biostudies-arrayexpressDomenico PalumboHomo sapiensDESeq2https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15354To understand molecules involved in DOT1L-menin-ERα complex formation, we performed a native nuclear RIP-Seq approach in MCF-7 BC cell line. Here, we submit 3 samples immunoprecipitated with anti-MEN1 and two samples with anti-IgG (E-MTAB-14147).biostudies-arrayexpressSample Collection - Cells were washed twice with cold PBS supplemented with 0.1% of EDTA (500 mM), harvested by scraping and collected in a tube. After a centrifugation at 3000 rpm for 5 min at 4°C, the nuclear fraction was extracted by resuspending the pellet in nuclear isolation Buffer (NIB) (1.28 M Sucrose, 40 mM Tris-HCl pH 7.5, 20 mM MgCl2 and 4% Triton X-100) supplemented with 100 U/ml RNAse inhibitor (RiboLock RNase Inhibitor, Invitrogen) and proteinase inhibitors (1mM PMSF and 1x PIC). Samples were incubated on ice for 20 min and then centrifuged at 2500 x g at 4°C for 15 min. Once removed the supernatant, nuclear pellets were resuspended in 400 µl of RIP Buffer (150 mM KCl, 25 mM Tris pH 7.4, 5 mM EDTA, 0.5 mM DTT e 0.5% NP40) supplemented with 100 U/ml RNAse and proteinase (1mM PMSF and 1x PIC) inhibitors. Cell nuclei were sonicated for 10 cycles (15\" ON and 15\" OFF) using Bioruptor (Diagenode, Denville, New Jersey, USA) and subsequently centrifuged at 13000 rpm for 10 min at 4°C.Sequencing - RIP-Seq libraries were sequenced on NextSeq 500 (Illumina) using 2 x 75 bp paired endLibrary Construction - TruSeq Stranded Total RNA Library Prep Gold (Cat. 20020599, Illumina, San Diego, California, USA)Nucleic Acid Extraction - 1 ml of TRIzol (Life Technologies, Thermo Fisher) was added directly to the beads and RNA extraction was performed according to the manufacturer's guidelinesOrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Fastq were generated from bcl files using bcl2fastq (Illumina v2.20.0.422), while the quality check was assessed using FastQC (v0.11.9). The adapters were removed using cutadapt (v 3.3) and the resulted fastq were aligned on human genome (hg38) using STAR (v 2.7.8a) with assembly of GENCODE v37 as GTF file. Eventually, the raw counts were generated using featurecounts (v2.0.1). The differential expression analysis and the normalized counts were produced using DESeq2 (v 1.38.3) on R (4.2.2).MetabolomicsUnknownTranscriptomicsGenomicsProteomicsDELL PRECISION 7500noneNextSeq 500RNA-seq of coding RNAHomo sapiensDomenico PalumbofalseNuclear RNA immunoprecipitation of MEN1 in MCF-7 BC cell lineTo understand molecules involved in DOT1L-menin-ERα complex formation, we performed a native nuclear RIP-Seq approach in MCF-7 BC cell line. Here, we submit 3 samples immunoprecipitated with anti-MEN1 and two samples with anti-IgG (E-MTAB-14147).2026-01-30T00:00:00Z2026-01-30T17:18:41.753Z2025-07-14T13:06:12.246ZE-MTAB-15354ERP176752E-MTAB-14147EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184