{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Eleanor Wigmore"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16414"],"description":["MCF7, T47D and CAMA-1 cell lines were treated with long-term (continuous) capivasertib to induce resistant cell-lines (T47D P1, MCF7 P1 and CAMA-1 P1). The naïve (or parental) cell lines had RNAseq sequencing at treatment with DMSO and treatment with capivasertib. Resistant cell lines had RNAseq sequencing at treatment with continuous capivasertib, removal of continuous capivasertib and treatment with DMSO and then re-treatment with capivasertib monotherapy. This gave 5 time points across the different 3 different cell lines."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - ibraries were quantified with the D1000 ScreenTape assay (Agilent; 5067-5582, 5067-5583) on the Tapestation 4200 system (Agilent) and subsequently pooled equimolar. The final pooled library was loaded onto two lanes of a NovaSeq X Series 25B flow cell (Illumina; 20104706) and run at a paired end 150 base pair configuration (300 cycles) with 1% PhiX spiked in on a NovaSeq X Plus (Illumina).","Sequencing - Ooly(A)+ mRNA enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490L; New England Biolabs) with oligo‑dT magnetic beads, performed at the sequencing center/institute. Libraries represent poly(A)+ mRNA (not total RNA) prepared at the sequencing center/institute, enabling transcriptome profiling of coding genes without UMIs.","Sample Collection - Cells were cultured for 6 months with increasing doses of capivasertib up to 10μM. Once generated, CapiR cells were routinely cultured in RPMI media (Gibco #11835-063) supplemented with 10% Fetal Calf Serum (FCS), 1% Glutamax, 10μM capivasertib and incubated at 37°C, 5% CO2.","Nucleic Acid Extraction - RNA was extracted from the treated cells using the AllPrep RNA Mini Kit (Qiagen, 80504). RNA-Seq was performed with poly(A) selection using standard methods"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Quantification on the transcript and gene level was performed using the DRAGEN quantification module with enabled GC bias correction and automatic strand detection, resulting with the output of gene and transcript counts and normalized TPMs. Grch38 reference with decoys and HLA (GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set) was used in the quantification step and ERCCs were not included in the reference.","Sequence Alignment - The run was processed using Illumina DRAGEN pipeline, software version 4.0 (07.021.645.4.0.3). The demultiplexing step was executed using DRAGEN bcl-to-fastq conversion program bclConvert. The resulting fastq files were aligned to combined hg38-ERCC reference genome using the DRAGEN RNA-Seq spliced aligner. Quantification on the transcript and gene level was performed using the DRAGEN quantification module with enabled GC bias correction and automatic strand detection, resulting with the output of gene and transcript counts and normalized TPMs. Grch38 reference with decoys and HLA (GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set) was used in the quantification step and ERCCs were not included in the reference."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq X"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_title":["Targeting the epigenetic regulators KDM5C enhances  AKT inhibitor response in ER+ breast cancer."],"pubmed_authors":["Eleanor Wigmore","Simon Barry","Valentina Cutano, Shanade Dunn, Sungmi Park-Chouinard, Eleanor M. Wigmore, Qing Wu, Lambert Montava Garriga, Lorna Hopcroft, David Esopi, Michele Chirichella, Siyu Liu, Cath Eberlein, Ming Tang, Hyung Joo Lee, Wenhao Zhang, Megan Callahan, Barrett Nuttall, Daniel Barrell, Toby Gurran, Jennifer Hillis, Adam Spruce, Ramy Elgendy, Jenna Bradley, Chang Kim, Sara Talbot, Laura Rosenberg, Susana Ros, Huayang Liu, Neeraj Aryal, Functional Genomics Centre, Jerome T. Mettetal, Ho Man Chan, Ultan McDermott and Simon T. Barry"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of human breast cancer cell line MCF7, T47D and CAMA-1 treated that are naïve and resistant to capivasertib and have been treated with acute capivasertib, continuous capivasertib and DMSO","description":"MCF7, T47D and CAMA-1 cell lines were treated with long-term (continuous) capivasertib to induce resistant cell-lines (T47D P1, MCF7 P1 and CAMA-1 P1). The naïve (or parental) cell lines had RNAseq sequencing at treatment with DMSO and treatment with capivasertib. Resistant cell lines had RNAseq sequencing at treatment with continuous capivasertib, removal of continuous capivasertib and treatment with DMSO and then re-treatment with capivasertib monotherapy. This gave 5 time points across the different 3 different cell lines.","dates":{"release":"2026-05-25T00:00:00Z","modification":"2026-05-26T17:05:05.302Z","creation":"2025-12-18T18:12:47.393Z"},"accession":"E-MTAB-16414","cross_references":{"ENA":["ERP186784"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}