Staining:Article Title: Epigenome profiling identifies H3K27me3 regulation of extracellular matrix composition in human corticogenesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Maxpar Cell Staining Buffer Standard BioTools Cat # 201068 DPBS Corning Cat # 21-031-CV 16 % Formaldehyde (w/v), methanol-free Thermo Scientific Cat # 28906 Fetal Bovine Serum (FBS) Sigma Aldrich Cat # F7524 Maxpar Nuclear Antigen Staining Buffer Set Standard BioTools Cat # 201063 Maxpar Fix I Buffer Standard BioTools Cat # 201065 Maxpar 10X Barcode Perm Buffer Standard BioTools Cat # 201057 Cell-IDTM Intercalator-Iridium Standard BioTools Cat # 201192A Maxpar Water Standard BioTools Cat # 201069 Maxpar Cell Acquisition Solution Plus for CyTOF XT Standard BioTools Cat # 201244 EQTM Six Element Calibration Beads Standard BioTools Cat # 201245 Critical commercial assays MACS Neural Tissue Dissociation Kit P Miltenyi Biotec Inc. Cat # 130-092-628 RNeasy Mini Kit QIAGEN Cat # 74104 Neural Tissue Dissociation Kit (P) Miltenyi Biotec Inc. Cat # 130-092-628 Cell-ID 20-Plex Pd Barcoding Kit Standard BioTools Cat # 201060 Deposited data RNA-seq Florio et al.35 NCBI GEO: GSE65000 CUT&Tag Human tissue GW12-14 This paper Zenodo: https://doi.org/10.5281/ zenodo.13897222 CUT&Tag PRC2 inhibitor treated organoids W8 This paper Zenodo: https://doi.org/10.5281/ zenodo.13897222 Bulk RNA-seq PRC2 inhibitor treated organoids W8 This paper Zenodo: https://doi.org/10.5281/ zenodo.13897222 Epi-CyTOF This paper FlowRepository: FR-FCM-Z8DC Experimental models: Cell lines Human: CRTDi004-A iPSC Völkner et al.78 CRTDi004-A; RRID: CVCL_YR23 Human: HPSI0114i-kolf_2 iPSC Welcome Trust Sanger Institute, HipSci WTSIi018-B; RRID: CVCL_AE29 Oligonucleotides Primers, see Table S7 This paper N/A Software and algorithms Fiji/ImageJ Fiji/ImageJ https://imagej.nih.gov/ij/ Prism (8.4.3) GraphPad software N/A Affinity Photo + Designer (1.10.5.1342) Serif Ltd. N/A FACSDiva (8.0.2) BD Biosciences N/A FACSChorus BD Biosciences N/A CyTOF Software (v9.0.2) Standard BioTools N/A OMIQ Dotmatics N/A FastQC (v0.11.9) Babraham Bioinformatics https://www.bioinformatics.babraham. ac.uk/projects/fastqc/ nf-core/cutandrun (v3.2.2) Cheshire et al.79 N/A Diffbind (v3.12.0) Stark et al.80 N/A DESeq2 (v1.42.1) Love et al.81 N/A deeptools (v3.5.1) Yu et al.82 N/A ChIPseeker (v1.38.0) Yu et al.82 and Bioconductor Core Team and Bioconductor Package Maintainer83 N/A ReactomePA (v1.46.0) Yu et al.44 and Moore et al.45 N/A (Continued on next page) e4 Neuron 113, 2927–2944.e1–e10, September 17, 2025 ..
Magnetic Cell Separation:Article Title: Epigenome profiling identifies H3K27me3 regulation of extracellular matrix composition in human corticogenesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Maxpar Cell Staining Buffer Standard BioTools Cat # 201068 DPBS Corning Cat # 21-031-CV 16 % Formaldehyde (w/v), methanol-free Thermo Scientific Cat # 28906 Fetal Bovine Serum (FBS) Sigma Aldrich Cat # F7524 Maxpar Nuclear Antigen Staining Buffer Set Standard BioTools Cat # 201063 Maxpar Fix I Buffer Standard BioTools Cat # 201065 Maxpar 10X Barcode Perm Buffer Standard BioTools Cat # 201057 Cell-IDTM Intercalator-Iridium Standard BioTools Cat # 201192A Maxpar Water Standard BioTools Cat # 201069 Maxpar Cell Acquisition Solution Plus for CyTOF XT Standard BioTools Cat # 201244 EQTM Six Element Calibration Beads Standard BioTools Cat # 201245 Critical commercial assays MACS Neural Tissue Dissociation Kit P Miltenyi Biotec Inc. Cat # 130-092-628 RNeasy Mini Kit QIAGEN Cat # 74104 Neural Tissue Dissociation Kit (P) Miltenyi Biotec Inc. Cat # 130-092-628 Cell-ID 20-Plex Pd Barcoding Kit Standard BioTools Cat # 201060 Deposited data RNA-seq Florio et al.35 NCBI GEO: GSE65000 CUT&Tag Human tissue GW12-14 This paper Zenodo: https://doi.org/10.5281/ zenodo.13897222 CUT&Tag PRC2 inhibitor treated organoids W8 This paper Zenodo: https://doi.org/10.5281/ zenodo.13897222 Bulk RNA-seq PRC2 inhibitor treated organoids W8 This paper Zenodo: https://doi.org/10.5281/ zenodo.13897222 Epi-CyTOF This paper FlowRepository: FR-FCM-Z8DC Experimental models: Cell lines Human: CRTDi004-A iPSC Völkner et al.78 CRTDi004-A; RRID: CVCL_YR23 Human: HPSI0114i-kolf_2 iPSC Welcome Trust Sanger Institute, HipSci WTSIi018-B; RRID: CVCL_AE29 Oligonucleotides Primers, see Table S7 This paper N/A Software and algorithms Fiji/ImageJ Fiji/ImageJ https://imagej.nih.gov/ij/ Prism (8.4.3) GraphPad software N/A Affinity Photo + Designer (1.10.5.1342) Serif Ltd. N/A FACSDiva (8.0.2) BD Biosciences N/A FACSChorus BD Biosciences N/A CyTOF Software (v9.0.2) Standard BioTools N/A OMIQ Dotmatics N/A FastQC (v0.11.9) Babraham Bioinformatics https://www.bioinformatics.babraham. ac.uk/projects/fastqc/ nf-core/cutandrun (v3.2.2) Cheshire et al.79 N/A Diffbind (v3.12.0) Stark et al.80 N/A DESeq2 (v1.42.1) Love et al.81 N/A deeptools (v3.5.1) Yu et al.82 N/A ChIPseeker (v1.38.0) Yu et al.82 and Bioconductor Core Team and Bioconductor Package Maintainer83 N/A ReactomePA (v1.46.0) Yu et al.44 and Moore et al.45 N/A (Continued on next page) e4 Neuron 113, 2927–2944.e1–e10, September 17, 2025 ..
RNA Sequencing:Article Title: Epigenome profiling identifies H3K27me3 regulation of extracellular matrix composition in human corticogenesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Maxpar Cell Staining Buffer Standard BioTools Cat # 201068 DPBS Corning Cat # 21-031-CV 16 % Formaldehyde (w/v), methanol-free Thermo Scientific Cat # 28906 Fetal Bovine Serum (FBS) Sigma Aldrich Cat # F7524 Maxpar Nuclear Antigen Staining Buffer Set Standard BioTools Cat # 201063 Maxpar Fix I Buffer Standard BioTools Cat # 201065 Maxpar 10X Barcode Perm Buffer Standard BioTools Cat # 201057 Cell-IDTM Intercalator-Iridium Standard BioTools Cat # 201192A Maxpar Water Standard BioTools Cat # 201069 Maxpar Cell Acquisition Solution Plus for CyTOF XT Standard BioTools Cat # 201244 EQTM Six Element Calibration Beads Standard BioTools Cat # 201245 Critical commercial assays MACS Neural Tissue Dissociation Kit P Miltenyi Biotec Inc. Cat # 130-092-628 RNeasy Mini Kit QIAGEN Cat # 74104 Neural Tissue Dissociation Kit (P) Miltenyi Biotec Inc. Cat # 130-092-628 Cell-ID 20-Plex Pd Barcoding Kit Standard BioTools Cat # 201060 Deposited data RNA-seq Florio et al.35 NCBI GEO: GSE65000 CUT&Tag Human tissue GW12-14 This paper Zenodo: https://doi.org/10.5281/ zenodo.13897222 CUT&Tag PRC2 inhibitor treated organoids W8 This paper Zenodo: https://doi.org/10.5281/ zenodo.13897222 Bulk RNA-seq PRC2 inhibitor treated organoids W8 This paper Zenodo: https://doi.org/10.5281/ zenodo.13897222 Epi-CyTOF This paper FlowRepository: FR-FCM-Z8DC Experimental models: Cell lines Human: CRTDi004-A iPSC Völkner et al.78 CRTDi004-A; RRID: CVCL_YR23 Human: HPSI0114i-kolf_2 iPSC Welcome Trust Sanger Institute, HipSci WTSIi018-B; RRID: CVCL_AE29 Oligonucleotides Primers, see Table S7 This paper N/A Software and algorithms Fiji/ImageJ Fiji/ImageJ https://imagej.nih.gov/ij/ Prism (8.4.3) GraphPad software N/A Affinity Photo + Designer (1.10.5.1342) Serif Ltd. N/A FACSDiva (8.0.2) BD Biosciences N/A FACSChorus BD Biosciences N/A CyTOF Software (v9.0.2) Standard BioTools N/A OMIQ Dotmatics N/A FastQC (v0.11.9) Babraham Bioinformatics https://www.bioinformatics.babraham. ac.uk/projects/fastqc/ nf-core/cutandrun (v3.2.2) Cheshire et al.79 N/A Diffbind (v3.12.0) Stark et al.80 N/A DESeq2 (v1.42.1) Love et al.81 N/A deeptools (v3.5.1) Yu et al.82 N/A ChIPseeker (v1.38.0) Yu et al.82 and Bioconductor Core Team and Bioconductor Package Maintainer83 N/A ReactomePA (v1.46.0) Yu et al.44 and Moore et al.45 N/A (Continued on next page) e4 Neuron 113, 2927–2944.e1–e10, September 17, 2025 ..
Software:Article Title: Epigenome profiling identifies H3K27me3 regulation of extracellular matrix composition in human corticogenesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Maxpar Cell Staining Buffer Standard BioTools Cat # 201068 DPBS Corning Cat # 21-031-CV 16 % Formaldehyde (w/v), methanol-free Thermo Scientific Cat # 28906 Fetal Bovine Serum (FBS) Sigma Aldrich Cat # F7524 Maxpar Nuclear Antigen Staining Buffer Set Standard BioTools Cat # 201063 Maxpar Fix I Buffer Standard BioTools Cat # 201065 Maxpar 10X Barcode Perm Buffer Standard BioTools Cat # 201057 Cell-IDTM Intercalator-Iridium Standard BioTools Cat # 201192A Maxpar Water Standard BioTools Cat # 201069 Maxpar Cell Acquisition Solution Plus for CyTOF XT Standard BioTools Cat # 201244 EQTM Six Element Calibration Beads Standard BioTools Cat # 201245 Critical commercial assays MACS Neural Tissue Dissociation Kit P Miltenyi Biotec Inc. Cat # 130-092-628 RNeasy Mini Kit QIAGEN Cat # 74104 Neural Tissue Dissociation Kit (P) Miltenyi Biotec Inc. Cat # 130-092-628 Cell-ID 20-Plex Pd Barcoding Kit Standard BioTools Cat # 201060 Deposited data RNA-seq Florio et al.35 NCBI GEO: GSE65000 CUT&Tag Human tissue GW12-14 This paper Zenodo: https://doi.org/10.5281/ zenodo.13897222 CUT&Tag PRC2 inhibitor treated organoids W8 This paper Zenodo: https://doi.org/10.5281/ zenodo.13897222 Bulk RNA-seq PRC2 inhibitor treated organoids W8 This paper Zenodo: https://doi.org/10.5281/ zenodo.13897222 Epi-CyTOF This paper FlowRepository: FR-FCM-Z8DC Experimental models: Cell lines Human: CRTDi004-A iPSC Völkner et al.78 CRTDi004-A; RRID: CVCL_YR23 Human: HPSI0114i-kolf_2 iPSC Welcome Trust Sanger Institute, HipSci WTSIi018-B; RRID: CVCL_AE29 Oligonucleotides Primers, see Table S7 This paper N/A Software and algorithms Fiji/ImageJ Fiji/ImageJ https://imagej.nih.gov/ij/ Prism (8.4.3) GraphPad software N/A Affinity Photo + Designer (1.10.5.1342) Serif Ltd. N/A FACSDiva (8.0.2) BD Biosciences N/A FACSChorus BD Biosciences N/A CyTOF Software (v9.0.2) Standard BioTools N/A OMIQ Dotmatics N/A FastQC (v0.11.9) Babraham Bioinformatics https://www.bioinformatics.babraham. ac.uk/projects/fastqc/ nf-core/cutandrun (v3.2.2) Cheshire et al.79 N/A Diffbind (v3.12.0) Stark et al.80 N/A DESeq2 (v1.42.1) Love et al.81 N/A deeptools (v3.5.1) Yu et al.82 N/A ChIPseeker (v1.38.0) Yu et al.82 and Bioconductor Core Team and Bioconductor Package Maintainer83 N/A ReactomePA (v1.46.0) Yu et al.44 and Moore et al.45 N/A (Continued on next page) e4 Neuron 113, 2927–2944.e1–e10, September 17, 2025 ..
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