Recombinant:Article Title: Regulatory Dynamics of Tet1 and Oct4 Resolve Stages of Global DNA Demethylation and Transcriptomic Changes in Reprogramming.
Article Snippet: Recombinant DNA pHAGE-tetO-STEMCCA Sommer et al., 2009 N/A FUW-M2rtTA Addgene; Hockemeyer et al., 2008 Cat.# 20342 Software and Algorithms GraphPad Prism7 GraphPad https://www.graphpad.com/scientific-software/prism/; (RRID:SCR_002798) FlowJo X FlowJo, LLC https://www.flowjo.com/; (RRID:SCR_008520) Venn diagrams VIB / UGent http://bioinformatics.psb.ugent.be/webtools/Venn/ NIS-Element Nikon https://www.microscope.healthcare.nikon.com/ en_EU/products/software; (RRID:SCR_014329) ImageJ N/A https://imagej.net/Welcome; (RRID:SCR_003070) Hisat2 v2.1.0 Kim et al., 2015 https://ccb.jhu.edu/software/hisat2/index.shtml; (RRID:SCR_015530) featureCounts v1.5.3 Liao et al., 2014 http://bioinf.wehi.edu.au/featureCounts/; (RRID:SCR_012919) Salmon v0.8.1 Patro et al., 2017 https://combine-lab.github.io/salmon/; (RRID:SCR_017036) R v3.4.4 N/A https://www.R-project.org/; (RRID:SCR_001905) DESeq2 v1.18.1 Love et al., 2014 http://www.bioconductor.org/packages/release/bioc/ html/DESeq2.html; (RRID:SCR_015687) ggpubr v0.1.6 R package https://rpkgs.datanovia.com/ggpubr/index.html; (RRID:SCR_014601) clusterProfiler v3.6.0 R package, Yu et al., 2012 http://bioconductor.org/packages/release/bioc/html/ clusterProfiler.html; (RRID:SCR_016884) pheatmap v1.0.10 R package https://cran.r-project.org/web/packages/pheatmap/; (RRID:SCR_016418) Integrative Genomics Viewer (IGV) Broad Institute http://software.broadinstitute.org/software/igv/; (RRID:SCR_011793) Methyl Kit R-package (v1.4.1) R-package https://bioconductor.org/packages/release/bioc/html/ methylKit.html; (RRID:SCR_006442) ChipSeeker (v1.18.0) R-package; Yu et al., 2015 https://bioconductor.org/packages/release/bioc/html/ ChIPseeker.html; (RRID:SCR_006442) complex Heatmap (v1.20.0) Gu et al., 2016 https://bioconductor.org/packages/release/bioc/html/ ComplexHeatmap.html; (RRID:SCR_006442) AdapterTrim (v2) In-house GenomeScan BV N/A Bismark (v0.19.0) Krueger and Andrews, 2011 https://www.bioinformatics.babraham.ac.uk/projects/ bismark/; (RRID:SCR_005604) (Continued on next page) Cell Reports 30, 2150–2169.e1–e9, February 18, 2020 e2
Software:Article Title: Regulatory Dynamics of Tet1 and Oct4 Resolve Stages of Global DNA Demethylation and Transcriptomic Changes in Reprogramming.
Article Snippet: Recombinant DNA pHAGE-tetO-STEMCCA Sommer et al., 2009 N/A FUW-M2rtTA Addgene; Hockemeyer et al., 2008 Cat.# 20342 Software and Algorithms GraphPad Prism7 GraphPad https://www.graphpad.com/scientific-software/prism/; (RRID:SCR_002798) FlowJo X FlowJo, LLC https://www.flowjo.com/; (RRID:SCR_008520) Venn diagrams VIB / UGent http://bioinformatics.psb.ugent.be/webtools/Venn/ NIS-Element Nikon https://www.microscope.healthcare.nikon.com/ en_EU/products/software; (RRID:SCR_014329) ImageJ N/A https://imagej.net/Welcome; (RRID:SCR_003070) Hisat2 v2.1.0 Kim et al., 2015 https://ccb.jhu.edu/software/hisat2/index.shtml; (RRID:SCR_015530) featureCounts v1.5.3 Liao et al., 2014 http://bioinf.wehi.edu.au/featureCounts/; (RRID:SCR_012919) Salmon v0.8.1 Patro et al., 2017 https://combine-lab.github.io/salmon/; (RRID:SCR_017036) R v3.4.4 N/A https://www.R-project.org/; (RRID:SCR_001905) DESeq2 v1.18.1 Love et al., 2014 http://www.bioconductor.org/packages/release/bioc/ html/DESeq2.html; (RRID:SCR_015687) ggpubr v0.1.6 R package https://rpkgs.datanovia.com/ggpubr/index.html; (RRID:SCR_014601) clusterProfiler v3.6.0 R package, Yu et al., 2012 http://bioconductor.org/packages/release/bioc/html/ clusterProfiler.html; (RRID:SCR_016884) pheatmap v1.0.10 R package https://cran.r-project.org/web/packages/pheatmap/; (RRID:SCR_016418) Integrative Genomics Viewer (IGV) Broad Institute http://software.broadinstitute.org/software/igv/; (RRID:SCR_011793) Methyl Kit R-package (v1.4.1) R-package https://bioconductor.org/packages/release/bioc/html/ methylKit.html; (RRID:SCR_006442) ChipSeeker (v1.18.0) R-package; Yu et al., 2015 https://bioconductor.org/packages/release/bioc/html/ ChIPseeker.html; (RRID:SCR_006442) complex Heatmap (v1.20.0) Gu et al., 2016 https://bioconductor.org/packages/release/bioc/html/ ComplexHeatmap.html; (RRID:SCR_006442) AdapterTrim (v2) In-house GenomeScan BV N/A Bismark (v0.19.0) Krueger and Andrews, 2011 https://www.bioinformatics.babraham.ac.uk/projects/ bismark/; (RRID:SCR_005604) (Continued on next page) Cell Reports 30, 2150–2169.e1–e9, February 18, 2020 e2
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