Nucleosome positioning maps in vivo
Below is the repository of nucleosome positioning datasets in vivo. This collection is part of NucPosDB, a manually curated database of experimental nucleosome maps in vivo, cfDNA and computational tools related to nucleosome positioning
Jump to: NucPosDB front page | stable nucleosomes of the human genome | experimental nucleosome maps in vivo | experimental cfDNA datasets | tools for analysis of nucleosome mapping experiments | tools for prediction of nucleosome maps from DNA sequence | tools for analysis of sequenced cfDNA
| Description | Organism | Cell type | Experiment type | GEO ID | Link (other ID) |
|---|---|---|---|---|---|
| Genome-wide MNase hypersensitivity assay unveils distinct classes of open chromatin associated with H3K27me3 and DNA methylation (Zhao et al., 2020). | Arabidopsis thaliana | MH-seq | GSE142495 | ||
| The histone variant H2A.Z and chromatin remodeler BRAHMA act coordinately and antagonistically to regulate transcription and nucleosome dynamics in Arabidopsis (Torres and Deal, 2019). | Arabidopsis thaliana | MNase-seq | GSE108450 | ||
| DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes (Lyons and Zilberman, 2017). | Arabidopsis thaliana | MNase-seq | GSE96994 | ||
| Genome-wide chromatin mapping with size resolution reveals a dynamic sub-nucleosomal landscape in Arabidopsis (Pass et al., 2017). | Arabidopsis thaliana | Col0 | MNase-seq | GSE94377 | |
| Arabidopsis Chromatin Assembly Factor 1 is required for occupancy and position of a subset of nucleosomes (Muñoz-Viana et al., 2017) | Arabidopsis thaliana | Col leaf, fas2 leaf, Col-0 seedling, fas2 seedling | MNase-seq | GSE87421 | |
| Transcriptional Regulation of the Ambient Temperature Response by H2A.Z Nucleosomes and HSF1 Transcription Factors in Arabidopsis (Cortijo et al., 2017) | Arabidopsis thaliana | Col0 seedlings | MNase-seq | GSE79355 | |
| Arabidopsis, Col-0 seeds; chr11-1 chr17-1, (Li et al. 2014) | Arabidopsis thaliana | Col-0 seeds | MNase-seq | GSE50242 | |
| Arabidopsis, Col-0 seeds; WT and inhibition of Pol V-produced lncRNAs. MNase-seq (Zhu et al. 2013) | Arabidopsis thaliana | Col-0 seeds | MNase-seq | GSE38401 | |
| Genome-wide identification of regulatory DNA elements and protein-binding footprints using signatures of open chromatin in Arabidopsis (Zhang et al., 2012). | Arabidopsis thaliana | MNase-seq | GSE34318 | ||
| Relationship between nucleosome positioning and methylation Chodavarapu et al., 2010). | Arabidopsis thaliana | MNase-seq, H3 ChIP-seq | GSE21821 | ||
| Col-0 seeds, shoots; MNase-seq, ChIP-seq, Bisulfite sequencing (Chodavarapu et al. 2010) | Arabidopsis thaliana | Col-0 seeds | MNase-seq | GSE21673 | |
| Nucleosome occupancy of C. elegans wild-type (N2) early stage embryos vs. mature sperm from him-8(e1489) males (Tabuchi, Rechtsteiner and Strome, 2018). | Caenorhabditis elegans | MNase-seq | GSE115705 | ||
| Chromatin accessibility dynamics across C. elegans development and ageing ( Jänes et al., 2018) | Caenorhabditis elegans | MNase-seq | GSE114481 | ||
| Nucleosome fragility is associates with future transcriptional response to developmental cues and stress in C. elegans ( Jeffers and Lieb, 2017) | Caenorhabditis elegans | MNase-seq | GSE79567 | ||
| A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning (Valouev et al, 2008). | Caenorhabditis elegans | Mixed stage, wild-type (N2) | MNase-seq | SRX000426 | |
| Chlamydomonas strain CC 1609. MNase-seq (Fu et al., 2015) | Chlamydomonas reinhardtii | strain: CC 1609 | MNase-seq | GSE62690 | |
| Genetic ablation of maternal SoxB1 results in the delay of gastrulation gene regulatory program in zebrafish (Gao, Veil and Onichtchouk, 2020). | Danio rerio | MNase-seq | GSE125945 | ||
| Pou5f3, SoxB1 and Nanog remodel chromatin on High Nucleosome Affinity Regions at Zygotic Genome Activation (Veil et al., 2019). | Danio rerio | MNase-seq | GSE109410 | ||
| Quantitative MNase-seq accurately maps nucleosome occupancy levels. (Chereji, Bryson and Henikoff, 2019). | Drosophila melanogaster | S2, Kc167 | MNase-seq | GSE128689 | |
| The NSL complex–mediated nucleosome landscape is required to maintain transcription fidelity and suppression of transcription noise (Lam et al., 2019). | Drosophila melanogaster | S2, Kc | MNase-seq | GSE118726 | |
| The NSL complex–mediated nucleosome landscape is required to maintain transcription fidelity and suppression of transcription noise (Lam et al., 2019). | Drosophila melanogaster | S2, Kc | MNase-ChIP | GSE118726 | |
| Genome-wide measurement of local nucleosome array regulatiry and spacing by nanopore sequencing (Baldi et al., 2018) | Drosophila melanogaster | Nanopore-seq, MNase-seq | GSE110807 | ||
| CHRAC/ACF contribute to the repressive ground stated of chromatin (Scacchetti et al., 2018) | Drosophila melanogaster | MNase-seq | GSE106731 | ||
| Nucleosome and H1 maps generated from AEL 3-4hr and 14-15hr D. melanogaster embryos (Hu et al., 2018). | Drosophila melanogaster | MNase-seq | GSE101327 | ||
| CBP regulates recruitment and release of promoter-proximal RNA polymerase II (Boija et al., 2017) | Drosophila melanogaster | S2 | MNase-seq | GSE100614 | |
| Enhanced chromatin accessibility of the dosage compensated Drosophila male X chromosome requires the CLAMP zinc finger protein (Urban et al., 2017) | Drosophila melanogaster | S2, Kc | MNase-seq | GSE99893 | |
| Transcription and Remodeling produce asymmetrically unwrapped nucleosomal intermediates (Ramachandran et al., 2017) | Drosophila melanogaster | S2 | MNase-seq | GSE98351 | |
| Widespread changes in nucleosome accessibility without changes in nucleosome occupancy during a rapid transcriptional induction (Mueller et al., 2017) | Drosophila melanogaster | S2 | MNase-seq | GSE95689 | |
| A comparison of nucleosome organization in Drosophila cell lines (Martin et al., 2017) | Drosophila melanogaster | S2, Cme-L1, ML-DmD11, ML-DmD20, ML-DmD17 | MNase-seq | GSE85584 | |
| ACF1 regulates nucleosome spacing in Drosophila chromatin (Baldi et al., 2018) | Drosophila melanogaster | BG3-c2 | MNase-seq, MNase-assisted H3 ChIP-seq | GSE85406, GSE85407 | |
| Using affinity purification approach to capture different stages of glial-specific information on gene expression, nucleosome occupancy and histone modifications (HMs) in Drosophila melanogaster embryo (Ye et al., 2016). | Drosophila melanogaster | Embryonic glial cells | MNase-seq | GSE83376 | |
| Chromatin remodeling during in vivo neural stem cells differentiating to neurons in early Drosophila embryos. (Ye et al., 2017). | Drosophila melanogaster | NSC, neurons | MNase-seq | GSE80457 | |
| GAGA factor, a positive regulator of global gene expression, modulates transcriptional pausing and organization of upstream nucleosomes (Tsai et al., 2016) | Drosophila melanogaster | MNase-seq | GSE70633 | ||
| Genome-wide profiling of nucleosome sensitivity and chromatin accessibility in D. melanogaster (Chereji et al., 2016). | Drosophila melanogaster | 12h embryo and S2 cells | MNase-seq | GSE69177 | |
| Genome-wide profiling of nucleosome sensitivity and chromatin accessibility in D. melanogaster (Chereji et al., 2016). | Drosophila melanogaster | 12h embryo and S2 cells | MNase-assisted H3 ChIP-seq | GSE69177 | |
| Active N6-Methyladenine demethylation by DMAD regulates gene expression by modulating the binding dynamics of Polycomb protein in neurons (Yao et al., 2018) | Drosophila melanogaster | BG3-c2 | MNase-seq | GSE67855 | |
| Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation (Sun et al., 2015) | Drosophila melanogaster | Orego-R | MNase-seq | GSE65441 | |
| S2 cell line. WT and stimulated by heat killed Salmonella typhimurium (Ren et al., 2015) | Drosophila melanogaster | S2 | MNase-seq | GSE64507 | |
| S2 cell line. WT; treated with RNAi against Beta-galactosidase or GAGA (Fuda et al., 2015) | Drosophila melanogaster | S2 | MNase-seq | GSE58957 | |
| RNAi-depleted GAF from Drosophila S2 cells and their the effects on promoter-proximal polymerase (Fuda and Lis, 2015). | Drosophila melanogaster | S2 | MNase-seq | GSE58956 | |
| S2 cell line. WT and Beaf32-depleted (Lhoumaud et al., 2014) | Drosophila melanogaster | S2 | MNase-seq | GSE57166 | |
| Genome-wide maps of PARP-1-bound nucleosomes (Matveeva et al., 2016) | Drosophila melanogaster | S2 | MNase-seq | GSE56120 | |
| CTCF/CP190 and ISWI dependent regulation of nucleosome occupancy (Bohla et al., 2014) | Drosophila melanogaster | S2 | H3 ChIP-seq | GSE51600 | |
| S2 cell line. WT and depletion of CTCF/P190 and ISWI (Bohla et al. 2014). | Drosophila melanogaster | S2 | MNase-seq | GSE51599 | |
| S2 cell line, WT (Nalabothula et al. 2014). | Drosophila melanogaster | S2 | MNase-seq | GSE49526 | |
| Staged Drosophila embryos (Chen et al. 2013). | Drosophila melanogaster | S2 | MNase-seq | GSE41686 | |
| Poised RNA Polymerase II changes over developmental time and prepares genes for future expression ( Gaertner et al., 2012) | Drosophila melanogaster | MNase-seq | GSE34283 | ||
| S2 cell line. WT, mock-treated, and NELF-depleted (Gilchrist et al. 2010). | Drosophila melanogaster | S2 | MNase-seq | GSE22119 | |
| Single-molecule Regulatory Architectures Captured by Chromatin Fiber Sequencing (Stergachis et al., 2020). | Homo sapiens | K562 | Fiber-seq | GSE146941 | |
| MNase sensitivity of promoter chromatin in GM12878 cells during stimulation with heat-killed Salmonella typhimurium (Cole and Dennis, 2019). | Homo sapiens | GM12878 | MNase-seq | GSE139224 | |
| Redefining the nucleosomal architecture of active and inactive promoters in the context of cellular plasticity and cancer (Dennis et al., 2020). | Homo sapiens | MCF10A, MCF10A-CA1a | MNase-seq | GSE134297 | |
| MYCN knock-down leads to DNA-repair deficiency in human neuroblastoma (Hu et al., 2019) | Homo sapiens | BE(2)C | MNase-seq | GSE120857 | |
| Genome-wide nucleosome positioning maps from undifferentiated human iPS cells (hIPS) and iPS cells differentiated to neural progenitor cells (NPC) (Harwood and Harwood, 2019). | Homo sapiens | hIPSC, NPC | MNase-seq | GSE117870 | |
| Characterising the nuclease accessibility of DNA in human cells to map higher order structures of chromatin (Schwartz et al., 2019) | Homo sapiens | HeLa | MNase-seq | GSE100401 | |
| Tyrosine-1 of RNAPII CTD controls global termination of gene transcription in mammals (Shah et al., 2018). | Homo sapiens | Raji B cells | MNase-seq | GSE94330 | |
| MNase titration with four different MNase amounts in K562 (low coverage) (Mieczkowski et al., 2016) | Homo sapiens | K562 | MNase-seq | GSE78984 | |
| Histone modification and nucleosome mapping in human liver cancer cells histone modification data at the single nucleosome resolution in human embryonic stem cells, normal hepatocytes, and liver cancer cells of both genders (Zheng et al., 2019). | Homo sapiens | HepG2 | MNase-seq | GSE76344 | |
| Genome-wide maps of chromatin state during the differentiation of hESC into hNECs (Du et al., 2017) | Homo sapiens | hESC; hESC-derived neuroectoderm cells | MNase-seq | GSE76083 | |
| Widespread Chromatin Accessibility at Repetitive Elements Links Stem Cells with Human Cancer (Gomez et al., 2016) | Homo sapiens | H1 ESC; Cultured Kidney Cell | MNase-seq | GSE75172 | |
| Antisense transcription predicts a distinct chromatin environment at mammalian promoters (Lavender et al., 2016) | Homo sapiens | T47D/A1-2 | MNase-seq | GSE74308 | |
| Targeting the SIN3A-PF1 Interaction inhibits Epithelial to Mesenchymal Transition and Maintenance of a Stem Cell Phenotype in Triple Negative Breast Cancer (Bansal et al., 2015) | Homo sapiens | MDA-MB-231 | MNase-seq | GSE73869 | |
| Nucleosome positioning and chromatin state in GATA3-mediated mesenchymal-epithelial transition (low coverage MNase-seq) (Takaku et al., 2016) | Homo sapiens | MDA-MB-231 | MNase-seq | GSE72141 | |
| Nucleosome Repositioning: Nicotine- and Cocaine-induced Changes (Brown et al., 2015). | Homo sapiens | SH-SY5Y | MNase-ChIP | GSE71795 | |
| Intrinsic histone acetyltransferase activity of BRD4 is responsible for nucleosome eviction and transcriptional activation (Devaiah et al., 2016) | Homo sapiens | U2OS | MNase-seq | GSE71577 | |
| Histone retention loci alteration in human sperm cell genome after density selection (Yu et al., 2015) | Homo sapiens | Sperm | MNase-seq | GSE71483 | |
| SF3B1 association with chromatin determines splicing outcomes (Kfir et al., 2015) | Homo sapiens | HeLa | MNase-seq | GSE65644 | |
| MNase-seq of chromatin from control and Snail2-expressing oral keratinocytes (Lyons and Delic, 2015) | Homo sapiens | HN13(TVA) | MNase-seq | GSE65191 | |
| HuRef lymphoblastoid line, α-satellite arrays of centromeres (Henikoff et al., 2015) | Homo sapiens | HuRef | MNase-seq | GSE60951 | |
| Human embryonic stem cells, induced pluripotent stem cells and differentiated fibroblasts (West et al., 2014) | Homo sapiens | hESC, hiPSC, hFib | MNase-seq | GSE59062 | |
| Chromatin modification dynamics at p53 binding sites upon treatment with DMSO or nutlin3-a (5uM) in IMR90 human lung fibroblasts using ChIP-seq and RNA-seq analyses; genomewide changes in H3, H3K4me3, H3K4me2, H3K4me1, H3K27ac, H4K16ac, RNA polymerase II, and p53 in response to p53 activation (Sammons et al., 2015). | Homo sapiens | IMR90 | H3 ChIP-seq | GSE58740 | |
| HCT116 colon cancer cells and their genetic derivatives which lack DNA methyltransferases DNMT3B and DNMT1 activity (Lay et al., 2015) | Homo sapiens | HCT116 | NOME-seq | GSE58638 | |
| HUVEC cells stimulated with tumour necrosis factor alpha (TNFalpha) (Diermeier et al. 2014) | Homo sapiens | HUVEC | MNase-seq | GSE53343 | |
| Tyrosine phosphorylation of RNA Polymerase II CTD is associated with antisense promoter transcription and active enhancers in mammalian cells | Homo sapiens | Raji B-cell line | MNase-seq | GSE52914 | |
| MCF-7 (breast cancer cell line) with and without MBD3 knockdown (Shimbo et al. 2013) | Homo sapiens | MCF-7 | MNase-seq | GSE51097 | |
| Nucleosome Organization in Human Embryonic Stem Cells (Yasdi et al., 2015). | Homo sapiens | H1, H9 hESC | MNase-seq | GSE49140 | |
| Human sperm (Samans et al. 2014). Limited regions retain nucleosomes in sperm. | Homo sapiens | Sperm | MNase-seq | GSE47843 | |
| Sequencing and genome-wide mapping of 146 bp mono-nucleosomal DNA from human and bovine sperm | Homo sapiens | Sperm | MNase-seq | GSE47843 | |
| Human colo829 cell line | Homo sapiens | colo829 | MNase-seq | GSE47802 | |
| Nucleosome positioning changes during human embryonic stem cell differentiation | Homo sapiens | hESC (WA09, WA09-INM, WA09-SMC) | MNase-seq | GSE46467 | |
| Nucleosome positioning changes during human embryonic stem cell differentiation | Homo sapiens | hESC (WA09, WA09-INM, WA09-SMC) | MNase-seq | GSE46461 | |
| DNA sequence explains seemingly disordered methylation levels in partially methylated domains of Mammalian genomes | Homo sapiens | IMR90 | MNase-seq | GSE44985 | |
| Raji cells (lymphoblastoid-like) with and without α-amanitin (Fenouil et al. 2012) | Homo sapiens | Raji cells | MNase-seq | GSE38563 | |
| 7 lymphoblastoid cell lines from the HapMap project (Gaffney et al. 2012). | All nucleosomes| Stable nucleosomes | Homo sapiens | lymphoblastoid cells | MNase-seq | GSE36979 | |
| Lymphoblastoid GM12878 and K562 cell lines (Kundaje et al. 2012) | Homo sapiens | GM12878, K562 | MNase-seq | GSE35586 | |
| CD36+ cells with and without BRG1 knockdown (Hu et al. 2011) | Homo sapiens | CD36+ | MNase-seq, ChIP-seq | GSE26501 | |
| Human embryonic carcinoma (NCCIT) cell line (Jung et al. 2012) | Homo sapiens | NCCIT | MNase-seq, ChIP-seq | GSE25882 | |
| Primary CD4+ T-cells, CD8+ T-cells and granulocytes (Valouev et al. 2011) | Homo sapiens | CD4+, CD8+ T-cells | MNase-seq | GSE25133 | |
| MCF7EcoR cells where P53 was either activated or not (Lidor Nili et al. 2010) | Homo sapiens | MCF-7, MCF7EcoR | MNase-seq | GSE22783 | |
| Nucleosome positioning and DNA methylation in IMR90 (Kelly et al. 2012). | Homo sapiens | IMR90 | NOME-seq | GSE21823 | |
| Pilot ENCODE: Determination of chromatin architecture along 44 human loci selected by the ENCODE consortium as common targets for genomic analysis, totalling 30 Mbp. The patterns of core histone H3 and five histone modifications were investigated: H3ac, H4ac, H3K4me1, H3K4me2, H3K4me3 (Heintzman et al., 2007). | Homo sapiens | HeLa | H3 ChIP-chip | GSE6273 | |
| Resting and activated CD4+ T cells (Schones et al., 2008). | Homo sapiens | CD4+ T cells | MNase-seq | SRA000234 | |
| Resting and activated CD4+ T cells (Schones et al., 2008). | Homo sapiens | CD4+ T cells | H3 ChIP-seq | SRA000234 | |
| Integrative Analysis of Multi-omics Data Reveals AP-1 Is a Key Regulator in Intrahepatic Cholangiocarcinoma (He et al., 2020). | Homo sapiens | SSP-25, CCLP-1, TFK-1, HuCCT1, HIBEpic | PRJNA588522 SUB6386682 | ||
| Chromatin conformation identification by Cut-C ( Shimbo et al., 2019). | Homo sapiens | HEK293T | Micro-C | GSE125988 | |
| Investigation of Rsf1 genomic distribution and effect on gene expression (Zhang et al., 2017) | Homo sapiens, Mus musculus | V6.5 | MNase-seq | GSE83360 | PRJNA325671, SRP076563 |
| Human exonization through differential nucleosome occupancy (Li et al., 2018) | Homo sapiens, Mus musculus, Macaca mulatta, Sus scrofa, Tupaia belangeri | Brain, muscle, heart, kidney, liver | MNase-seq | GSE106578 | |
| Defining TP53 pioneering capabilities with competitive nucleosome binding assays (Yu and Buck, 2019). | Multispecies | MiSeq | PRJNA498696 | ||
| Polycomb repressive complex 1 shapes the nucleosome landscape but not accessibility at target genes (King et al.,2018) | Mus musculus | mESC | MNase-seq | GSE117767 | |
| BAF250a Protein Regulates Nucleosome Occupancy and Histone Modifications in Priming Embryonic Stem Cell Differentiation (Lei et al., 2015) | Mus musculus | mESC | MNase-seq | GSE59082 | PRJNA254343, SRP044051 |
| NF-Y controls fidelity of transcription initiation at gene promoters through maintenance of the nucleosome-depleted region ( Oldfield et al., 2019) | Mus musculus | mESC | MNase-seq | GSE115110 | PRJNA473812, , SRP149362 |
| Co-regulation of transcription factor binding and nucleosome occupancy through DNA features of mammalian enhancers (Barozzi et al., 2014) | Mus musculus | primary macrophage | MNase-seq | GSE50762 | PRJNA218857, SRP029883 |
| Regulation of nucleosome architecture and factor binding revealed by nuclease footprinting of the ESC genome (Hainer et al., 2015) | Mus musculus | mESC | MNase-seq | GSE68400 | PRJNA282642, SRP057797 |
| Replication-independent histone turnover confers regulatory genome for adult heart homeostasis (Li et al., 2019) | Mus musculus | cardiomyocytes | MNase-seq | GSE103680 | PRJNA404043, SRP117236 |
| Differential Nucleosome Spacing in Neurons and Glia (Clark et al., 2020). | Mus musculus | Neurons, glia | MNase-seq | GSE133966 | |
| MeCP2 regulates gene expression through recognition of H3K27me3 (Lee et al., 2020) | Mus musculus | SH-SY5Y | MNase-seq | GSE125585 | |
| High-resolution analysis of chromatin structure by MNase-SSP (Ramani, Qui and Shendure, 2019). | Mus musculus | mESC | MNase-SSP | GSE125053 | |
| Contribution of H3K4 demethylase KDM5B to nucleosome organization in embryonic stem cells revealed by micrococcal nuclease sequencing (Kurup, Campeanu and Kidder, 2019). | Mus musculus | mESC | MNase-seq | GSE123249 | |
| NOMe-seq data obtained from mouse embryonic stem cells (Requena et al., 2019). | Mus musculus | mESC | NOME-seq | GSE122964 | |
| Transcription factor activity and nucleosome organisation in mitosis (Owens and Navarro, 2019). | Mus musculus | mESC | MNase-seq | GSE122589 | |
| Transcription factor activity and nucleosome organisation in mitosis (Owens and Navarro, 2019). | Mus musculus | mESC | MNase-assisted H3 ChIP-seq | GSE122589 | |
| Polycomb repressive complex 1 shapes the nucleosome landscape but not accessibility at target genes (King et al., 2018) | Mus musculus | mESC | MNase-seq | GSE117767 | |
| DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries (Wiehle et al., 2019). | Mus musculus | mESC | MNase-assisted H3 ChIP-seq | GSE114599 | |
| Mammalian ISWI and SWI/SNF selectively mediate binding of distinct groups of transcription factors (Barisic et al., 2019). | Mus musculus | mESC | MNase-seq | GSE112134 | |
| Single-cell MNase-seq (scMNase-seq) measures genome-wide nucleosome positioning and chromatin accessibility simultaneously in single cell (Lai et al., 2018). | Mus musculus | NIH3T3, mESC, naïve CD4 T cells | scMNase-seq | GSE96688 | |
| Histone variant H2A.L.2 guides transition protein - dependent protamine assembly in male germ cells (Barral et al., 2017). | Mus musculus | Spermatocyte, spermatid | MNase-seq | GSE93251 | |
| Mouse adenocarcinoma cells, untreated and treated with dexamethasone. Conventional and pioneer modes of glucocorticoid receptor interaction with enhancer chromatin in vivo (Johnson et al., 2018). | Mus musculus | 3134 adenocarcinoma cells | MNase-seq | GSE92505 | |
| Transcriptional repression by FACT is linked to regulation of chromatin accessibility at the promoter of ES cells (Mylonas and Tessarz, 2018) | Mus musculus | mESC | MNase-seq | GSE90906 | |
| Early-life gene expression in neurons modulates lasting epigenetic states (Stroud et al., 2017) | Mus musculus | Neuron | MNase-seq | GSE90906 | |
| A high-resolution map of transcriptional repression (Liang et al., 2017). | Mus musculus | pre-B cell line B3 | MNase-seq | GSE89716 | |
| Functional Roles of Acetylated Histone Marks at Mouse Meiotic Recombination Hot Spots (Getun et al., 2017) | Mus musculus | Testis | MNase-seq | GSE87057 | |
| Epigenetic silencing of miR-125b is required for normal B-cell development (Li et al., 2018) | Mus musculus | MNase-seq | GSE82144 | ||
| Insights into Nucleosome Organization in Mouse Embryonic Stem Cells through Chemical Mapping (Voong et al., 2016) | Mus musculus | mESC | MNase-seq | GSE82127 | |
| MNase titration reveals differences between nucleosome occupancy and chromatin accessibility (Mieczkowski et al., 2016) | Mus musculus | mESC, NPC | MNase-seq | GSE78984 | |
| Nuclease footprints in sperm project past and future chromatin regulatory events (Johnson et al., 2016) | Mus musculus | C57BL/6 | MNase-seq | GSE78075 | |
| Whole genome nucleosome positioning by MNase-seq on the mouse tumor line, RMA (Wight et al., 2016) | Mus musculus | NK-T, RMA | MNase-seq | GSE71863 | |
| Rube et al. Sequence features accurately predict genome-wide MeCP2 binding in vivo. Nat Commun 2016 Mar 24;7:11025 (Rube et al., 2016) | Mus musculus | Olfactory epithelium | MNase-seq | GSE71126 | |
| Mouse thymocytes (Teng et al., 2015) | Mus musculus | thymocytes | MNase-seq | GSE69474 | |
| Mouse ESCs (Ishii et al. 2015) (Ishii et al., 2015) | Mus musculus | mESC | MNase-seq, MPE-seq | GSE69098 | |
| Hypothalamus from MeCP2 knockout mice and control mice (Chen et al., 2015) | Mus musculus | Hypothalamus | MNase-seq | GSE66869 | |
| Mouse ESCs, wild type (WT) and Dnmt1/3a/3b triple knockout (Yearim et al., 2015) | Mus musculus | mESC | MNase-seq | GSE64910 | |
| Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells (de Dieuleveult et al., 2016) | Mus musculus | mESC | MNase-seq | GSE64825 | |
| Mouse bone marrow-derived macrophages (BMDMs) (Scruggs et al., 2015) | Mus musculus | BMDM, macrophage | MNase-seq | GSE62151 | |
| Dynamically reorganized chromatin is the key for the reprogramming of somatic cells to pluripotent cells (Huang et al., 2015) | Mus musculus | MEF | MNase-assisted H3 ChIP-seq | GSE60627 | |
| WCE and histone H3 ChIP-seq samples are compared to H3K27me3 ChIP-seq and RNA-seq (Flensburg et al., 2014). | Mus musculus | H3 ChIP-seq | GSE59419 | ||
| Mouse EScs, WT and remodeler BAF250a knockout (Lei et al., 2015) | Mus musculus | mESC | MNase-seq | GSE59082 | |
| Mouse ESCs, induced pluripotent stem cells (iPSCs), somatic tail-tip fibroblasts (TTF) and liver (West et al., 2014) | Mus musculus | mESC, iPSC, TTF | MNase-seq | GSE59062 | |
| Mouse ESCs and sperm. Different size-selection of MNase-seq fragments (Carone et al., 2014) | Mus musculus | mESC | MNase-seq | GSE58101 | |
| Mouse liver, 3-mohth and 21-month old mice (Bochkis et al., 2014) | Mus musculus | Liver | MNase-seq | GSE58005 | |
| Hypersensitive Nucleosomes in Chromatin Are Intrinsic to the Structure of Active, Tissue-Specific Enhancers. The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation (Iwafuchi-Doi et al., 2016) | Mus musculus | Liver | MNase-seq | GSE57558 | |
| Mouse ESCs, siRNA knockdown of EGFP, Smarca4 or MBD3 (Hainer et al., 2015) | Mus musculus | mESC | MNase-seq | GSE57170 | |
| Mouse ESCs, low MNase digestion; dinucleosome fraction (Teif et al. 2014) | Mus musculus | mESC | MNase-seq | GSE56938 | |
| Primary CD4+ CD8+ DP thymocytes and Rag2 -/- thymocytes (Zacarias-Cabeza et al. 2015) | Mus musculus | CD4+, CD8+, DP thymocytes | MNase-seq | GSE56395 | |
| Transcriptional landscape of Rag2 -/- thymocytes. Cauchy et al. Dynamic recruitment of Ets1 to both nucleosome-occupied and -depleted enhancer regions mediates a transcriptional program switch during early T-cell differentiation. Nucleic Acids Res 2016 May 5;44(8):3567-85 | Mus musculus | Rag2 -/- thymocytes, primary CD4+ CD8+ DP thymocytes | MNase-seq | GSE56360 | |
| Siklenka et al. Disruption of histone methylation in developing sperm impairs offspring health transgenerationally. Science 2015 Nov 6;350(6261):aab2006 | Mus musculus | sperm | MNase-seq | GSE55471 | |
| Cultured germline stem cells with and without Scml2 knockout (Hasegawa et al. 2015). | Mus musculus | Cultured germline stem cells | MNase-seq | GSE55060 | |
| ACF chromatin remodeling complex mediates stress-induced depressive-like behavior through nucleosome repositioning and transcriptional regulation. | Mus musculus | nucleus accumbens | MNase-assisted H3 ChIP-seq | GSE54263 | |
| Mouse B-cell to macrophage lineage switching, several time points. | Mus musculus | B-cell, macrophage | MNase-seq | GSE53460 | |
| Nucleosome density map during B-cell to Macrophage lineage switching. van Oevelen et al. C/EBPα Activates Pre-existing and De Novo Macrophage Enhancers during Induced Pre-B Cell Transdifferentiation and Myelopoiesis. Stem Cell Reports 2015 Aug 11;5(2):232-47 | Mus musculus | HAFTL (pre-B cells) | MNase-seq | GSE53460 | |
| Mouse ESCs and differentiated iMEFs. RED-seq | Mus musculus | mESC | RED-seq | GSE51821 | |
| Mouse ESCs (J1) (Zhang et al. 2014) | Mus musculus | mESC | MNase-seq, ChIP-seq | GSE51766 | |
| Mouse ESCs, low MNase digestion (Chen et al. 2013) | Mus musculus | mESC | MNase-seq | GSE50706 | |
| Mouse ESCs (E14) and SMARCAD1-knock down cells. | Mus musculus | mESC | MNase-seq | GSE47802 | |
| Mouse liver, 6 time points of the 24h light:dark cycle; WT and Bmal1-/- (Menet et al. 2014). | Mus musculus | Liver | MNase-seq | GSE47142 | |
| Mouse ESCs and induced pluripotent cells (iPSC) from different layers (Tao et al. 2014) | Mus musculus | mESC, iPSC | MNase-seq | GSE46716 | |
| Mouse ESCs, neural progenitor cells (NPCs) and neurons with and without HMGN1 knockout. MNase-seq using high and low MNase digestion levels (Deng et al. 2013). | Mus musculus | mESC, NPC | MNase-seq | GSE44175 | |
| Mouse ESCs, NPCs and embryonic fibroblasts (MEFs) (Teif et al. 2012). | Mus musculus | mESC, NPC, MEF | MNase-seq | GSE40951 | |
| Genome-wide nucleosome positioning during embryonic stem cell development (Teif et al., 2012). | Mus musculus | mESC, NPC, MEF | MNase-seq | GSE40910 | |
| Fibroblasts from E13.5 embryos. WT, Snf5-/- and Brg1-/- (Tolstorukov et al. 2013). | Mus musculus | MEF | MNase-seq | GSE38670 | |
| CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters (Fenouil et al., 2012) | Mus musculus | CD4+, CD8+, DP, Raji, ESC | MNase-seq | GSE38577 | |
| Mouse liver (Li et al. 2012). | Mus musculus | Liver | MNase-seq, ChIP-seq | GSE26729 | |
| Resolving the 3D landscape of transcription-linked mammalian chromatin folding (Hsieh et al., 2020). | Mus musculus | mESC | Micro-C | GSE130275 | |
| 3D ATAC-PALM: Super-resolution Imaging of the Accessible Genome (Xie et al., 2020). | Mus musculus | mESC | Micro-C | GSE126112 | |
| An RNA binding region in CTCF regulates chromatin looping and CTCF nuclear organization ( Hansen et al., 2019). | Mus musculus | mES | Micro-C | GSE123636 | |
| Novel nucleosomal particles containing core histones and linker DNA but no histone H1 (Cole et al., 2016) | Mus musculus, Saccharomyces cerevisiae | MNase-seq | GSE65889 | ||
| Proper nucleosome positioning by the DIM-1 chromatin remodeler prevents intergenic cytosine methylation but allows DNA damage by 5-azacytidine in Neurospora crassa (Klocko et al., 2019). | Neurospora crassa | MNase-seq | GSE98911 | ||
| Proper nucleosome positioning by the DIM-1 chromatin remodeler prevents intergenic cytosine methylation but allows DNA damage by 5-azacytidine in Neurospora crassa (Klocko et al., 2019). | Neurospora crassa | H3 ChIP-seq | GSE98911 | ||
| Genomic analysis of N. crassa histone H1 ( Seymour et al., 2016) | Neurospora crassa | MNase-seq | GSE78157 | ||
| Genome-wide nucleosome positioning is orchestrated by genomic regions associated with DNase I hypersensitivity in rice (Wu, Zhang and Jiang, 2014). | Oryza sativa | MNase-seq | GSE53027 | SRR1536110 | |
| The nucleosome landscape of P. falciparum reveals chromatin architecture and dynamics of regulatory sequences ( Kensche et al., 2016) | Plasmodium falciparum | MNase-seq | GSE66185 | ||
| Genome information processing by the INO80 chromatin remodeler positions nucleosomes ( Oberbeckmann et al., 2020) | Saccharomyces cerevisiae | Hu0303 | MNase-seq | GSE145093 | |
| Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome ( Oberbeckmann et al., 2019) | Saccharomyces cerevisiae | MNase-seq | GSE141043 | ||
| Ruler elements in chromatin remodelers set nucleosome array spacing and phasing (Oberbeckmann et al., 2020) | Saccharomyces cerevisiae | MNase-seq | GSE140614 | ||
| Nucleosome profiles in strains with different number of nucleosomes at HML and HMR ( Saxton and Rine, 2019 ) | Saccharomyces cerevisiae | MNase-seq | GSE136897 | ||
| Topoisomerases modulate the timing of meiotic DNA breakage and chromosome morphogenesis in Saccharomyces cerevisiae ( Heldrich et al., 2020) | Saccharomyces cerevisiae | MNase-seq | GSE131994 | ||
| Sir2 suppresses transcription-mediates displacement of Mcm2-7 replicative helicases at the ribosomal DNA repeats ( Foss et al., 2019 ) | Saccharomyces cerevisiae | MNase-seq | GSE130273 | ||
| Distinct transcriptional roles for Histone H3-K56 acetylation during cell cycle ( Topal et al., 2019 ) | Saccharomyces cerevisiae | MNase-seq | GSE126686 | ||
| Engineered Chromatin Remodeling Proteins for Precise Nucleosome Positioning ( Donovan et al., 2019 ) | Saccharomyces cerevisiae | MNase-seq | GSE123237 | ||
| The nucleosome acidic patch directly interacts with subunits of the Paf1 and FACT complexes and controls chromatin architecture in vivo (Cucinotta et al., 2019). | Saccharomyces cerevisiae | MNase-seq | GSE121543 | ||
| The nucleosome acidic patch directly interacts with subunits of the Paf1 and FACT complexes and controls chromatin architecture in vivo (Cucinotta et al., 2019). | Saccharomyces cerevisiae | H3 ChIP-seq | GSE121543 | ||
| Crosstalk between chromatin structure, cohesin activity and transcription ( Maya-Miles et al., 2019 ) | Saccharomyces cerevisiae | MNase-seq | GSE121067 | ||
| FACT mediates cohesin function on chromatin ( Garcia-Luis et al., 2019) | Saccharomyces cerevisiae | MNase-seq | GSE118534 | ||
| FACT activity and histone H3-K56 acetylation promote optimal establishment of chromatin architecture independent of ongoing transcription in Saccharomyces cerevisiae ( McCullough et al., 2019 ) | Saccharomyces cerevisiae | MNase-seq | GSE118330 | ||
| A role for Chromatin Remodeling in Cohesin Loading onto Chromosomes ( Muñoz et al., 2019 ) | Saccharomyces cerevisiae | MNase-seq | GSE117881 | ||
| Nucleosome positioning - Transient Depletion and Recovery of the Essential RSC Chromatin Remodelin Complex ( Klein-Brill et al., 2019) | Saccharomyces cerevisiae | MNase-seq | GSE117598 | ||
| Contrasting role of the RSC and ISW1/CHD1 chromatin remodelers in RNA polymerase II elongation and termination ( Ocampo et al., 2019) | Saccharomyces cerevisiae | MNase-seq | GSE117514 | ||
| Nucleosome position mapping by micrococcal nuclease analysis of S. cerevisiae cells in raffinose and galactose containing media ( Donovan et al., 2019 ) | Saccharomyces cerevisiae | MNase-seq | GSE116337 | ||
| Spt6 is requires for the fidelity of promoter selectivity ( Doris et al., 2018) | Saccharomyces cerevisiae | MNase-seq | GSE115775 | ||
| Genome-wide maps of nucleosome positioning in asynchronously growing yeast cells ( Cutler et al., 2018) | Saccharomyces cerevisiae | MNase-seq | GSE112427 | ||
| MNase-seq for budding yeast Saccharomyces cerevisiae ( Miura et al., 2018) | Saccharomyces cerevisiae | MNase-seq | GSE110666 | ||
| Histone exchange assay in loss of DOT1 ( Lee et al., 2018) | Saccharomyces cerevisiae | MNase-seq | GSE106450 | ||
| Deciphering cis-regulatory logic with 100 million synthetic promoters ( Ocampo et al., 2019) | Saccharomyces cerevisiae | MNase-seq | GSE104903 | ||
| Viral proteins as a potential driver of histone depletion in dinoflagellates ( Irwin et al., 2018) | Saccharomyces cerevisiae | MNase-seq | GSE102280 | ||
| Transfer RNA Genes Affect Chromsome Architecture and Function ( Hamdadi et al., 2019 ) | Saccharomyces cerevisiae | MNase-seq | GSE98304 | ||
| Subtracting the sequence bias from partially digested MNase-seq data reveals a general contribution of TFIIS to nucleosome positioning ( Gutiérrez et al., 2017) | Saccharomyces cerevisiae | MNase-seq | GSE94313 | ||
| Dynamics of chromatin maturation after genome replication ( Vasseur et al., 2016) | Saccharomyces cerevisiae | MNase-seq | GSE74090 | ||
| Divergent residues within histone H3 define a unique chromatin structure in S. cerevisiae ( McBurney et al., 2016) | Saccharomyces cerevisiae | MNase-seq | GSE73425 | ||
| Genomic nucleosome organisation recontrituted with pure proteins ( Krietenstein et al., 2016) | Saccharomyces cerevisiae | MNase-seq | GSE72106 | ||
| The ISW1 and CHD1 ATP-dependent chromatin remodelers compete to set nucleosome spacing in vivo (Ocampo et al., 2016). | Saccharomyces cerevisiae | MNase-seq | GSE69400 | ||
| Rpd3 drives transcriptional quiescence ( McKnight et al., 2015) | Saccharomyces cerevisiae | H3 ChIP-seq | GSE67151 | ||
| Rpd3 drives transcriptional quiescence ( McKnight et al., 2015) | Saccharomyces cerevisiae | MNase-seq | GSE67148 | ||
| S. cerevisiae hho1, ioc3isw1, and chd1 deletion mutants complemented with the corresponding copies from K. lactis (Hughes and Rando, 2015) | Saccharomyces cerevisiae | S. cerevisiae hho1, ioc3isw1, and chd1 deletion mutants; K. lactis | MNase-seq | GSE66979 | |
| Strain W303, stationary growth phase. Wild type (WT) and with introduced DNMT3b (Morselli et al., 2015) | Saccharomyces cerevisiae | Strain W303, stationary growth phase | MNase-seq | GSE66907 | |
| Cryptic transcription is the primary driving force for nucleosome instability in Spt16 mutant cells ( Feng et al., 2016) | Saccharomyces cerevisiae | MNase-seq | GSE66215 | ||
| S. cerevisiae. Strains carrying the Sth1 degron allele and either pGal-UBR1 (YBC3386) or ubr1 null (YBC3387) represent RSC null and RSC wild type correspondingly (Parnell et al. 2015) | Saccharomyces cerevisiae | MNase-seq | GSE65593 | ||
| High resolution chromatin dynamics during a yeast stress response (Weiner et al., 2015). | Saccharomyces cerevisiae | MNase-assisted H3 ChIP-seq | GSE61888 | ||
| WT and Snf2 K1493R, K1497R strains; unstressed/stressed (Dutta et al., 2014) | Saccharomyces cerevisiae | K1493R, K1497R strains | MNase-seq | GSE61210 | |
| WT and modification affecting one of the following chromatin remodelers: ISW1, CHD1, FUN30, IOC3 (Ramachandran et al., 2015) | Saccharomyces cerevisiae | Strain W303 | MNase-seq | GSE59523 | |
| Acetylation of histone H4 at lysine 44 facilitates meiotic recombination by creating accessible chromatin ( Hu et al., 2015) | Saccharomyces cerevisiae | MNase-seq | GSE59004 | ||
| S. cerevisiae. Strain W303. Affected histone deacetylases Sir2 and Rpd3 (Yoshida et al., 2014) | Saccharomyces cerevisiae | Strain W303 | MNase-seq | GSE57618 | |
| S. cerevisiae. Strain YK699, WT and changes addressing the following: Scc2-4; Sth1-3; a2/MCM1; TATAC; TATA∆. Replicates at 25C and 37C (Lopez-Serra et al. 2014). | Saccharomyces cerevisiae | Strain YK699 | MNase-seq | GSE56994 | |
| Dang et al. Inactivation of yeast Isw2 chromatin remodeling enzyme mimics longevity effect of calorie restriction via induction of genotoxic stress response. Cell Metab 2014 Jun 3;19(6):952-66 | Saccharomyces cerevisiae | Calorie restricted and non-restricted WT, ISW2DEL and ISW2K215R strains | MNase-seq | GSE53718 | |
| Genome-wide nucleosome maps for wild type and Rsc8-depleted Saccharomyces cerevisiae (Ganguli, Cole and Clark, 2014). | Saccharomyces cerevisiae | MNase-seq | GSE49512 | ||
| Woo S, Zhang X, Sauteraud R, Robert F et al. PING 2.0: an R/Bioconductor package for nucleosome positioning using next-generation sequencing data. Bioinformatics 2013 Aug 15;29(16):2049-50 | Saccharomyces cerevisiae | Strain W303 (yFR212) | MNase-seq | GSE47073 | |
| Hu et al. Nucleosome loss leads to global transcriptional up-regulation and genomic instability during yeast aging. Genes Dev 2014 Feb 15;28(4):396-408 | Saccharomyces cerevisiae | Strain S288c (BY4741). | MNase-seq | GSE47023 | |
| Exposed/not exposed to osmostress. Nadal-Ribelles et al. Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling. Genome Biol 2012 Nov 18;13(11):R106 | Saccharomyces cerevisiae | Strain BY4741, WT and Hog1 mutant | MNase-seq | GSE41494 | |
| Chen et al. Stabilization of the promoter nucleosomes in nucleosome-free regions by the yeast Cyc8-Tup1 corepressor. Genome Res 2013 Feb;23(2):312-22 | Saccharomyces cerevisiae | Strain BY4742, WT, Ssn6 KO and Tup1 KO | MNase-seq | GSE37465 | |
| Van de Vosse et al. A role for the nucleoporin Nup170p in chromatin structure and gene silencing. Cell 2013 Feb 28;152(5):969-83 | Saccharomyces cerevisiae | Strain S288C. WT, Nup170∆ and Sth1p depletion | MNase-seq | GSE36792 | |
| In vivo nucleosome occupancy in yeast ( Chai et al., 2013) | Saccharomyces cerevisiae | MNase-seq | GSE34923 | ||
| Huebert DJ, Kuan PF, Keleş S, Gasch AP. Dynamic changes in nucleosome occupancy are not predictive of gene expression dynamics but are linked to transcription and chromatin regulators. Mol Cell Biol 2012 May;32(9):1645-53 | Saccharomyces cerevisiae | Strain BY4741 | MNase-seq | GSE30900 | |
| Gossett AJ, Lieb JD. In vivo effects of histone H3 depletion on nucleosome occupancy and position in Saccharomyces cerevisiae. PLoS Genet 2012;8(6):e1002771 | Saccharomyces cerevisiae | Strain YEF473A | MNase-seq | GSE29292 | |
| Structural mapping of regulatory function of histone H3 and H4 residues ( Jung et al., 2015) | Saccharomyces cerevisiae | MNase-seq | GSE29064 | ||
| Tsankov et al. Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization. Genome Res 2011 Nov;21(11):1851-62. | Saccharomyces cerevisiae | S. cerevisiae, C. albicans, S. pombe | MNase-seq | GSE28839 | |
| Activation-induced disruption of nucleosome position clusters on the coding regions of Gcn4-dependent genes extends into neighbouring genes (Cole et al., 2011) | Saccharomyces cerevisiae | MNase-seq | GSE26493 | ||
| S. cerevisiae in varying phosphate concentrations | Saccharomyces cerevisiae | Saccharomyces cerevisiae | MNase-seq | GSE26392 | |
| Tsankov et al. The role of nucleosome positioning in the evolution of gene regulation. PLoS Biol 2010 Jul 6;8(7):e1000414 | Saccharomyces cerevisiae | MNase-seq | GSE22211 | ||
| MNase titration series from three different titration levels – underdigested, typical digestion, and overdigested BY4741 cells. Time dependence series: MNase-seq at 0, 20, and 120 minutes after shifting RPO21 cells from 25 C to 37 C (Weiner et al. 2010). | Saccharomyces cerevisiae | Strains BY4741 and RPO21. | MNase-seq | GSE18530 | |
| Chromatin remodelling by Isw2 (Whitehouse et al. 2007). http://research.fhcrc.org/tsukiyama/en/genomics-data/global_nucleosomemapping.html | Saccharomyces cerevisiae | Saccharomyces cerevisiae | Tiling microarrays | GSE8814 | |
| Chromatin remodelling by Isw2 (Whitehouse et al. 2007). http://research.fhcrc.org/tsukiyama/en/genomics-data/global_nucleosomemapping.html | Saccharomyces cerevisiae | Saccharomyces cerevisiae | Tiling microarrays | GSE8813 | |
| Nascent chromatin occupancy profiling reveals locus- and factor-specific chromatin maturation dynamics behind the DNA replication fork (Gutiérrez, MacAlpine and MacAlpine, 2018). | Saccharomyces cerevisiae | MNase-seq | SRP158706 | ||
| Condensin-dependent chromatin condensation represses transcription globally during quiescence (Swygert et al., 2019). | Saccharomyces cerevisiae | Micro-C XL | GSE120605 | ||
| Transfer RNA Genes Affect Chromosome Architecture and Function (Hamdani et al., 2019). | Saccharomyces cerevisiae | Micro-C | GSE98543 | ||
| Mapping nucleosome resolution chromosome folding in yeast by Micro-C (Hsieh et al., 2015). | Saccharomyces cerevisiae | Micro-C | GSE68016 | ||
| The Penn State Genome Cartography Project. (Mavrich et al. 2008; Zhang and Pugh 2011; Zhang et al. 2011; Yen et al. 2013). Tiling microarrays. | Saccharomyces cerevisiae, Drosophila melanogaster | S. cerevisiae and D. melanogaster | MNase-seq | ||
| Comparison of nucleosome positioning in S. cerevisiae, S. paradoxus and their hybrid for wild-type and deletion mutant strains (Tirosh et al. 2010). | Saccharomyces cerevisiae, Saccharomyces paradoxus | S. cerevisiae, S. paradoxus | MNase-seq | GSE18939 | |
| The chaperone FACT and H2B ubiquitination maintain S. pombe genome architecture through genic and subtelomeric functions ( Seymour et al., 2016) | Schizosaccharomyces pombe | MNase-seq | GSE124091 | ||
| Shelterin and subtelomeric DNA sequences control nucleosome maintenance and genome stability (van Emden et al., 2019). | Schizosaccharomyces pombe | H3 ChIP-seq | GSE121502 | ||
| Spt6 regulates intragenic and antisense transcription, nucleosome positioning, and histone modifications genome-wide in fission yeast ( DeGennaro et al., 2013) | Schizosaccharomyces pombe | MNase-seq | GSE49572 | ||
| Hrp3 controls nucleosome positioning to suppress non-coding transcription in eu- and heterochromatin ( Shim et al., 2012) | Schizosaccharomyces pombe | MNase-seq | GSE40451 | ||
| Chromatin architectures at fission yeast transcriptional promoters and replication origins ( Givens et al., 2011) | Schizosaccharomyces pombe | MNase-seq | GSE28071 | ||
| Micro-C XL: assaying chromosome conformation at length scales from the nucleosome to the entire genome (Hsieh et al., 2016). | Schizosaccharomyces pombe, Saccharomyces cerevisiae | Micro-C XL | GSE85220 | ||
| Rapid and Inexpensive Preparation of Genome-Wide Nucleosome Footprints from Model and Non-Model Organisms (McKnight et al., 2019). | Schizosaccharomyces pombe, Saccharomyces cerevisiae, Neurospora crassa | MNase-seq | GSE141676 | ||
| N6-adenine DNA methylation is associated with the linker DNA of H2A.Z-containing well-positioned nucleosomes in Pol II-transcribed genes in Tetrahymena ( Wang et al., 2017) | Tetrahymena thermophila | MNase-seq | GSE96521 | ||
| MNase-seq of Tetrahymena thermophila macronucleus (MAC) and micronucleus (MIC) ( Jeffers and Lieb, 2017) | Tetrahymena thermophila | MNase-seq | GSE77660 | ||
| Genomic features shaping the landscape of meiotic double-strand break hotspots in maize ( He et al., 2017) | Zea mays | MNase-seq | GSE84368 | ||