{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Andrew Holding"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15329"],"description":["While many studies have investigated the effects of hypoxia on the progression of ER-positive (ER⁺) breast cancer, the impact of hypoxia on estrogen receptor alpha (ERα) signalling remains relatively understudied. In this dataset, we examine how the hypoxia mimetic DMOG influences ERα chromatin binding in MCF7 cells using ChIP-seq."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - MCF7 cells (RRID:CVCL_0031) were cultured in DMEM (Gibco) with 10% FBS. Cells were seeded at 2 × 10⁶ per 15 cm dish and grown for 3 days. On day 4, media was replaced and cells were treated with 2 mM DMOG (or vehicle control). After 16 hours, cells were washed with PBS and crosslinked using 1% formaldehyde.","Nucleic Acid Extraction - Following immunoprecipitation, protein–DNA complexes were eluted, reverse crosslinked, and treated with RNase and proteinase K. DNA was purified using phenol-chloroform extraction and ethanol precipitation.","Sequencing - Libraries were sequenced on an Illumina NovaSeq 6000 (S4 flow cell) with 150 bp paired-end reads by Novogene.","Library Construction - ChIP DNA was used as input for library prep using the NEBNext Ultra II DNA Library Prep Kit, including end repair, adaptor ligation, size selection, and PCR amplification."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Reads were aligned to the human genome (GRCh38/hg38) using BWA-MEM (v1.1).","Data Transformation - Samples were normalised using total mapped reads. Signal intensities (e.g., coverage tracks and peak calling) were scaled by reads per million (RPM) to correct for sequencing depth differences between samples."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["ChIP-seq"],"species":["Homo sapiens"],"pubmed_authors":["Andrew Holding"],"additional_accession":[]},"is_claimable":false,"name":"ChIP-seq of ERα in MCF7 cells treated with the hypoxia mimetic DMOG versus vehicle control","description":"While many studies have investigated the effects of hypoxia on the progression of ER-positive (ER⁺) breast cancer, the impact of hypoxia on estrogen receptor alpha (ERα) signalling remains relatively understudied. In this dataset, we examine how the hypoxia mimetic DMOG influences ERα chromatin binding in MCF7 cells using ChIP-seq.","dates":{"release":"2025-07-21T00:00:00Z","modification":"2025-07-07T15:24:41.172Z","creation":"2025-07-07T15:24:41.172Z"},"accession":"E-MTAB-15329","cross_references":{"ENA":["ERP174880"],"EFO":["EFO_0002944","EFO_0004170","EFO_0002692","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"]}}