{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Ye Liu"],"organism":["Mus musculus"],"software":["Bowtie2"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17175"],"description":["To examine the impaired osteoclastogenic program in Senp6^LysM BMMs, we performed H3K9me3 CUT&RUN on WT and Senp6^LysM BMMs stimulated with RANKL for 16 h (R16) corresponding to sequential stages of early osteoclastogenesis."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - EpiCypher CUT&RUN Kit","Library Construction - CUT&RUN libraries were prepared by the Van Andel Institute Genomics Core using a standard ChIP-style library preparation workflow.","Sample Collection - BMMs from Ctrl (n = 3) and Senp6LysM (n = 2) mice were seeded into 12-well plates and treated with RANKL for 16 h. H3K9me3 CUT&RUN libraries were prepared from 50,000 cells per sample according to the EpiCypher CUT&RUN Kit v6 protocol.","Sequencing - Element AVITI 2x75bp"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Raw CUT&RUN reads were adapter-trimmed and aligned to the mm39 reference genome using Bowtie2 v2.5.4, with parallel alignment to the E. coli spike-in genome for normalization."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Element AVITI"],"study_type":["CUT&RUN"],"species":["Mus musculus"],"pubmed_title":["The deSUMOlyase SENP6 represses transposable elements-induced innate immune response to support osteoclastogenesis"],"pubmed_authors":["Ye Liu; Huadie Liu; Vladimir Molchanov; Yaguang Zhao; Saumya Bhagat; Lukai Zhai; Minmin Liu; Di Lu; H. Josh Jang; Tao Yang","Ye Liu"],"additional_accession":[]},"is_claimable":false,"name":"H3K9me3 CUT&RUN of mouse bone-marrow–derived macrophages and osteoclast precursors (RANKL-16h) from wild-type and Senp6 conditional knockout mice","description":"To examine the impaired osteoclastogenic program in Senp6^LysM BMMs, we performed H3K9me3 CUT&RUN on WT and Senp6^LysM BMMs stimulated with RANKL for 16 h (R16) corresponding to sequential stages of early osteoclastogenesis.","dates":{"release":"2026-09-28T00:00:00Z","modification":"2026-09-28T15:03:24.128Z","creation":"2026-06-16T21:15:13.149Z"},"accession":"E-MTAB-17175","cross_references":{"ENA":["ERP195219"],"Biostudies":["E-MTAB-16140","E-MTAB-16167"],"EFO":["EFO_0002944","EFO_0009973","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0004184"]}}