{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Domenico Memoli"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16473"],"description":["AKAP1 is highly expressed in glioblastoma and is required for tumor growth. We therefore analyzed the AKAP1 RNA interactome in glioblastoma cells. Native RNA immunoprecipitation followed by high-throughput sequencing (RIP-Seq) was performed in U87MG cells transiently expressing V5-tagged mouse wild-type AKAP1, as well as deletion mutants lacking either the KH (Δ563–630) or Tudor (Δ709–786) domain, to assess domain-specific RNA binding."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Growth Protocol - The human glioblastoma cell line U87MG was cultured in Dulbecco’s Modified Eagle Medium supplemented with 10% fetal bovine serum, L-glutamine, penicillin, streptomycin, and Amphotericin B in a humidified incubater in the presence of 5% CO2.","Sample Collection - For each AKAP1-associated RNA immunoprecipitation (RIP) reaction, an anti-V5 antibody was conjugated to sheep anti-mouse IgG–conjugated beads. Protein lysates prepared from U87MG cells transiently transfected with empty vector, wild-type AKAP1, or AKAP1 deletion mutants were incubated with the antibody-conjugated beads. An aliquot of diluted protein lysate was reserved for subsequent RNA extraction as the “input” control. Bead–lysate mixtures were incubated overnight at 4 °C with rotation, followed by four washes with NT2 buffer.","Nucleic Acid Extraction - Input samples and washed post-IP reaction beads were resuspended in NT2 buffer and treated with proteinase K to release RNAs from RNA–protein complexes. RNA was then purified using the RNA Clean & Concentrator™-5 Kit (Zymo Research) according to the manufacturer’s instructions.","Sequencing - An equimolar pool of libraries at a concentration of 1.2 nM was sequenced on the NovaSeq 6000 platform (Illumina) using 2 × 100 bp paired-end mode.","Library Construction - Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Gold kit (Illumina).","Sample Treatment - Vectors encoding wild-type or mutant AKAP1 were transiently transfected into U87MG cells using linear polyethylenimine."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - normalization performed using deseq2 default procedure","Sequence Alignment - we used STAR alignment tool using human h38 as reference"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RIP-seq"],"species":["Homo sapiens"],"pubmed_authors":["Domenico Memoli"],"additional_accession":[]},"is_claimable":false,"name":"RNA sequencing–based determination of the RNA interactome of wild-type AKAP1 and its deletion mutants deficient for the KH or Tudor domain.","description":"AKAP1 is highly expressed in glioblastoma and is required for tumor growth. We therefore analyzed the AKAP1 RNA interactome in glioblastoma cells. Native RNA immunoprecipitation followed by high-throughput sequencing (RIP-Seq) was performed in U87MG cells transiently expressing V5-tagged mouse wild-type AKAP1, as well as deletion mutants lacking either the KH (Δ563–630) or Tudor (Δ709–786) domain, to assess domain-specific RNA binding.","dates":{"release":"2026-09-01T00:00:00Z","modification":"2026-09-01T01:00:38.746Z","creation":"2025-12-22T18:55:40.225Z"},"accession":"E-MTAB-16473","cross_references":{"ENA":["ERP187053"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005310","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184","EFO_0003969"]}}