESR1 binding in MCF-7 cells (ChIP-seq)					
Comment[Submitted Name]	Genome-wide mapping of SPDEF and ESR1 binding in MCF-7 cells (ChIP-seq)
Experiment Description	Using a transcriptional network derived from 2000 breast cancer gene expression profiles we identify the master regulators (MRs) of FGFR2 signalling. To validate the identified regulons, we examined whether there was enrichment of TF binding near the transcription start sites (TSS) of genes found in the regulons of a particular MR. For ESR1 and SPDEF, ChIP-seq experiments were performed in MCF-7 cells, while existing data was analysed for FOXA1 (Hurtado et al. Nature Genetics, 43:27–33, 2010) and GATA3 (Theodorou, et al., Genome Res 23: 12-22, 2013). ChIP-seq experiments were performed on three biological replicates per each transcription factor. For each sample, 36bp single-end reads were obtained. Peak regions were identified in all ChIP-seq TF data sets using the peak caller algorithm MACS (Zhang et al., Genome Biology, 9(9):R137, 2008) with default parameters.					
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	Alves Castro	Castro	Fletcher	de Santiago	Markowetz	Meyer
Person First Name	Mauro	Mauro	Michael	Ines	Florian	Kerstin
Person Mid Initials	Antonio					
Person Email	mauro.a.castro@gmail.com					
Person Affiliation	Cambridge Research Institute					
Person Address	Cambridge Research Institute, Robinson Way, Cambridge, United Kingdom					
Person Roles	submitter					
Protocol Name	P-GSE48930-4	P-GSE48930-1	P-GSE48930-3	P-GSE48930-2		
Protocol Description	ChIP-Seq reads were aligned to genome build hg18 and filtered by removing reads either with quality less than 5 or overlapping signal artefact regions (regions obtained from http://hgdownload-test.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeMapability/). Peaks were called using model-based analysis for ChIP-Seq (MACS) (Zhang et al., Genome Biology, 9(9):R137, 2008), run using default parameters. Quality control of the raw sequenced data was conducted using the FastQC software (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) and good quality scores across all bases were observed. To evaluate the consistency of signal between replicates we measured the read coverage over all genomic regions covering peak regions that were called in at least two of the three replicates. There is a good correlation between pairs of replicates, with Spearman’s correlation coefficients ranging from 0.51 to 0.74 Genome_build: hg18 Supplementary_files_format_and_content: Files produced by MACS that report peak positons, summit and statistics. The files named NAME_peaks.bed are in BED format which contains the peak locations and in the 5th column is the -10*log10pvalue of peak region. The files names NAME_summits.bed is in BED format, which contains the peak summits locations for every peaks, and in the 5th column in this file is the summit height of fragment pileup.	Cells growing asynchronously in full media were fixed for ChIP.	ChIP of DNA was performed as described in Schmidt et al., Methods (2009) doi: 10.1016/j.ymeth.2009.03.001 Illumina sequencing libraries were prepared as described in Schmidt et al., Methods (2009) doi: 10.1016/j.ymeth.2009.03.001	MCF7 cells were grown in DMEM supplemented with 10% heat-inactivated foetal calf serum and 1% penicillin-streptomycin.		
Protocol Type	normalization data transformation protocol	sample treatment protocol	nucleic acid library construction protocol	growth protocol		
Experimental Factor Name	CHIP TREATMENT CONDITIONS	CHIP ANTIBODY				
Experimental Factor Type	chip treatment conditions	chip antibody				
Comment[SecondaryAccession]	GSE48930					
Comment[GEOReleaseDate]	2013-07-17					
Comment[ArrayExpressSubmissionDate]	2013-07-16					
Comment[GEOLastUpdateDate]	2013-07-29					
Comment[AEExperimentType]	ChIP-seq					
Comment[SecondaryAccession]	SRP027513					
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR935442-SRR935447					
SDRF File	E-GEOD-48930.sdrf.txt