{"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-16514"],"description":["Bulk RNA-seq profiling of untreated human cell lines derived from blood, breast and bladder tissues (MCF7, MDA-MB-231, KMCB2, Jurkat) to characterise baseline transcriptional differences across cellular contexts."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - MCF7 and MDA-MB-231 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% L-glutamine. KMBC2 cells were cultured in a 1:1 mixture of DMEM and RPMI supplemented with 5% FBS. Adherent cells were maintained under standard conditions and harvested at ~90% confluence. Jurkat cells were cultured in RPMI supplemented with 10% FBS according to ATCC handling guidelines and maintained between 1 x 10^5 and 1 × 10^6 viable cells/mL. Cells were harvested and processed immediately for RNA extraction.","Nucleic Acid Extraction - Cells were stabilised in RNA later prior to extraction. Total RNA was isolated using the Monarch RNA purification column system with on-column DNase I treatment, following the manufacturer’s instructions. RNA concentration and purity were assessed prior to library preparation.","Sequencing - Illumina-compatible RNA-seq libraries were sequenced by Azenta Life Sciences using an Illumina NovaSeq platform with a 2 x 150 bp paired-end configuration.","Library Construction - Purified total RNA was submitted to the University of York Bioscience Technology Facility (BTF) Genomics Laboratory for library preparation. Poly(A) RNA was enriched from total RNA and used for stranded library construction according to standard Illumina-compatible protocols. Libraries were indexed and amplified prior to sequencing."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Monarch RNA purification column system","Illumina NovaSeq 6000","Standard mammalian cell culture equipment","Illumina-compatible library preparation equipment"],"pubmed_abstract":["The glucocorticoid receptor (GR) coordinates diverse transcriptional responses to glucocorticoids, regulating metabolism, inflammation, homeostasis, and development. Although GR is expressed in nearly every cell type, its activity is tissue-specific and shaped by context-dependent protein interactions. To enable comprehensive, quantitative profiling of GR interactomes across tissue types and cell states, we developed DIANNeR: a label-free proteomic pipeline combining immunoprecipitation with data-independent acquisition mass spectrometry (DIA-MS) and the DIA-NN software. DIANNeR provides a 2-fold increase in quantification of specific protein–protein interactions over DDA-RIME, without requiring isotopic labelling. Applied to GR, DIANNeR revealed distinct context-dependent interaction networks. We observed loss of a HOXA5–GR interaction during the transition from breast epithelium to cancer lines and patient-derived xenografts (PDXs), and a CD4  + T cell-specific GR interaction with FOXP3 and BCL11B, not detected in epithelial or Jurkat cells. Conversely, the SWI/SNF complex subunit SMARCD3 was consistently enriched in GR interactomes from normal human breast and urothelial cells but absent in CD4  + T cells, suggesting lineage-specific roles and the potential for selective modulation of GR activity in different contexts.  Our findings establish DIANNeR as a robust, scalable platform for resolving tissue-specific transcription factor interactomes, and reveal features of GR signalling with implications for cancer biology and immunology. <h4>Abstract Figure</h4>"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_title":["Label-free DIA-NN enabled RIME (DIANNeR) reveals glucocorticoid receptor interaction networks in breast, bladder, and blood across normal untransformed cells, cancer cell lines, and PDXs"],"pubmed_authors":["Weiye Zhao, Susanna F Rose, Thomas F Grimes, Jack Stenning, Chris Taylor, Chloë Baldreki, Iain Goulding, Ros Duke, Simon C Baker, Marcela Montes de Oca, Aparna Sinha, Jenny Hinley, James M Fox, Paul M Kaye, Jennifer J Gomm, Louise J Jones, Elisabetta Marangoni, Bruno M Simões, Robert B Clarke, Jennifer Southgate, Katherine S Bridge, Adam Dowle, Andrew N Holding","Andrew Holding"],"additional_accession":[]},"is_claimable":false,"name":"Bulk RNA-seq of untreated human cell lines from multiple tissues","description":"Bulk RNA-seq profiling of untreated human cell lines derived from blood, breast and bladder tissues (MCF7, MDA-MB-231, KMCB2, Jurkat) to characterise baseline transcriptional differences across cellular contexts.","dates":{"release":"2026-01-25T00:00:00Z","modification":"2026-01-25T02:01:51.895Z","creation":"2026-01-12T15:56:31.674Z"},"accession":"E-MTAB-16514","cross_references":{"ENA":["ERP187486"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003738","EFO_0004184"],"doi":["10.1101/2025.08.07.669166"]}}