Journal: Cell reports

Article Title: Stochastic models of nucleosome dynamics reveal regulatory rules of stimulus-induced epigenome remodeling

doi: 10.1016/j.celrep.2022.111076

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, Peptides, and Recombinant Proteins LPS Sigma, B5:055 L2880 murine TNF Roche 11271156001 Experimental Models: Cell lines Immortalized Myeloid Progenitor-derived macrophages ( Singh et al., 2022 ) N/A Experimental Models: Organisms C57Bl/6 mouse Nfkbia −/− Rel −/− Tnf −/− Nfkbie −/− BMDMs ( Cheng et al., 2021 ) N/A Deposited Data Macrophage PE ATACseq This paper GSE156385 Macrophage SE ATACseq ( Cheng et al., 2021 ) GSE146068 Software and Algorithms MATLAB 2016b https://matlab.mathworks.com/ R (version 4.0.3) https://www.r-project.org/ ENCODE-DCC ATACseq Pipeline https://github.com/ENCODE-DCC/atac-seq-pipeline bedtools ( Quinlan and Hall, 2010 ) https://bedtools.readthedocs.io/en/latest/ NucleoATAC ( Schep et al., 2015 ) https://github.com/GreenleafLab/NucleoATAC HOMER ( Heinz et al., 2010 ) http://homer.ucsd.edu/homer/ngs/peakMotifs.html Nucleosome Model Code This paper DOI: 10.5281/zenodo.6503369 ( https://github.com/signalingsystemslab/nucleosome_stochasticModel ) Open in a separate window KEY RESOURCES TABLE.

Techniques: Recombinant, Software

Journal: Cell reports

Article Title: Stochastic models of nucleosome dynamics reveal regulatory rules of stimulus-induced epigenome remodeling

doi: 10.1016/j.celrep.2022.111076

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, Peptides, and Recombinant Proteins LPS Sigma, B5:055 L2880 murine TNF Roche 11271156001 Experimental Models: Cell lines Immortalized Myeloid Progenitor-derived macrophages ( Singh et al., 2022 ) N/A Experimental Models: Organisms C57Bl/6 mouse Nfkbia −/− Rel −/− Tnf −/− Nfkbie −/− BMDMs ( Cheng et al., 2021 ) N/A Deposited Data Macrophage PE ATACseq This paper GSE156385 Macrophage SE ATACseq ( Cheng et al., 2021 ) GSE146068 Software and Algorithms MATLAB 2016b https://matlab.mathworks.com/ R (version 4.0.3) https://www.r-project.org/ ENCODE-DCC ATACseq Pipeline https://github.com/ENCODE-DCC/atac-seq-pipeline bedtools ( Quinlan and Hall, 2010 ) https://bedtools.readthedocs.io/en/latest/ NucleoATAC ( Schep et al., 2015 ) https://github.com/GreenleafLab/NucleoATAC HOMER ( Heinz et al., 2010 ) http://homer.ucsd.edu/homer/ngs/peakMotifs.html Nucleosome Model Code This paper DOI: 10.5281/zenodo.6503369 ( https://github.com/signalingsystemslab/nucleosome_stochasticModel ) Open in a separate window KEY RESOURCES TABLE.

Techniques: Recombinant, Software