{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["veronica manicardi"],"instrument_platform":["NextSeq 500"],"study_type":["ChIP-seq"],"organism":["Homo sapiens"],"species":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14152"],"description":["The aim of the experiment was to explore the RUNX2 genomic functions in the papillary thyroid carcinoma. To this end, we performed Chromatin Immunoprecipitation followed by deep-sequencing using an antibody against RUNX2, RNA-Polymerase II and Histone Marks (H3K27ac, H3K4me1, H3K4me3) in MDA-T41  thyroid cancer cell line, in order to define the genomic regions bound by this transcription factor."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Sequencing was performed by Illumina Nextseq 500 instrument (High output kit v2, 1x75 cycles)","Growth Protocol - MDA-T41 cells were grown in RPMI-1640 supplemented with 1% non-essential amino acids, 10% FBS and 1% penicillin-streptomycin. All cell lines were grown at 37°C/ 5% CO2 and routinely tested for mycoplasma infection.","Library Construction - Libraries were obtained starting from 3ng of ChIP and Input samples following ThruPLEX DNA-Seq Kit (Takara Bio Ink) protocol.","Nucleic Acid Extraction - ChIP samples were purified with PCR Purification Kit (Qiagen) and eluted in 50ul of Elution Buffer.","Sample Collection - 20M cells were collected for Chromatin Immunoprecipitation."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["veronica manicardi"],"additional_accession":[]},"is_claimable":false,"name":"ChIP-seq  against RUNX2, RNA-Polymerase II and Histone Marks (H3K27ac, H3K4me1, H3K4me3) in human Papillary Thyroid Cancer cell line (MDA-T41)","description":"The aim of the experiment was to explore the RUNX2 genomic functions in the papillary thyroid carcinoma. To this end, we performed Chromatin Immunoprecipitation followed by deep-sequencing using an antibody against RUNX2, RNA-Polymerase II and Histone Marks (H3K27ac, H3K4me1, H3K4me3) in MDA-T41  thyroid cancer cell line, in order to define the genomic regions bound by this transcription factor.","dates":{"release":"2025-12-31T00:00:00Z","modification":"2025-12-31T02:02:13.684Z","creation":"2024-06-06T09:47:33.354Z"},"accession":"E-MTAB-14152","cross_references":{"ENA":["ERP160916"],"Biostudies":["E-MTAB-13777"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0002692","EFO_0005518","EFO_0004184"]}}