{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE335nnn/GSE335614/"]},"type":"primary"},"statusCodeValue":200,"statusCode":"OK"}],"scores":null,"additional":{"omics_type":["Genomics"],"species":["Homo sapiens"],"gds_type":["Genome binding/occupancy profiling by high throughput sequencing"],"full_dataset_link":["https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE335614"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"Concentration-dependent MNase-seq with yeast spike-in normalization resolves nucleosome occupancy and accessibility in human induced pluripotent stem cells (nucMACC)","description":"Micrococcal nuclease sequencing (MNase-seq) maps nucleosome occupancy and positioning genome-wide but is sensitive to digestion conditions and lacks standardized, quantitative normalization. We developed a refined, scalable MNase-seq workflow and applied it to human induced pluripotent stem cells (hiPSCs; FUCCI-reporter line PB010.5) across a five-point MNase digestion titration (0.5, 1, 3, 6, and 10 U), with an in-house Saccharomyces cerevisiae mononucleosomal spike-in (~5% of input DNA) added for cross-sample normalization. Libraries were sequenced on two platforms (Illumina NovaSeq X, 150 bp paired-end; Illumina NextSeq 2000, 50 bp paired-end) and analyzed with the nucMACC pipeline to quantify concentration-dependent shifts between mononucleosomal and subnucleosomal fragments and to resolve the nucleosome-depleted region and +1/-1 nucleosome positioning at transcription start sites. nucMACC accessibility scores stratified nucleosomes into hyper- and hypo-accessible classes corresponding to active and repressive chromatin states.","dates":{"publication":"2026/07/28"},"accession":"GSE335614","cross_references":{"GSM":["GSM9816380","GSM9816379","GSM9816378","GSM9816377","GSM9816376","GSM9816375","GSM9816374","GSM9816373","GSM9816372","GSM9816371"],"GPL":["30173","34281"],"GSE":["335614"],"taxon":["Homo sapiens"],"PMID":["[42558761]"]}}