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Series GSE48930 Query DataSets for GSE48930
Status Public on Jul 17, 2013
Title Genome-wide mapping of SPDEF and ESR1 binding in MCF-7 cells (ChIP-seq)
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary 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.
Overall design 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.
Contributor(s) Castro M, Fletcher M, de Santiago I, Markowetz F, Meyer K
Citation(s) 24043118, 27236187
Submission date Jul 16, 2013
Last update date May 15, 2019
Contact name Mauro Antonio Alves Castro
Organization name Cambridge Research Institute
Street address Robinson Way
City Cambridge
ZIP/Postal code CB2 0RE
Country United Kingdom
Platforms (1)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
Samples (6)
GSM1187116 s01_MCF7_ER_rep1
GSM1187117 s02_MCF7_ER_rep2
GSM1187118 s03_MCF7_ER_rep3
This SubSeries is part of SuperSeries:
GSE48931 Master regulators of FGFR2 signalling and breast cancer risk
BioProject PRJNA212328
SRA SRP027513

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Supplementary file Size Download File type/resource
GSE48930_RAW.tar 9.2 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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