Project description:Sequencing of mononucleosomal DNA during asynchronous mitosis in Schizosaccharomyces pombe, Schizosaccharomyces octosporus, Schizosaccharomyces japonicus and Saccharomyces cerevisiae Samples from mononucleosomal DNA from asynchronous mitosis of four species of budding (Saccharomyces cerevisiae W303-1a) and fission yeasts (S. pombe wild type 972h-, S. octosporus CBS1804, S. japonicus var. japonicus ade12- FY53) were sequenced (Illumina Genome Analyzer IIx and HiSeq 2500) using the single read and paired end protocol.
Project 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.
2026-07-28 | GSE335614 | GEO
Project description:27 ILLUMINA paired-end RNAseq samples of Saccharomyces cerevisiae industrial strains under suboptimal temperature conditions
Project description:MNase-Seq and ChIP-Seq have evolved as popular techniques to study chromatin and histone modification. Although many tools have been developed to identify enriched regions, software tools for nucleosome positioning are still limited. We introduce a flexible and powerful open-source R package, PING 2.0, for nucleosome positioning using MNase-Seq data or MNase- or sonicated- ChIP-Seq data combined with either single-end or paired-end sequencing. PING uses a model-based approach, which enables nucleosome predictions even in the presence of low read counts. We illustrate PING using two paired-end datasets from Saccharomyces cerevisiae and compare its performance to nucleR and ChIPseqR.
Project description:Intact nuclei from an asynchronous population of W303 Saccharomyces cerevisiae in log-phase growth were subjected to a 16-minute DNase I digestion (0.1 U/μL) at 37 °C. DNA was then recovered, and single-end Illumina sequencing libraries were prepared using the Crawford DNase-seq method (Song and Crawford, 2010).
2016-01-08 | GSE69651 | GEO
Project description:Illumina NextSeq 500 paired end sequencing