{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Giulio Aceto"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15707"],"description":["To examine the role SMARCA4-p53 regulatory axis in SCCOHT cells we performed RNA-seq in BIN-67 cells with SMARCA4 restoration, p53ko alone or combined with SMARCA4 and idasanutlin treatment (0.5μM, 24h) which increase the stability of p53 and its protein levels in SCCOHT."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - 1ug total RNA was used for the library construction. RNA libraries for RNA-Seq were prepared using the SMARTER mRNA-Seq library.","Sequencing - Samples were collected with an illumination Next Sequence 500 instrument.","Sample Collection - BIN-67, BIN-67 p53ko, BIN-67 with SMARCA4 restoration and BIN-67 p53ko cells with SMARCA4 restoration were cultured in Roswell Park Memorial Institute 1640 Medium (RPMI, Thermo Fisher Scientific, Cat# 11875-093; no pyruvate) with 6% fetal bovine serum (Sigma, Cat# F1051), 1% penicillin/streptomycin (Thermo Fisher Scientific, Cat# 15140-122), and 2 mM L-glutamine (Thermo Fisher Scientific, Cat# 25030-081). Cells were maintained in a humidified 5% CO2-containing incubator at 37°C and regular Mycoplasma test was performed using Mycoalert Detection Kit (Lonza, Cat# LT07-318).  Cells were treated with 0.5μM idasanutlin for 24h. Total RNA was collected with the RNeasy Mini Kit (Qiagen, Hilden, Germany).","Nucleic Acid Extraction - Total RNA was extracted with the RNeasy Mini Kit (Qiagen, Hilden, Germany)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Sequencing files were aligned to the human reference genome (hg38) using STAR (v2.6.1c). Gene expression levels were quantified using Homer or HTseq  with Gencode gene annotation (GTF) files. Differentially expressed genes were identified using Edger."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 500"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Giulio Aceto","Sidong Huang"],"additional_accession":[]},"is_claimable":false,"name":"Examining the effect of SMARCA4–p53 regulatory axis on SCCOHT cells transcription","description":"To examine the role SMARCA4-p53 regulatory axis in SCCOHT cells we performed RNA-seq in BIN-67 cells with SMARCA4 restoration, p53ko alone or combined with SMARCA4 and idasanutlin treatment (0.5μM, 24h) which increase the stability of p53 and its protein levels in SCCOHT.","dates":{"release":"2026-05-05T00:00:00Z","modification":"2026-05-05T17:59:05.116Z","creation":"2025-10-09T21:45:50.627Z"},"accession":"E-MTAB-15707","cross_references":{"ENA":["ERP181314"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}