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anna katerina hadjantonakis  (Addgene inc)


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    Structured Review

    Addgene inc anna katerina hadjantonakis
    Anna Katerina Hadjantonakis, supplied by Addgene inc, used in various techniques. Bioz Stars score: 93/100, based on 20 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/pcag-gfp/pCAG%3AGPI-GFP+(Plasmid+%2332601)/bio_rxiv__64898__2026__03__22__713470-230-19-21
    Average 93 stars, based on 20 article reviews
    anna katerina hadjantonakis - by Bioz Stars, 2026-10
    93/100 stars

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    Related Articles

    Knock-Out:

    Article Title: In situ cell-type-specific cell-surface proteomic profiling in mice.
    Article Snippet: Nelson; Clark et al., 2020 N/A Mouse: MADM6-GT Contreras et al., 2021 N/A Mouse: MADM6-TG Contreras et al., 2021 N/A Oligonucleotides See Table S2 for a complete list of sequences Recombinant DNA See Table S2 for a complete list of gR and miR sequences integrated into plasmids pCAG-GFP Matsuda and Cepko, 2004 RRID:Addgene_11150 pCAG-tdTomato W. Joo, unpublished N/A pX333 Maddalo et al., 2014 RRID:Addgene_64073 pX333-CBh-Cas9-U6-2xsgRNA-LacZ Takeo et al., 2021 N/A pX333-CBh-Cas9-U6-2xsgRNA-Armh4 This paper N/A pCAG-EmGFP-miR Gift from M. Yuzaki N/A pCAG-EmGFP-LacZ-miR This paper N/A pCAG-EmGFP-Armh4-miR This paper N/A pCAG-2xHA-Armh4WT This paper N/A pCAG-V5-Armh4WT This paper N/A pCAG-Armh4WT-2xHA This paper N/A pCAG-2xHA-Armh4DICD This paper N/A pCAG-Armh4Endo6A-2xHA This paper N/A Software and algorithms ZEN Carl Zeiss RRID: SCR_013672 Imaris 9.3 Oxford Instruments RRID:SCR_007370; https://imaris.oxinst.com/ ImageJ (Fiji) NIH https://imagej.net/Fiji/Downloads Prism 9 GraphPad RRID:SCR_002798; https://www.graphpad.com/ Excel Microsoft RRID:SCR_016137 Spectrum Mill Agilent https://proteomics.broadinstitute. org/millhome.htm

    Article Title: Visualizing and manipulating the production and accumulation of hyaluronan for functional assessment in chicken embryos
    Article Snippet: pCAG - GFP , Matsuda and Cepko 4 , pCAG-GFP was a gift from Connie Cepko (Addgene plasmid # 11150; http://n2t.net/addgene:11150 ; RRID:Addgene_11150).

    Article Title: PCSK9 deficiency alters brain lipid composition without affecting brain development and function
    Article Snippet: We transfected the cells with the PCSK9 plasmid or an empty pCAGEN vector and stained with an anti-PCSK9 antibody (Goat-a-PCSK9: AF3985 (anti mouse/rat PCSK9, 0.2 mg/mL), dilution 1:50) and used immunofluorescence to confirm specific PCSK9 expression. pCAG-GFP was purchased from Addgene #11150. pCX::myr-Venus plasmid was a gift from Anna-Katerina Hadjantonalis.

    Article Title: DCX knockout ferret reveals a neurogenic mechanism in cortical development.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains Ferrets: WT This paper N/A Ferrets: DCX knockout mutants This paper N/A Mice: ICR This paper N/A Recombinant DNA pCAG-GFP Addgene Cat#11150 pCAG-DCX-GFP This paper N/A Software and algorithms Spaceranger v 1.0.0 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/ software/downloads/latest R v.4.1.0 R Core Team https://www.R-project.org/ CellRanger v.6.1.2 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/installation Seurat v4.3.0 Stuart et al., 201953 https://satijalab.org/seurat/install.html scrubletR v0.1.0 https://github.com/Moonerss/scrubletR CytoTRACE v0.3.3 Gulati et al., 201934 https://github.com/seqyuan/CytoTRACE SAW-5.4.0 BGIResearch https://github.com/STOmics/SAW stereopy-0.8.0 BGIResearch https://github.com/BGIResearch/stereopy scanpy-1.9.3 the Scanpy development team https://github.com/scverse/scanpy ggplot2 v3.3.2 Wickham, 201654 https://ggplot2.tidyverse.org scran v1.10.2 Lun et al., 201655 https://bioconductor.statistik.tu- dortmund.de/packages/3.8/bioc/ html/scran.html ggtree https://github.com/YuLab- SMU/ggtree V3.0.4 clusterProfiler v4.4.4 Wu et al., 2021.56 http://www.bioconductor.org/packages/ release/bioc/html/clusterProfiler.html ggpubr GitHub - kassambara/ ggpubr: ’ggplot20 V0.5.0 tidyverse https://bioconductor.org/ packages/release/ bioc/html/enrichplot.html V1.14.2 GSEA v4.1.0 Subramanian et al., 200557 http://software.broadinstitute.org/ gsea/index.jsp Cytoscape v3.8.2 Shannon et al. 200358 https://cytoscape.org/ ImageJ (1.5.3a) NIH https://imagej.nih.gov/ij/ Adobe Photoshop CC2020 Adobe Systems http://www.adobe.com GraphPad Prism 8.0 GraphPad Software http://www.graphpad.com/scientific- software/prism/

    Article Title: Sensor systems for target ligands and uses thereof
    Article Snippet: Miscellaneous Plasmids—pCAG-GFP (Addgene plasmid 11150)39, pCAG-YFP (Addgene plasmid 11180)39, pCAG-DsRed (Addgene 11151)39. pRho-GFP-IRES-AP (referred to as Rho-GFP)40. pCAG-nlacZ (Cepko lab, Harvard Medical School), pCAGEN (Addgene plasmid 11160)39. pCALNL-DsRed (Addgene plasmid 13769)39. pCAFNF-DsRed (Addgene plasmid 13771)39. pCALNL-luc28. pRL-TK (Promega, 4E2241).

    Article Title: Polysaccharide-Polyplex Nanofilm Coatings Enhance Nanoneedle-Based Gene Delivery and Transfection Efficiency.
    Article Snippet: Anti-mouse CD44 was purchased from BD Biosciences. pCAG-GFP and pCAG-dsRFP were obtained from Addgene (MA, USA) and developed by Cepko C, et al.[103] Fluc-pcDNA3 was obtained from Addgene (MA, USA) and developed by Safran M, et al.[104] pABOL was obtained in-house and synthesized as previously described.

    Article Title: The mTOR pathway genes mTOR, Rheb, Depdc5, Pten , and Tsc1 have convergent and divergent impacts on cortical neuron development and function
    Article Snippet: pCAG-GFP , Addgene plasmid #11150; deposited by Dr. Connie Cepko.

    Article Title: Caveolin-3 prevents swelling-induced membrane damage via regulation of I Cl,swell activity.
    Article Snippet: Caveola membrane structures harbor mechanosensitive chloride channels (MCCs; including chloride channel 2, chloride channel 3, and SWELL1, also known as LRRC8A) that form a swelling-activated chloride current (ICl,swell) and play an important role in cell volume regulation and mechanoelectrical signal transduction.. However, the role of the muscle-specific caveolar scaffolding protein caveolin-3 (Cav3) in regulation of MCC expression, activity, and contribution to membrane integrity in response to mechanical stress remains unclear.. Here we showed that Cav3-transfected (Cav3-positive) HEK293 cells were significantly resistant to extreme (<20 milliosmole) hypotonic swelling compared with native (Cav3-negative) HEK293 cells; the percentage of cells with membrane damage decreased from 45% in Cav3-negative cells to 17% in Cav3-positive cells (p < 0.05).

    Mouse Assay:

    Article Title: In situ cell-type-specific cell-surface proteomic profiling in mice.
    Article Snippet: Nelson; Clark et al., 2020 N/A Mouse: MADM6-GT Contreras et al., 2021 N/A Mouse: MADM6-TG Contreras et al., 2021 N/A Oligonucleotides See Table S2 for a complete list of sequences Recombinant DNA See Table S2 for a complete list of gR and miR sequences integrated into plasmids pCAG-GFP Matsuda and Cepko, 2004 RRID:Addgene_11150 pCAG-tdTomato W. Joo, unpublished N/A pX333 Maddalo et al., 2014 RRID:Addgene_64073 pX333-CBh-Cas9-U6-2xsgRNA-LacZ Takeo et al., 2021 N/A pX333-CBh-Cas9-U6-2xsgRNA-Armh4 This paper N/A pCAG-EmGFP-miR Gift from M. Yuzaki N/A pCAG-EmGFP-LacZ-miR This paper N/A pCAG-EmGFP-Armh4-miR This paper N/A pCAG-2xHA-Armh4WT This paper N/A pCAG-V5-Armh4WT This paper N/A pCAG-Armh4WT-2xHA This paper N/A pCAG-2xHA-Armh4DICD This paper N/A pCAG-Armh4Endo6A-2xHA This paper N/A Software and algorithms ZEN Carl Zeiss RRID: SCR_013672 Imaris 9.3 Oxford Instruments RRID:SCR_007370; https://imaris.oxinst.com/ ImageJ (Fiji) NIH https://imagej.net/Fiji/Downloads Prism 9 GraphPad RRID:SCR_002798; https://www.graphpad.com/ Excel Microsoft RRID:SCR_016137 Spectrum Mill Agilent https://proteomics.broadinstitute. org/millhome.htm

    Article Title: Visualizing and manipulating the production and accumulation of hyaluronan for functional assessment in chicken embryos
    Article Snippet: pCAG - GFP , Matsuda and Cepko 4 , pCAG-GFP was a gift from Connie Cepko (Addgene plasmid # 11150; http://n2t.net/addgene:11150 ; RRID:Addgene_11150).

    Article Title: PCSK9 deficiency alters brain lipid composition without affecting brain development and function
    Article Snippet: We transfected the cells with the PCSK9 plasmid or an empty pCAGEN vector and stained with an anti-PCSK9 antibody (Goat-a-PCSK9: AF3985 (anti mouse/rat PCSK9, 0.2 mg/mL), dilution 1:50) and used immunofluorescence to confirm specific PCSK9 expression. pCAG-GFP was purchased from Addgene #11150. pCX::myr-Venus plasmid was a gift from Anna-Katerina Hadjantonalis.

    Article Title: DCX knockout ferret reveals a neurogenic mechanism in cortical development.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains Ferrets: WT This paper N/A Ferrets: DCX knockout mutants This paper N/A Mice: ICR This paper N/A Recombinant DNA pCAG-GFP Addgene Cat#11150 pCAG-DCX-GFP This paper N/A Software and algorithms Spaceranger v 1.0.0 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/ software/downloads/latest R v.4.1.0 R Core Team https://www.R-project.org/ CellRanger v.6.1.2 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/installation Seurat v4.3.0 Stuart et al., 201953 https://satijalab.org/seurat/install.html scrubletR v0.1.0 https://github.com/Moonerss/scrubletR CytoTRACE v0.3.3 Gulati et al., 201934 https://github.com/seqyuan/CytoTRACE SAW-5.4.0 BGIResearch https://github.com/STOmics/SAW stereopy-0.8.0 BGIResearch https://github.com/BGIResearch/stereopy scanpy-1.9.3 the Scanpy development team https://github.com/scverse/scanpy ggplot2 v3.3.2 Wickham, 201654 https://ggplot2.tidyverse.org scran v1.10.2 Lun et al., 201655 https://bioconductor.statistik.tu- dortmund.de/packages/3.8/bioc/ html/scran.html ggtree https://github.com/YuLab- SMU/ggtree V3.0.4 clusterProfiler v4.4.4 Wu et al., 2021.56 http://www.bioconductor.org/packages/ release/bioc/html/clusterProfiler.html ggpubr GitHub - kassambara/ ggpubr: ’ggplot20 V0.5.0 tidyverse https://bioconductor.org/ packages/release/ bioc/html/enrichplot.html V1.14.2 GSEA v4.1.0 Subramanian et al., 200557 http://software.broadinstitute.org/ gsea/index.jsp Cytoscape v3.8.2 Shannon et al. 200358 https://cytoscape.org/ ImageJ (1.5.3a) NIH https://imagej.nih.gov/ij/ Adobe Photoshop CC2020 Adobe Systems http://www.adobe.com GraphPad Prism 8.0 GraphPad Software http://www.graphpad.com/scientific- software/prism/

    Article Title: Sensor systems for target ligands and uses thereof
    Article Snippet: Miscellaneous Plasmids—pCAG-GFP (Addgene plasmid 11150)39, pCAG-YFP (Addgene plasmid 11180)39, pCAG-DsRed (Addgene 11151)39. pRho-GFP-IRES-AP (referred to as Rho-GFP)40. pCAG-nlacZ (Cepko lab, Harvard Medical School), pCAGEN (Addgene plasmid 11160)39. pCALNL-DsRed (Addgene plasmid 13769)39. pCAFNF-DsRed (Addgene plasmid 13771)39. pCALNL-luc28. pRL-TK (Promega, 4E2241).

    Article Title: Polysaccharide-Polyplex Nanofilm Coatings Enhance Nanoneedle-Based Gene Delivery and Transfection Efficiency.
    Article Snippet: Anti-mouse CD44 was purchased from BD Biosciences. pCAG-GFP and pCAG-dsRFP were obtained from Addgene (MA, USA) and developed by Cepko C, et al.[103] Fluc-pcDNA3 was obtained from Addgene (MA, USA) and developed by Safran M, et al.[104] pABOL was obtained in-house and synthesized as previously described.

    Article Title: The mTOR pathway genes mTOR, Rheb, Depdc5, Pten , and Tsc1 have convergent and divergent impacts on cortical neuron development and function
    Article Snippet: pCAG-GFP , Addgene plasmid #11150; deposited by Dr. Connie Cepko.

    Article Title: Caveolin-3 prevents swelling-induced membrane damage via regulation of I Cl,swell activity.
    Article Snippet: Caveola membrane structures harbor mechanosensitive chloride channels (MCCs; including chloride channel 2, chloride channel 3, and SWELL1, also known as LRRC8A) that form a swelling-activated chloride current (ICl,swell) and play an important role in cell volume regulation and mechanoelectrical signal transduction.. However, the role of the muscle-specific caveolar scaffolding protein caveolin-3 (Cav3) in regulation of MCC expression, activity, and contribution to membrane integrity in response to mechanical stress remains unclear.. Here we showed that Cav3-transfected (Cav3-positive) HEK293 cells were significantly resistant to extreme (<20 milliosmole) hypotonic swelling compared with native (Cav3-negative) HEK293 cells; the percentage of cells with membrane damage decreased from 45% in Cav3-negative cells to 17% in Cav3-positive cells (p < 0.05).

    Recombinant:

    Article Title: In situ cell-type-specific cell-surface proteomic profiling in mice.
    Article Snippet: Nelson; Clark et al., 2020 N/A Mouse: MADM6-GT Contreras et al., 2021 N/A Mouse: MADM6-TG Contreras et al., 2021 N/A Oligonucleotides See Table S2 for a complete list of sequences Recombinant DNA See Table S2 for a complete list of gR and miR sequences integrated into plasmids pCAG-GFP Matsuda and Cepko, 2004 RRID:Addgene_11150 pCAG-tdTomato W. Joo, unpublished N/A pX333 Maddalo et al., 2014 RRID:Addgene_64073 pX333-CBh-Cas9-U6-2xsgRNA-LacZ Takeo et al., 2021 N/A pX333-CBh-Cas9-U6-2xsgRNA-Armh4 This paper N/A pCAG-EmGFP-miR Gift from M. Yuzaki N/A pCAG-EmGFP-LacZ-miR This paper N/A pCAG-EmGFP-Armh4-miR This paper N/A pCAG-2xHA-Armh4WT This paper N/A pCAG-V5-Armh4WT This paper N/A pCAG-Armh4WT-2xHA This paper N/A pCAG-2xHA-Armh4DICD This paper N/A pCAG-Armh4Endo6A-2xHA This paper N/A Software and algorithms ZEN Carl Zeiss RRID: SCR_013672 Imaris 9.3 Oxford Instruments RRID:SCR_007370; https://imaris.oxinst.com/ ImageJ (Fiji) NIH https://imagej.net/Fiji/Downloads Prism 9 GraphPad RRID:SCR_002798; https://www.graphpad.com/ Excel Microsoft RRID:SCR_016137 Spectrum Mill Agilent https://proteomics.broadinstitute. org/millhome.htm

    Article Title: Visualizing and manipulating the production and accumulation of hyaluronan for functional assessment in chicken embryos
    Article Snippet: pCAG - GFP , Matsuda and Cepko 4 , pCAG-GFP was a gift from Connie Cepko (Addgene plasmid # 11150; http://n2t.net/addgene:11150 ; RRID:Addgene_11150).

    Article Title: PCSK9 deficiency alters brain lipid composition without affecting brain development and function
    Article Snippet: We transfected the cells with the PCSK9 plasmid or an empty pCAGEN vector and stained with an anti-PCSK9 antibody (Goat-a-PCSK9: AF3985 (anti mouse/rat PCSK9, 0.2 mg/mL), dilution 1:50) and used immunofluorescence to confirm specific PCSK9 expression. pCAG-GFP was purchased from Addgene #11150. pCX::myr-Venus plasmid was a gift from Anna-Katerina Hadjantonalis.

    Article Title: DCX knockout ferret reveals a neurogenic mechanism in cortical development.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains Ferrets: WT This paper N/A Ferrets: DCX knockout mutants This paper N/A Mice: ICR This paper N/A Recombinant DNA pCAG-GFP Addgene Cat#11150 pCAG-DCX-GFP This paper N/A Software and algorithms Spaceranger v 1.0.0 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/ software/downloads/latest R v.4.1.0 R Core Team https://www.R-project.org/ CellRanger v.6.1.2 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/installation Seurat v4.3.0 Stuart et al., 201953 https://satijalab.org/seurat/install.html scrubletR v0.1.0 https://github.com/Moonerss/scrubletR CytoTRACE v0.3.3 Gulati et al., 201934 https://github.com/seqyuan/CytoTRACE SAW-5.4.0 BGIResearch https://github.com/STOmics/SAW stereopy-0.8.0 BGIResearch https://github.com/BGIResearch/stereopy scanpy-1.9.3 the Scanpy development team https://github.com/scverse/scanpy ggplot2 v3.3.2 Wickham, 201654 https://ggplot2.tidyverse.org scran v1.10.2 Lun et al., 201655 https://bioconductor.statistik.tu- dortmund.de/packages/3.8/bioc/ html/scran.html ggtree https://github.com/YuLab- SMU/ggtree V3.0.4 clusterProfiler v4.4.4 Wu et al., 2021.56 http://www.bioconductor.org/packages/ release/bioc/html/clusterProfiler.html ggpubr GitHub - kassambara/ ggpubr: ’ggplot20 V0.5.0 tidyverse https://bioconductor.org/ packages/release/ bioc/html/enrichplot.html V1.14.2 GSEA v4.1.0 Subramanian et al., 200557 http://software.broadinstitute.org/ gsea/index.jsp Cytoscape v3.8.2 Shannon et al. 200358 https://cytoscape.org/ ImageJ (1.5.3a) NIH https://imagej.nih.gov/ij/ Adobe Photoshop CC2020 Adobe Systems http://www.adobe.com GraphPad Prism 8.0 GraphPad Software http://www.graphpad.com/scientific- software/prism/

    Article Title: Sensor systems for target ligands and uses thereof
    Article Snippet: Miscellaneous Plasmids—pCAG-GFP (Addgene plasmid 11150)39, pCAG-YFP (Addgene plasmid 11180)39, pCAG-DsRed (Addgene 11151)39. pRho-GFP-IRES-AP (referred to as Rho-GFP)40. pCAG-nlacZ (Cepko lab, Harvard Medical School), pCAGEN (Addgene plasmid 11160)39. pCALNL-DsRed (Addgene plasmid 13769)39. pCAFNF-DsRed (Addgene plasmid 13771)39. pCALNL-luc28. pRL-TK (Promega, 4E2241).

    Article Title: Polysaccharide-Polyplex Nanofilm Coatings Enhance Nanoneedle-Based Gene Delivery and Transfection Efficiency.
    Article Snippet: Anti-mouse CD44 was purchased from BD Biosciences. pCAG-GFP and pCAG-dsRFP were obtained from Addgene (MA, USA) and developed by Cepko C, et al.[103] Fluc-pcDNA3 was obtained from Addgene (MA, USA) and developed by Safran M, et al.[104] pABOL was obtained in-house and synthesized as previously described.

    Article Title: The mTOR pathway genes mTOR, Rheb, Depdc5, Pten , and Tsc1 have convergent and divergent impacts on cortical neuron development and function
    Article Snippet: pCAG-GFP , Addgene plasmid #11150; deposited by Dr. Connie Cepko.

    Article Title: Caveolin-3 prevents swelling-induced membrane damage via regulation of I Cl,swell activity.
    Article Snippet: Caveola membrane structures harbor mechanosensitive chloride channels (MCCs; including chloride channel 2, chloride channel 3, and SWELL1, also known as LRRC8A) that form a swelling-activated chloride current (ICl,swell) and play an important role in cell volume regulation and mechanoelectrical signal transduction.. However, the role of the muscle-specific caveolar scaffolding protein caveolin-3 (Cav3) in regulation of MCC expression, activity, and contribution to membrane integrity in response to mechanical stress remains unclear.. Here we showed that Cav3-transfected (Cav3-positive) HEK293 cells were significantly resistant to extreme (<20 milliosmole) hypotonic swelling compared with native (Cav3-negative) HEK293 cells; the percentage of cells with membrane damage decreased from 45% in Cav3-negative cells to 17% in Cav3-positive cells (p < 0.05).

    Software:

    Article Title: In situ cell-type-specific cell-surface proteomic profiling in mice.
    Article Snippet: Nelson; Clark et al., 2020 N/A Mouse: MADM6-GT Contreras et al., 2021 N/A Mouse: MADM6-TG Contreras et al., 2021 N/A Oligonucleotides See Table S2 for a complete list of sequences Recombinant DNA See Table S2 for a complete list of gR and miR sequences integrated into plasmids pCAG-GFP Matsuda and Cepko, 2004 RRID:Addgene_11150 pCAG-tdTomato W. Joo, unpublished N/A pX333 Maddalo et al., 2014 RRID:Addgene_64073 pX333-CBh-Cas9-U6-2xsgRNA-LacZ Takeo et al., 2021 N/A pX333-CBh-Cas9-U6-2xsgRNA-Armh4 This paper N/A pCAG-EmGFP-miR Gift from M. Yuzaki N/A pCAG-EmGFP-LacZ-miR This paper N/A pCAG-EmGFP-Armh4-miR This paper N/A pCAG-2xHA-Armh4WT This paper N/A pCAG-V5-Armh4WT This paper N/A pCAG-Armh4WT-2xHA This paper N/A pCAG-2xHA-Armh4DICD This paper N/A pCAG-Armh4Endo6A-2xHA This paper N/A Software and algorithms ZEN Carl Zeiss RRID: SCR_013672 Imaris 9.3 Oxford Instruments RRID:SCR_007370; https://imaris.oxinst.com/ ImageJ (Fiji) NIH https://imagej.net/Fiji/Downloads Prism 9 GraphPad RRID:SCR_002798; https://www.graphpad.com/ Excel Microsoft RRID:SCR_016137 Spectrum Mill Agilent https://proteomics.broadinstitute. org/millhome.htm

    Article Title: Visualizing and manipulating the production and accumulation of hyaluronan for functional assessment in chicken embryos
    Article Snippet: pCAG - GFP , Matsuda and Cepko 4 , pCAG-GFP was a gift from Connie Cepko (Addgene plasmid # 11150; http://n2t.net/addgene:11150 ; RRID:Addgene_11150).

    Article Title: PCSK9 deficiency alters brain lipid composition without affecting brain development and function
    Article Snippet: We transfected the cells with the PCSK9 plasmid or an empty pCAGEN vector and stained with an anti-PCSK9 antibody (Goat-a-PCSK9: AF3985 (anti mouse/rat PCSK9, 0.2 mg/mL), dilution 1:50) and used immunofluorescence to confirm specific PCSK9 expression. pCAG-GFP was purchased from Addgene #11150. pCX::myr-Venus plasmid was a gift from Anna-Katerina Hadjantonalis.

    Article Title: DCX knockout ferret reveals a neurogenic mechanism in cortical development.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains Ferrets: WT This paper N/A Ferrets: DCX knockout mutants This paper N/A Mice: ICR This paper N/A Recombinant DNA pCAG-GFP Addgene Cat#11150 pCAG-DCX-GFP This paper N/A Software and algorithms Spaceranger v 1.0.0 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/ software/downloads/latest R v.4.1.0 R Core Team https://www.R-project.org/ CellRanger v.6.1.2 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/installation Seurat v4.3.0 Stuart et al., 201953 https://satijalab.org/seurat/install.html scrubletR v0.1.0 https://github.com/Moonerss/scrubletR CytoTRACE v0.3.3 Gulati et al., 201934 https://github.com/seqyuan/CytoTRACE SAW-5.4.0 BGIResearch https://github.com/STOmics/SAW stereopy-0.8.0 BGIResearch https://github.com/BGIResearch/stereopy scanpy-1.9.3 the Scanpy development team https://github.com/scverse/scanpy ggplot2 v3.3.2 Wickham, 201654 https://ggplot2.tidyverse.org scran v1.10.2 Lun et al., 201655 https://bioconductor.statistik.tu- dortmund.de/packages/3.8/bioc/ html/scran.html ggtree https://github.com/YuLab- SMU/ggtree V3.0.4 clusterProfiler v4.4.4 Wu et al., 2021.56 http://www.bioconductor.org/packages/ release/bioc/html/clusterProfiler.html ggpubr GitHub - kassambara/ ggpubr: ’ggplot20 V0.5.0 tidyverse https://bioconductor.org/ packages/release/ bioc/html/enrichplot.html V1.14.2 GSEA v4.1.0 Subramanian et al., 200557 http://software.broadinstitute.org/ gsea/index.jsp Cytoscape v3.8.2 Shannon et al. 200358 https://cytoscape.org/ ImageJ (1.5.3a) NIH https://imagej.nih.gov/ij/ Adobe Photoshop CC2020 Adobe Systems http://www.adobe.com GraphPad Prism 8.0 GraphPad Software http://www.graphpad.com/scientific- software/prism/

    Article Title: Sensor systems for target ligands and uses thereof
    Article Snippet: Miscellaneous Plasmids—pCAG-GFP (Addgene plasmid 11150)39, pCAG-YFP (Addgene plasmid 11180)39, pCAG-DsRed (Addgene 11151)39. pRho-GFP-IRES-AP (referred to as Rho-GFP)40. pCAG-nlacZ (Cepko lab, Harvard Medical School), pCAGEN (Addgene plasmid 11160)39. pCALNL-DsRed (Addgene plasmid 13769)39. pCAFNF-DsRed (Addgene plasmid 13771)39. pCALNL-luc28. pRL-TK (Promega, 4E2241).

    Article Title: Polysaccharide-Polyplex Nanofilm Coatings Enhance Nanoneedle-Based Gene Delivery and Transfection Efficiency.
    Article Snippet: Anti-mouse CD44 was purchased from BD Biosciences. pCAG-GFP and pCAG-dsRFP were obtained from Addgene (MA, USA) and developed by Cepko C, et al.[103] Fluc-pcDNA3 was obtained from Addgene (MA, USA) and developed by Safran M, et al.[104] pABOL was obtained in-house and synthesized as previously described.

    Article Title: The mTOR pathway genes mTOR, Rheb, Depdc5, Pten , and Tsc1 have convergent and divergent impacts on cortical neuron development and function
    Article Snippet: pCAG-GFP , Addgene plasmid #11150; deposited by Dr. Connie Cepko.

    Article Title: Caveolin-3 prevents swelling-induced membrane damage via regulation of I Cl,swell activity.
    Article Snippet: Caveola membrane structures harbor mechanosensitive chloride channels (MCCs; including chloride channel 2, chloride channel 3, and SWELL1, also known as LRRC8A) that form a swelling-activated chloride current (ICl,swell) and play an important role in cell volume regulation and mechanoelectrical signal transduction.. However, the role of the muscle-specific caveolar scaffolding protein caveolin-3 (Cav3) in regulation of MCC expression, activity, and contribution to membrane integrity in response to mechanical stress remains unclear.. Here we showed that Cav3-transfected (Cav3-positive) HEK293 cells were significantly resistant to extreme (<20 milliosmole) hypotonic swelling compared with native (Cav3-negative) HEK293 cells; the percentage of cells with membrane damage decreased from 45% in Cav3-negative cells to 17% in Cav3-positive cells (p < 0.05).

    Plasmid Preparation:

    Article Title: In situ cell-type-specific cell-surface proteomic profiling in mice.
    Article Snippet: Nelson; Clark et al., 2020 N/A Mouse: MADM6-GT Contreras et al., 2021 N/A Mouse: MADM6-TG Contreras et al., 2021 N/A Oligonucleotides See Table S2 for a complete list of sequences Recombinant DNA See Table S2 for a complete list of gR and miR sequences integrated into plasmids pCAG-GFP Matsuda and Cepko, 2004 RRID:Addgene_11150 pCAG-tdTomato W. Joo, unpublished N/A pX333 Maddalo et al., 2014 RRID:Addgene_64073 pX333-CBh-Cas9-U6-2xsgRNA-LacZ Takeo et al., 2021 N/A pX333-CBh-Cas9-U6-2xsgRNA-Armh4 This paper N/A pCAG-EmGFP-miR Gift from M. Yuzaki N/A pCAG-EmGFP-LacZ-miR This paper N/A pCAG-EmGFP-Armh4-miR This paper N/A pCAG-2xHA-Armh4WT This paper N/A pCAG-V5-Armh4WT This paper N/A pCAG-Armh4WT-2xHA This paper N/A pCAG-2xHA-Armh4DICD This paper N/A pCAG-Armh4Endo6A-2xHA This paper N/A Software and algorithms ZEN Carl Zeiss RRID: SCR_013672 Imaris 9.3 Oxford Instruments RRID:SCR_007370; https://imaris.oxinst.com/ ImageJ (Fiji) NIH https://imagej.net/Fiji/Downloads Prism 9 GraphPad RRID:SCR_002798; https://www.graphpad.com/ Excel Microsoft RRID:SCR_016137 Spectrum Mill Agilent https://proteomics.broadinstitute. org/millhome.htm

    Article Title: Visualizing and manipulating the production and accumulation of hyaluronan for functional assessment in chicken embryos
    Article Snippet: pCAG - GFP , Matsuda and Cepko 4 , pCAG-GFP was a gift from Connie Cepko (Addgene plasmid # 11150; http://n2t.net/addgene:11150 ; RRID:Addgene_11150).

    Article Title: PCSK9 deficiency alters brain lipid composition without affecting brain development and function
    Article Snippet: We transfected the cells with the PCSK9 plasmid or an empty pCAGEN vector and stained with an anti-PCSK9 antibody (Goat-a-PCSK9: AF3985 (anti mouse/rat PCSK9, 0.2 mg/mL), dilution 1:50) and used immunofluorescence to confirm specific PCSK9 expression. pCAG-GFP was purchased from Addgene #11150. pCX::myr-Venus plasmid was a gift from Anna-Katerina Hadjantonalis.

    Article Title: DCX knockout ferret reveals a neurogenic mechanism in cortical development.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains Ferrets: WT This paper N/A Ferrets: DCX knockout mutants This paper N/A Mice: ICR This paper N/A Recombinant DNA pCAG-GFP Addgene Cat#11150 pCAG-DCX-GFP This paper N/A Software and algorithms Spaceranger v 1.0.0 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/ software/downloads/latest R v.4.1.0 R Core Team https://www.R-project.org/ CellRanger v.6.1.2 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/installation Seurat v4.3.0 Stuart et al., 201953 https://satijalab.org/seurat/install.html scrubletR v0.1.0 https://github.com/Moonerss/scrubletR CytoTRACE v0.3.3 Gulati et al., 201934 https://github.com/seqyuan/CytoTRACE SAW-5.4.0 BGIResearch https://github.com/STOmics/SAW stereopy-0.8.0 BGIResearch https://github.com/BGIResearch/stereopy scanpy-1.9.3 the Scanpy development team https://github.com/scverse/scanpy ggplot2 v3.3.2 Wickham, 201654 https://ggplot2.tidyverse.org scran v1.10.2 Lun et al., 201655 https://bioconductor.statistik.tu- dortmund.de/packages/3.8/bioc/ html/scran.html ggtree https://github.com/YuLab- SMU/ggtree V3.0.4 clusterProfiler v4.4.4 Wu et al., 2021.56 http://www.bioconductor.org/packages/ release/bioc/html/clusterProfiler.html ggpubr GitHub - kassambara/ ggpubr: ’ggplot20 V0.5.0 tidyverse https://bioconductor.org/ packages/release/ bioc/html/enrichplot.html V1.14.2 GSEA v4.1.0 Subramanian et al., 200557 http://software.broadinstitute.org/ gsea/index.jsp Cytoscape v3.8.2 Shannon et al. 200358 https://cytoscape.org/ ImageJ (1.5.3a) NIH https://imagej.nih.gov/ij/ Adobe Photoshop CC2020 Adobe Systems http://www.adobe.com GraphPad Prism 8.0 GraphPad Software http://www.graphpad.com/scientific- software/prism/

    Article Title: Sensor systems for target ligands and uses thereof
    Article Snippet: Miscellaneous Plasmids—pCAG-GFP (Addgene plasmid 11150)39, pCAG-YFP (Addgene plasmid 11180)39, pCAG-DsRed (Addgene 11151)39. pRho-GFP-IRES-AP (referred to as Rho-GFP)40. pCAG-nlacZ (Cepko lab, Harvard Medical School), pCAGEN (Addgene plasmid 11160)39. pCALNL-DsRed (Addgene plasmid 13769)39. pCAFNF-DsRed (Addgene plasmid 13771)39. pCALNL-luc28. pRL-TK (Promega, 4E2241).

    Article Title: Polysaccharide-Polyplex Nanofilm Coatings Enhance Nanoneedle-Based Gene Delivery and Transfection Efficiency.
    Article Snippet: Anti-mouse CD44 was purchased from BD Biosciences. pCAG-GFP and pCAG-dsRFP were obtained from Addgene (MA, USA) and developed by Cepko C, et al.[103] Fluc-pcDNA3 was obtained from Addgene (MA, USA) and developed by Safran M, et al.[104] pABOL was obtained in-house and synthesized as previously described.

    Article Title: The mTOR pathway genes mTOR, Rheb, Depdc5, Pten , and Tsc1 have convergent and divergent impacts on cortical neuron development and function
    Article Snippet: pCAG-GFP , Addgene plasmid #11150; deposited by Dr. Connie Cepko.

    Article Title: Caveolin-3 prevents swelling-induced membrane damage via regulation of I Cl,swell activity.
    Article Snippet: Caveola membrane structures harbor mechanosensitive chloride channels (MCCs; including chloride channel 2, chloride channel 3, and SWELL1, also known as LRRC8A) that form a swelling-activated chloride current (ICl,swell) and play an important role in cell volume regulation and mechanoelectrical signal transduction.. However, the role of the muscle-specific caveolar scaffolding protein caveolin-3 (Cav3) in regulation of MCC expression, activity, and contribution to membrane integrity in response to mechanical stress remains unclear.. Here we showed that Cav3-transfected (Cav3-positive) HEK293 cells were significantly resistant to extreme (<20 milliosmole) hypotonic swelling compared with native (Cav3-negative) HEK293 cells; the percentage of cells with membrane damage decreased from 45% in Cav3-negative cells to 17% in Cav3-positive cells (p < 0.05).

    Incubation:

    Article Title: In situ cell-type-specific cell-surface proteomic profiling in mice.
    Article Snippet: Nelson; Clark et al., 2020 N/A Mouse: MADM6-GT Contreras et al., 2021 N/A Mouse: MADM6-TG Contreras et al., 2021 N/A Oligonucleotides See Table S2 for a complete list of sequences Recombinant DNA See Table S2 for a complete list of gR and miR sequences integrated into plasmids pCAG-GFP Matsuda and Cepko, 2004 RRID:Addgene_11150 pCAG-tdTomato W. Joo, unpublished N/A pX333 Maddalo et al., 2014 RRID:Addgene_64073 pX333-CBh-Cas9-U6-2xsgRNA-LacZ Takeo et al., 2021 N/A pX333-CBh-Cas9-U6-2xsgRNA-Armh4 This paper N/A pCAG-EmGFP-miR Gift from M. Yuzaki N/A pCAG-EmGFP-LacZ-miR This paper N/A pCAG-EmGFP-Armh4-miR This paper N/A pCAG-2xHA-Armh4WT This paper N/A pCAG-V5-Armh4WT This paper N/A pCAG-Armh4WT-2xHA This paper N/A pCAG-2xHA-Armh4DICD This paper N/A pCAG-Armh4Endo6A-2xHA This paper N/A Software and algorithms ZEN Carl Zeiss RRID: SCR_013672 Imaris 9.3 Oxford Instruments RRID:SCR_007370; https://imaris.oxinst.com/ ImageJ (Fiji) NIH https://imagej.net/Fiji/Downloads Prism 9 GraphPad RRID:SCR_002798; https://www.graphpad.com/ Excel Microsoft RRID:SCR_016137 Spectrum Mill Agilent https://proteomics.broadinstitute. org/millhome.htm

    Article Title: Visualizing and manipulating the production and accumulation of hyaluronan for functional assessment in chicken embryos
    Article Snippet: pCAG - GFP , Matsuda and Cepko 4 , pCAG-GFP was a gift from Connie Cepko (Addgene plasmid # 11150; http://n2t.net/addgene:11150 ; RRID:Addgene_11150).

    Article Title: PCSK9 deficiency alters brain lipid composition without affecting brain development and function
    Article Snippet: We transfected the cells with the PCSK9 plasmid or an empty pCAGEN vector and stained with an anti-PCSK9 antibody (Goat-a-PCSK9: AF3985 (anti mouse/rat PCSK9, 0.2 mg/mL), dilution 1:50) and used immunofluorescence to confirm specific PCSK9 expression. pCAG-GFP was purchased from Addgene #11150. pCX::myr-Venus plasmid was a gift from Anna-Katerina Hadjantonalis.

    Article Title: DCX knockout ferret reveals a neurogenic mechanism in cortical development.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains Ferrets: WT This paper N/A Ferrets: DCX knockout mutants This paper N/A Mice: ICR This paper N/A Recombinant DNA pCAG-GFP Addgene Cat#11150 pCAG-DCX-GFP This paper N/A Software and algorithms Spaceranger v 1.0.0 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/ software/downloads/latest R v.4.1.0 R Core Team https://www.R-project.org/ CellRanger v.6.1.2 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/installation Seurat v4.3.0 Stuart et al., 201953 https://satijalab.org/seurat/install.html scrubletR v0.1.0 https://github.com/Moonerss/scrubletR CytoTRACE v0.3.3 Gulati et al., 201934 https://github.com/seqyuan/CytoTRACE SAW-5.4.0 BGIResearch https://github.com/STOmics/SAW stereopy-0.8.0 BGIResearch https://github.com/BGIResearch/stereopy scanpy-1.9.3 the Scanpy development team https://github.com/scverse/scanpy ggplot2 v3.3.2 Wickham, 201654 https://ggplot2.tidyverse.org scran v1.10.2 Lun et al., 201655 https://bioconductor.statistik.tu- dortmund.de/packages/3.8/bioc/ html/scran.html ggtree https://github.com/YuLab- SMU/ggtree V3.0.4 clusterProfiler v4.4.4 Wu et al., 2021.56 http://www.bioconductor.org/packages/ release/bioc/html/clusterProfiler.html ggpubr GitHub - kassambara/ ggpubr: ’ggplot20 V0.5.0 tidyverse https://bioconductor.org/ packages/release/ bioc/html/enrichplot.html V1.14.2 GSEA v4.1.0 Subramanian et al., 200557 http://software.broadinstitute.org/ gsea/index.jsp Cytoscape v3.8.2 Shannon et al. 200358 https://cytoscape.org/ ImageJ (1.5.3a) NIH https://imagej.nih.gov/ij/ Adobe Photoshop CC2020 Adobe Systems http://www.adobe.com GraphPad Prism 8.0 GraphPad Software http://www.graphpad.com/scientific- software/prism/

    Article Title: Sensor systems for target ligands and uses thereof
    Article Snippet: Miscellaneous Plasmids—pCAG-GFP (Addgene plasmid 11150)39, pCAG-YFP (Addgene plasmid 11180)39, pCAG-DsRed (Addgene 11151)39. pRho-GFP-IRES-AP (referred to as Rho-GFP)40. pCAG-nlacZ (Cepko lab, Harvard Medical School), pCAGEN (Addgene plasmid 11160)39. pCALNL-DsRed (Addgene plasmid 13769)39. pCAFNF-DsRed (Addgene plasmid 13771)39. pCALNL-luc28. pRL-TK (Promega, 4E2241).

    Article Title: Polysaccharide-Polyplex Nanofilm Coatings Enhance Nanoneedle-Based Gene Delivery and Transfection Efficiency.
    Article Snippet: Anti-mouse CD44 was purchased from BD Biosciences. pCAG-GFP and pCAG-dsRFP were obtained from Addgene (MA, USA) and developed by Cepko C, et al.[103] Fluc-pcDNA3 was obtained from Addgene (MA, USA) and developed by Safran M, et al.[104] pABOL was obtained in-house and synthesized as previously described.

    Article Title: The mTOR pathway genes mTOR, Rheb, Depdc5, Pten , and Tsc1 have convergent and divergent impacts on cortical neuron development and function
    Article Snippet: pCAG-GFP , Addgene plasmid #11150; deposited by Dr. Connie Cepko.

    Article Title: Caveolin-3 prevents swelling-induced membrane damage via regulation of I Cl,swell activity.
    Article Snippet: Caveola membrane structures harbor mechanosensitive chloride channels (MCCs; including chloride channel 2, chloride channel 3, and SWELL1, also known as LRRC8A) that form a swelling-activated chloride current (ICl,swell) and play an important role in cell volume regulation and mechanoelectrical signal transduction.. However, the role of the muscle-specific caveolar scaffolding protein caveolin-3 (Cav3) in regulation of MCC expression, activity, and contribution to membrane integrity in response to mechanical stress remains unclear.. Here we showed that Cav3-transfected (Cav3-positive) HEK293 cells were significantly resistant to extreme (<20 milliosmole) hypotonic swelling compared with native (Cav3-negative) HEK293 cells; the percentage of cells with membrane damage decreased from 45% in Cav3-negative cells to 17% in Cav3-positive cells (p < 0.05).

    Paraffin Wax:

    Article Title: In situ cell-type-specific cell-surface proteomic profiling in mice.
    Article Snippet: Nelson; Clark et al., 2020 N/A Mouse: MADM6-GT Contreras et al., 2021 N/A Mouse: MADM6-TG Contreras et al., 2021 N/A Oligonucleotides See Table S2 for a complete list of sequences Recombinant DNA See Table S2 for a complete list of gR and miR sequences integrated into plasmids pCAG-GFP Matsuda and Cepko, 2004 RRID:Addgene_11150 pCAG-tdTomato W. Joo, unpublished N/A pX333 Maddalo et al., 2014 RRID:Addgene_64073 pX333-CBh-Cas9-U6-2xsgRNA-LacZ Takeo et al., 2021 N/A pX333-CBh-Cas9-U6-2xsgRNA-Armh4 This paper N/A pCAG-EmGFP-miR Gift from M. Yuzaki N/A pCAG-EmGFP-LacZ-miR This paper N/A pCAG-EmGFP-Armh4-miR This paper N/A pCAG-2xHA-Armh4WT This paper N/A pCAG-V5-Armh4WT This paper N/A pCAG-Armh4WT-2xHA This paper N/A pCAG-2xHA-Armh4DICD This paper N/A pCAG-Armh4Endo6A-2xHA This paper N/A Software and algorithms ZEN Carl Zeiss RRID: SCR_013672 Imaris 9.3 Oxford Instruments RRID:SCR_007370; https://imaris.oxinst.com/ ImageJ (Fiji) NIH https://imagej.net/Fiji/Downloads Prism 9 GraphPad RRID:SCR_002798; https://www.graphpad.com/ Excel Microsoft RRID:SCR_016137 Spectrum Mill Agilent https://proteomics.broadinstitute. org/millhome.htm

    Article Title: Visualizing and manipulating the production and accumulation of hyaluronan for functional assessment in chicken embryos
    Article Snippet: pCAG - GFP , Matsuda and Cepko 4 , pCAG-GFP was a gift from Connie Cepko (Addgene plasmid # 11150; http://n2t.net/addgene:11150 ; RRID:Addgene_11150).

    Article Title: PCSK9 deficiency alters brain lipid composition without affecting brain development and function
    Article Snippet: We transfected the cells with the PCSK9 plasmid or an empty pCAGEN vector and stained with an anti-PCSK9 antibody (Goat-a-PCSK9: AF3985 (anti mouse/rat PCSK9, 0.2 mg/mL), dilution 1:50) and used immunofluorescence to confirm specific PCSK9 expression. pCAG-GFP was purchased from Addgene #11150. pCX::myr-Venus plasmid was a gift from Anna-Katerina Hadjantonalis.

    Article Title: DCX knockout ferret reveals a neurogenic mechanism in cortical development.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains Ferrets: WT This paper N/A Ferrets: DCX knockout mutants This paper N/A Mice: ICR This paper N/A Recombinant DNA pCAG-GFP Addgene Cat#11150 pCAG-DCX-GFP This paper N/A Software and algorithms Spaceranger v 1.0.0 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/ software/downloads/latest R v.4.1.0 R Core Team https://www.R-project.org/ CellRanger v.6.1.2 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/installation Seurat v4.3.0 Stuart et al., 201953 https://satijalab.org/seurat/install.html scrubletR v0.1.0 https://github.com/Moonerss/scrubletR CytoTRACE v0.3.3 Gulati et al., 201934 https://github.com/seqyuan/CytoTRACE SAW-5.4.0 BGIResearch https://github.com/STOmics/SAW stereopy-0.8.0 BGIResearch https://github.com/BGIResearch/stereopy scanpy-1.9.3 the Scanpy development team https://github.com/scverse/scanpy ggplot2 v3.3.2 Wickham, 201654 https://ggplot2.tidyverse.org scran v1.10.2 Lun et al., 201655 https://bioconductor.statistik.tu- dortmund.de/packages/3.8/bioc/ html/scran.html ggtree https://github.com/YuLab- SMU/ggtree V3.0.4 clusterProfiler v4.4.4 Wu et al., 2021.56 http://www.bioconductor.org/packages/ release/bioc/html/clusterProfiler.html ggpubr GitHub - kassambara/ ggpubr: ’ggplot20 V0.5.0 tidyverse https://bioconductor.org/ packages/release/ bioc/html/enrichplot.html V1.14.2 GSEA v4.1.0 Subramanian et al., 200557 http://software.broadinstitute.org/ gsea/index.jsp Cytoscape v3.8.2 Shannon et al. 200358 https://cytoscape.org/ ImageJ (1.5.3a) NIH https://imagej.nih.gov/ij/ Adobe Photoshop CC2020 Adobe Systems http://www.adobe.com GraphPad Prism 8.0 GraphPad Software http://www.graphpad.com/scientific- software/prism/

    Article Title: Sensor systems for target ligands and uses thereof
    Article Snippet: Miscellaneous Plasmids—pCAG-GFP (Addgene plasmid 11150)39, pCAG-YFP (Addgene plasmid 11180)39, pCAG-DsRed (Addgene 11151)39. pRho-GFP-IRES-AP (referred to as Rho-GFP)40. pCAG-nlacZ (Cepko lab, Harvard Medical School), pCAGEN (Addgene plasmid 11160)39. pCALNL-DsRed (Addgene plasmid 13769)39. pCAFNF-DsRed (Addgene plasmid 13771)39. pCALNL-luc28. pRL-TK (Promega, 4E2241).

    Article Title: Polysaccharide-Polyplex Nanofilm Coatings Enhance Nanoneedle-Based Gene Delivery and Transfection Efficiency.
    Article Snippet: Anti-mouse CD44 was purchased from BD Biosciences. pCAG-GFP and pCAG-dsRFP were obtained from Addgene (MA, USA) and developed by Cepko C, et al.[103] Fluc-pcDNA3 was obtained from Addgene (MA, USA) and developed by Safran M, et al.[104] pABOL was obtained in-house and synthesized as previously described.

    Article Title: The mTOR pathway genes mTOR, Rheb, Depdc5, Pten , and Tsc1 have convergent and divergent impacts on cortical neuron development and function
    Article Snippet: pCAG-GFP , Addgene plasmid #11150; deposited by Dr. Connie Cepko.

    Article Title: Caveolin-3 prevents swelling-induced membrane damage via regulation of I Cl,swell activity.
    Article Snippet: Caveola membrane structures harbor mechanosensitive chloride channels (MCCs; including chloride channel 2, chloride channel 3, and SWELL1, also known as LRRC8A) that form a swelling-activated chloride current (ICl,swell) and play an important role in cell volume regulation and mechanoelectrical signal transduction.. However, the role of the muscle-specific caveolar scaffolding protein caveolin-3 (Cav3) in regulation of MCC expression, activity, and contribution to membrane integrity in response to mechanical stress remains unclear.. Here we showed that Cav3-transfected (Cav3-positive) HEK293 cells were significantly resistant to extreme (<20 milliosmole) hypotonic swelling compared with native (Cav3-negative) HEK293 cells; the percentage of cells with membrane damage decreased from 45% in Cav3-negative cells to 17% in Cav3-positive cells (p < 0.05).

    Binding Assay:

    Article Title: In situ cell-type-specific cell-surface proteomic profiling in mice.
    Article Snippet: Nelson; Clark et al., 2020 N/A Mouse: MADM6-GT Contreras et al., 2021 N/A Mouse: MADM6-TG Contreras et al., 2021 N/A Oligonucleotides See Table S2 for a complete list of sequences Recombinant DNA See Table S2 for a complete list of gR and miR sequences integrated into plasmids pCAG-GFP Matsuda and Cepko, 2004 RRID:Addgene_11150 pCAG-tdTomato W. Joo, unpublished N/A pX333 Maddalo et al., 2014 RRID:Addgene_64073 pX333-CBh-Cas9-U6-2xsgRNA-LacZ Takeo et al., 2021 N/A pX333-CBh-Cas9-U6-2xsgRNA-Armh4 This paper N/A pCAG-EmGFP-miR Gift from M. Yuzaki N/A pCAG-EmGFP-LacZ-miR This paper N/A pCAG-EmGFP-Armh4-miR This paper N/A pCAG-2xHA-Armh4WT This paper N/A pCAG-V5-Armh4WT This paper N/A pCAG-Armh4WT-2xHA This paper N/A pCAG-2xHA-Armh4DICD This paper N/A pCAG-Armh4Endo6A-2xHA This paper N/A Software and algorithms ZEN Carl Zeiss RRID: SCR_013672 Imaris 9.3 Oxford Instruments RRID:SCR_007370; https://imaris.oxinst.com/ ImageJ (Fiji) NIH https://imagej.net/Fiji/Downloads Prism 9 GraphPad RRID:SCR_002798; https://www.graphpad.com/ Excel Microsoft RRID:SCR_016137 Spectrum Mill Agilent https://proteomics.broadinstitute. org/millhome.htm

    Article Title: Visualizing and manipulating the production and accumulation of hyaluronan for functional assessment in chicken embryos
    Article Snippet: pCAG - GFP , Matsuda and Cepko 4 , pCAG-GFP was a gift from Connie Cepko (Addgene plasmid # 11150; http://n2t.net/addgene:11150 ; RRID:Addgene_11150).

    Article Title: PCSK9 deficiency alters brain lipid composition without affecting brain development and function
    Article Snippet: We transfected the cells with the PCSK9 plasmid or an empty pCAGEN vector and stained with an anti-PCSK9 antibody (Goat-a-PCSK9: AF3985 (anti mouse/rat PCSK9, 0.2 mg/mL), dilution 1:50) and used immunofluorescence to confirm specific PCSK9 expression. pCAG-GFP was purchased from Addgene #11150. pCX::myr-Venus plasmid was a gift from Anna-Katerina Hadjantonalis.

    Article Title: DCX knockout ferret reveals a neurogenic mechanism in cortical development.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains Ferrets: WT This paper N/A Ferrets: DCX knockout mutants This paper N/A Mice: ICR This paper N/A Recombinant DNA pCAG-GFP Addgene Cat#11150 pCAG-DCX-GFP This paper N/A Software and algorithms Spaceranger v 1.0.0 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/ software/downloads/latest R v.4.1.0 R Core Team https://www.R-project.org/ CellRanger v.6.1.2 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/installation Seurat v4.3.0 Stuart et al., 201953 https://satijalab.org/seurat/install.html scrubletR v0.1.0 https://github.com/Moonerss/scrubletR CytoTRACE v0.3.3 Gulati et al., 201934 https://github.com/seqyuan/CytoTRACE SAW-5.4.0 BGIResearch https://github.com/STOmics/SAW stereopy-0.8.0 BGIResearch https://github.com/BGIResearch/stereopy scanpy-1.9.3 the Scanpy development team https://github.com/scverse/scanpy ggplot2 v3.3.2 Wickham, 201654 https://ggplot2.tidyverse.org scran v1.10.2 Lun et al., 201655 https://bioconductor.statistik.tu- dortmund.de/packages/3.8/bioc/ html/scran.html ggtree https://github.com/YuLab- SMU/ggtree V3.0.4 clusterProfiler v4.4.4 Wu et al., 2021.56 http://www.bioconductor.org/packages/ release/bioc/html/clusterProfiler.html ggpubr GitHub - kassambara/ ggpubr: ’ggplot20 V0.5.0 tidyverse https://bioconductor.org/ packages/release/ bioc/html/enrichplot.html V1.14.2 GSEA v4.1.0 Subramanian et al., 200557 http://software.broadinstitute.org/ gsea/index.jsp Cytoscape v3.8.2 Shannon et al. 200358 https://cytoscape.org/ ImageJ (1.5.3a) NIH https://imagej.nih.gov/ij/ Adobe Photoshop CC2020 Adobe Systems http://www.adobe.com GraphPad Prism 8.0 GraphPad Software http://www.graphpad.com/scientific- software/prism/

    Article Title: Sensor systems for target ligands and uses thereof
    Article Snippet: Miscellaneous Plasmids—pCAG-GFP (Addgene plasmid 11150)39, pCAG-YFP (Addgene plasmid 11180)39, pCAG-DsRed (Addgene 11151)39. pRho-GFP-IRES-AP (referred to as Rho-GFP)40. pCAG-nlacZ (Cepko lab, Harvard Medical School), pCAGEN (Addgene plasmid 11160)39. pCALNL-DsRed (Addgene plasmid 13769)39. pCAFNF-DsRed (Addgene plasmid 13771)39. pCALNL-luc28. pRL-TK (Promega, 4E2241).

    Article Title: Polysaccharide-Polyplex Nanofilm Coatings Enhance Nanoneedle-Based Gene Delivery and Transfection Efficiency.
    Article Snippet: Anti-mouse CD44 was purchased from BD Biosciences. pCAG-GFP and pCAG-dsRFP were obtained from Addgene (MA, USA) and developed by Cepko C, et al.[103] Fluc-pcDNA3 was obtained from Addgene (MA, USA) and developed by Safran M, et al.[104] pABOL was obtained in-house and synthesized as previously described.

    Article Title: The mTOR pathway genes mTOR, Rheb, Depdc5, Pten , and Tsc1 have convergent and divergent impacts on cortical neuron development and function
    Article Snippet: pCAG-GFP , Addgene plasmid #11150; deposited by Dr. Connie Cepko.

    Article Title: Caveolin-3 prevents swelling-induced membrane damage via regulation of I Cl,swell activity.
    Article Snippet: Caveola membrane structures harbor mechanosensitive chloride channels (MCCs; including chloride channel 2, chloride channel 3, and SWELL1, also known as LRRC8A) that form a swelling-activated chloride current (ICl,swell) and play an important role in cell volume regulation and mechanoelectrical signal transduction.. However, the role of the muscle-specific caveolar scaffolding protein caveolin-3 (Cav3) in regulation of MCC expression, activity, and contribution to membrane integrity in response to mechanical stress remains unclear.. Here we showed that Cav3-transfected (Cav3-positive) HEK293 cells were significantly resistant to extreme (<20 milliosmole) hypotonic swelling compared with native (Cav3-negative) HEK293 cells; the percentage of cells with membrane damage decreased from 45% in Cav3-negative cells to 17% in Cav3-positive cells (p < 0.05).

    Blocking Assay:

    Article Title: In situ cell-type-specific cell-surface proteomic profiling in mice.
    Article Snippet: Nelson; Clark et al., 2020 N/A Mouse: MADM6-GT Contreras et al., 2021 N/A Mouse: MADM6-TG Contreras et al., 2021 N/A Oligonucleotides See Table S2 for a complete list of sequences Recombinant DNA See Table S2 for a complete list of gR and miR sequences integrated into plasmids pCAG-GFP Matsuda and Cepko, 2004 RRID:Addgene_11150 pCAG-tdTomato W. Joo, unpublished N/A pX333 Maddalo et al., 2014 RRID:Addgene_64073 pX333-CBh-Cas9-U6-2xsgRNA-LacZ Takeo et al., 2021 N/A pX333-CBh-Cas9-U6-2xsgRNA-Armh4 This paper N/A pCAG-EmGFP-miR Gift from M. Yuzaki N/A pCAG-EmGFP-LacZ-miR This paper N/A pCAG-EmGFP-Armh4-miR This paper N/A pCAG-2xHA-Armh4WT This paper N/A pCAG-V5-Armh4WT This paper N/A pCAG-Armh4WT-2xHA This paper N/A pCAG-2xHA-Armh4DICD This paper N/A pCAG-Armh4Endo6A-2xHA This paper N/A Software and algorithms ZEN Carl Zeiss RRID: SCR_013672 Imaris 9.3 Oxford Instruments RRID:SCR_007370; https://imaris.oxinst.com/ ImageJ (Fiji) NIH https://imagej.net/Fiji/Downloads Prism 9 GraphPad RRID:SCR_002798; https://www.graphpad.com/ Excel Microsoft RRID:SCR_016137 Spectrum Mill Agilent https://proteomics.broadinstitute. org/millhome.htm

    Article Title: Visualizing and manipulating the production and accumulation of hyaluronan for functional assessment in chicken embryos
    Article Snippet: pCAG - GFP , Matsuda and Cepko 4 , pCAG-GFP was a gift from Connie Cepko (Addgene plasmid # 11150; http://n2t.net/addgene:11150 ; RRID:Addgene_11150).

    Article Title: PCSK9 deficiency alters brain lipid composition without affecting brain development and function
    Article Snippet: We transfected the cells with the PCSK9 plasmid or an empty pCAGEN vector and stained with an anti-PCSK9 antibody (Goat-a-PCSK9: AF3985 (anti mouse/rat PCSK9, 0.2 mg/mL), dilution 1:50) and used immunofluorescence to confirm specific PCSK9 expression. pCAG-GFP was purchased from Addgene #11150. pCX::myr-Venus plasmid was a gift from Anna-Katerina Hadjantonalis.

    Article Title: DCX knockout ferret reveals a neurogenic mechanism in cortical development.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains Ferrets: WT This paper N/A Ferrets: DCX knockout mutants This paper N/A Mice: ICR This paper N/A Recombinant DNA pCAG-GFP Addgene Cat#11150 pCAG-DCX-GFP This paper N/A Software and algorithms Spaceranger v 1.0.0 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/ software/downloads/latest R v.4.1.0 R Core Team https://www.R-project.org/ CellRanger v.6.1.2 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/installation Seurat v4.3.0 Stuart et al., 201953 https://satijalab.org/seurat/install.html scrubletR v0.1.0 https://github.com/Moonerss/scrubletR CytoTRACE v0.3.3 Gulati et al., 201934 https://github.com/seqyuan/CytoTRACE SAW-5.4.0 BGIResearch https://github.com/STOmics/SAW stereopy-0.8.0 BGIResearch https://github.com/BGIResearch/stereopy scanpy-1.9.3 the Scanpy development team https://github.com/scverse/scanpy ggplot2 v3.3.2 Wickham, 201654 https://ggplot2.tidyverse.org scran v1.10.2 Lun et al., 201655 https://bioconductor.statistik.tu- dortmund.de/packages/3.8/bioc/ html/scran.html ggtree https://github.com/YuLab- SMU/ggtree V3.0.4 clusterProfiler v4.4.4 Wu et al., 2021.56 http://www.bioconductor.org/packages/ release/bioc/html/clusterProfiler.html ggpubr GitHub - kassambara/ ggpubr: ’ggplot20 V0.5.0 tidyverse https://bioconductor.org/ packages/release/ bioc/html/enrichplot.html V1.14.2 GSEA v4.1.0 Subramanian et al., 200557 http://software.broadinstitute.org/ gsea/index.jsp Cytoscape v3.8.2 Shannon et al. 200358 https://cytoscape.org/ ImageJ (1.5.3a) NIH https://imagej.nih.gov/ij/ Adobe Photoshop CC2020 Adobe Systems http://www.adobe.com GraphPad Prism 8.0 GraphPad Software http://www.graphpad.com/scientific- software/prism/

    Article Title: Sensor systems for target ligands and uses thereof
    Article Snippet: Miscellaneous Plasmids—pCAG-GFP (Addgene plasmid 11150)39, pCAG-YFP (Addgene plasmid 11180)39, pCAG-DsRed (Addgene 11151)39. pRho-GFP-IRES-AP (referred to as Rho-GFP)40. pCAG-nlacZ (Cepko lab, Harvard Medical School), pCAGEN (Addgene plasmid 11160)39. pCALNL-DsRed (Addgene plasmid 13769)39. pCAFNF-DsRed (Addgene plasmid 13771)39. pCALNL-luc28. pRL-TK (Promega, 4E2241).

    Article Title: Polysaccharide-Polyplex Nanofilm Coatings Enhance Nanoneedle-Based Gene Delivery and Transfection Efficiency.
    Article Snippet: Anti-mouse CD44 was purchased from BD Biosciences. pCAG-GFP and pCAG-dsRFP were obtained from Addgene (MA, USA) and developed by Cepko C, et al.[103] Fluc-pcDNA3 was obtained from Addgene (MA, USA) and developed by Safran M, et al.[104] pABOL was obtained in-house and synthesized as previously described.

    Article Title: The mTOR pathway genes mTOR, Rheb, Depdc5, Pten , and Tsc1 have convergent and divergent impacts on cortical neuron development and function
    Article Snippet: pCAG-GFP , Addgene plasmid #11150; deposited by Dr. Connie Cepko.

    Article Title: Caveolin-3 prevents swelling-induced membrane damage via regulation of I Cl,swell activity.
    Article Snippet: Caveola membrane structures harbor mechanosensitive chloride channels (MCCs; including chloride channel 2, chloride channel 3, and SWELL1, also known as LRRC8A) that form a swelling-activated chloride current (ICl,swell) and play an important role in cell volume regulation and mechanoelectrical signal transduction.. However, the role of the muscle-specific caveolar scaffolding protein caveolin-3 (Cav3) in regulation of MCC expression, activity, and contribution to membrane integrity in response to mechanical stress remains unclear.. Here we showed that Cav3-transfected (Cav3-positive) HEK293 cells were significantly resistant to extreme (<20 milliosmole) hypotonic swelling compared with native (Cav3-negative) HEK293 cells; the percentage of cells with membrane damage decreased from 45% in Cav3-negative cells to 17% in Cav3-positive cells (p < 0.05).

    Dissection:

    Article Title: In situ cell-type-specific cell-surface proteomic profiling in mice.
    Article Snippet: Nelson; Clark et al., 2020 N/A Mouse: MADM6-GT Contreras et al., 2021 N/A Mouse: MADM6-TG Contreras et al., 2021 N/A Oligonucleotides See Table S2 for a complete list of sequences Recombinant DNA See Table S2 for a complete list of gR and miR sequences integrated into plasmids pCAG-GFP Matsuda and Cepko, 2004 RRID:Addgene_11150 pCAG-tdTomato W. Joo, unpublished N/A pX333 Maddalo et al., 2014 RRID:Addgene_64073 pX333-CBh-Cas9-U6-2xsgRNA-LacZ Takeo et al., 2021 N/A pX333-CBh-Cas9-U6-2xsgRNA-Armh4 This paper N/A pCAG-EmGFP-miR Gift from M. Yuzaki N/A pCAG-EmGFP-LacZ-miR This paper N/A pCAG-EmGFP-Armh4-miR This paper N/A pCAG-2xHA-Armh4WT This paper N/A pCAG-V5-Armh4WT This paper N/A pCAG-Armh4WT-2xHA This paper N/A pCAG-2xHA-Armh4DICD This paper N/A pCAG-Armh4Endo6A-2xHA This paper N/A Software and algorithms ZEN Carl Zeiss RRID: SCR_013672 Imaris 9.3 Oxford Instruments RRID:SCR_007370; https://imaris.oxinst.com/ ImageJ (Fiji) NIH https://imagej.net/Fiji/Downloads Prism 9 GraphPad RRID:SCR_002798; https://www.graphpad.com/ Excel Microsoft RRID:SCR_016137 Spectrum Mill Agilent https://proteomics.broadinstitute. org/millhome.htm

    Article Title: Visualizing and manipulating the production and accumulation of hyaluronan for functional assessment in chicken embryos
    Article Snippet: pCAG - GFP , Matsuda and Cepko 4 , pCAG-GFP was a gift from Connie Cepko (Addgene plasmid # 11150; http://n2t.net/addgene:11150 ; RRID:Addgene_11150).

    Article Title: PCSK9 deficiency alters brain lipid composition without affecting brain development and function
    Article Snippet: We transfected the cells with the PCSK9 plasmid or an empty pCAGEN vector and stained with an anti-PCSK9 antibody (Goat-a-PCSK9: AF3985 (anti mouse/rat PCSK9, 0.2 mg/mL), dilution 1:50) and used immunofluorescence to confirm specific PCSK9 expression. pCAG-GFP was purchased from Addgene #11150. pCX::myr-Venus plasmid was a gift from Anna-Katerina Hadjantonalis.

    Article Title: DCX knockout ferret reveals a neurogenic mechanism in cortical development.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains Ferrets: WT This paper N/A Ferrets: DCX knockout mutants This paper N/A Mice: ICR This paper N/A Recombinant DNA pCAG-GFP Addgene Cat#11150 pCAG-DCX-GFP This paper N/A Software and algorithms Spaceranger v 1.0.0 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/ software/downloads/latest R v.4.1.0 R Core Team https://www.R-project.org/ CellRanger v.6.1.2 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/installation Seurat v4.3.0 Stuart et al., 201953 https://satijalab.org/seurat/install.html scrubletR v0.1.0 https://github.com/Moonerss/scrubletR CytoTRACE v0.3.3 Gulati et al., 201934 https://github.com/seqyuan/CytoTRACE SAW-5.4.0 BGIResearch https://github.com/STOmics/SAW stereopy-0.8.0 BGIResearch https://github.com/BGIResearch/stereopy scanpy-1.9.3 the Scanpy development team https://github.com/scverse/scanpy ggplot2 v3.3.2 Wickham, 201654 https://ggplot2.tidyverse.org scran v1.10.2 Lun et al., 201655 https://bioconductor.statistik.tu- dortmund.de/packages/3.8/bioc/ html/scran.html ggtree https://github.com/YuLab- SMU/ggtree V3.0.4 clusterProfiler v4.4.4 Wu et al., 2021.56 http://www.bioconductor.org/packages/ release/bioc/html/clusterProfiler.html ggpubr GitHub - kassambara/ ggpubr: ’ggplot20 V0.5.0 tidyverse https://bioconductor.org/ packages/release/ bioc/html/enrichplot.html V1.14.2 GSEA v4.1.0 Subramanian et al., 200557 http://software.broadinstitute.org/ gsea/index.jsp Cytoscape v3.8.2 Shannon et al. 200358 https://cytoscape.org/ ImageJ (1.5.3a) NIH https://imagej.nih.gov/ij/ Adobe Photoshop CC2020 Adobe Systems http://www.adobe.com GraphPad Prism 8.0 GraphPad Software http://www.graphpad.com/scientific- software/prism/

    Article Title: Sensor systems for target ligands and uses thereof
    Article Snippet: Miscellaneous Plasmids—pCAG-GFP (Addgene plasmid 11150)39, pCAG-YFP (Addgene plasmid 11180)39, pCAG-DsRed (Addgene 11151)39. pRho-GFP-IRES-AP (referred to as Rho-GFP)40. pCAG-nlacZ (Cepko lab, Harvard Medical School), pCAGEN (Addgene plasmid 11160)39. pCALNL-DsRed (Addgene plasmid 13769)39. pCAFNF-DsRed (Addgene plasmid 13771)39. pCALNL-luc28. pRL-TK (Promega, 4E2241).

    Article Title: Polysaccharide-Polyplex Nanofilm Coatings Enhance Nanoneedle-Based Gene Delivery and Transfection Efficiency.
    Article Snippet: Anti-mouse CD44 was purchased from BD Biosciences. pCAG-GFP and pCAG-dsRFP were obtained from Addgene (MA, USA) and developed by Cepko C, et al.[103] Fluc-pcDNA3 was obtained from Addgene (MA, USA) and developed by Safran M, et al.[104] pABOL was obtained in-house and synthesized as previously described.

    Article Title: The mTOR pathway genes mTOR, Rheb, Depdc5, Pten , and Tsc1 have convergent and divergent impacts on cortical neuron development and function
    Article Snippet: pCAG-GFP , Addgene plasmid #11150; deposited by Dr. Connie Cepko.

    Article Title: Caveolin-3 prevents swelling-induced membrane damage via regulation of I Cl,swell activity.
    Article Snippet: Caveola membrane structures harbor mechanosensitive chloride channels (MCCs; including chloride channel 2, chloride channel 3, and SWELL1, also known as LRRC8A) that form a swelling-activated chloride current (ICl,swell) and play an important role in cell volume regulation and mechanoelectrical signal transduction.. However, the role of the muscle-specific caveolar scaffolding protein caveolin-3 (Cav3) in regulation of MCC expression, activity, and contribution to membrane integrity in response to mechanical stress remains unclear.. Here we showed that Cav3-transfected (Cav3-positive) HEK293 cells were significantly resistant to extreme (<20 milliosmole) hypotonic swelling compared with native (Cav3-negative) HEK293 cells; the percentage of cells with membrane damage decreased from 45% in Cav3-negative cells to 17% in Cav3-positive cells (p < 0.05).

    Microscopy:

    Article Title: In situ cell-type-specific cell-surface proteomic profiling in mice.
    Article Snippet: Nelson; Clark et al., 2020 N/A Mouse: MADM6-GT Contreras et al., 2021 N/A Mouse: MADM6-TG Contreras et al., 2021 N/A Oligonucleotides See Table S2 for a complete list of sequences Recombinant DNA See Table S2 for a complete list of gR and miR sequences integrated into plasmids pCAG-GFP Matsuda and Cepko, 2004 RRID:Addgene_11150 pCAG-tdTomato W. Joo, unpublished N/A pX333 Maddalo et al., 2014 RRID:Addgene_64073 pX333-CBh-Cas9-U6-2xsgRNA-LacZ Takeo et al., 2021 N/A pX333-CBh-Cas9-U6-2xsgRNA-Armh4 This paper N/A pCAG-EmGFP-miR Gift from M. Yuzaki N/A pCAG-EmGFP-LacZ-miR This paper N/A pCAG-EmGFP-Armh4-miR This paper N/A pCAG-2xHA-Armh4WT This paper N/A pCAG-V5-Armh4WT This paper N/A pCAG-Armh4WT-2xHA This paper N/A pCAG-2xHA-Armh4DICD This paper N/A pCAG-Armh4Endo6A-2xHA This paper N/A Software and algorithms ZEN Carl Zeiss RRID: SCR_013672 Imaris 9.3 Oxford Instruments RRID:SCR_007370; https://imaris.oxinst.com/ ImageJ (Fiji) NIH https://imagej.net/Fiji/Downloads Prism 9 GraphPad RRID:SCR_002798; https://www.graphpad.com/ Excel Microsoft RRID:SCR_016137 Spectrum Mill Agilent https://proteomics.broadinstitute. org/millhome.htm

    Article Title: Visualizing and manipulating the production and accumulation of hyaluronan for functional assessment in chicken embryos
    Article Snippet: pCAG - GFP , Matsuda and Cepko 4 , pCAG-GFP was a gift from Connie Cepko (Addgene plasmid # 11150; http://n2t.net/addgene:11150 ; RRID:Addgene_11150).

    Article Title: PCSK9 deficiency alters brain lipid composition without affecting brain development and function
    Article Snippet: We transfected the cells with the PCSK9 plasmid or an empty pCAGEN vector and stained with an anti-PCSK9 antibody (Goat-a-PCSK9: AF3985 (anti mouse/rat PCSK9, 0.2 mg/mL), dilution 1:50) and used immunofluorescence to confirm specific PCSK9 expression. pCAG-GFP was purchased from Addgene #11150. pCX::myr-Venus plasmid was a gift from Anna-Katerina Hadjantonalis.

    Article Title: DCX knockout ferret reveals a neurogenic mechanism in cortical development.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains Ferrets: WT This paper N/A Ferrets: DCX knockout mutants This paper N/A Mice: ICR This paper N/A Recombinant DNA pCAG-GFP Addgene Cat#11150 pCAG-DCX-GFP This paper N/A Software and algorithms Spaceranger v 1.0.0 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/ software/downloads/latest R v.4.1.0 R Core Team https://www.R-project.org/ CellRanger v.6.1.2 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/installation Seurat v4.3.0 Stuart et al., 201953 https://satijalab.org/seurat/install.html scrubletR v0.1.0 https://github.com/Moonerss/scrubletR CytoTRACE v0.3.3 Gulati et al., 201934 https://github.com/seqyuan/CytoTRACE SAW-5.4.0 BGIResearch https://github.com/STOmics/SAW stereopy-0.8.0 BGIResearch https://github.com/BGIResearch/stereopy scanpy-1.9.3 the Scanpy development team https://github.com/scverse/scanpy ggplot2 v3.3.2 Wickham, 201654 https://ggplot2.tidyverse.org scran v1.10.2 Lun et al., 201655 https://bioconductor.statistik.tu- dortmund.de/packages/3.8/bioc/ html/scran.html ggtree https://github.com/YuLab- SMU/ggtree V3.0.4 clusterProfiler v4.4.4 Wu et al., 2021.56 http://www.bioconductor.org/packages/ release/bioc/html/clusterProfiler.html ggpubr GitHub - kassambara/ ggpubr: ’ggplot20 V0.5.0 tidyverse https://bioconductor.org/ packages/release/ bioc/html/enrichplot.html V1.14.2 GSEA v4.1.0 Subramanian et al., 200557 http://software.broadinstitute.org/ gsea/index.jsp Cytoscape v3.8.2 Shannon et al. 200358 https://cytoscape.org/ ImageJ (1.5.3a) NIH https://imagej.nih.gov/ij/ Adobe Photoshop CC2020 Adobe Systems http://www.adobe.com GraphPad Prism 8.0 GraphPad Software http://www.graphpad.com/scientific- software/prism/

    Article Title: Sensor systems for target ligands and uses thereof
    Article Snippet: Miscellaneous Plasmids—pCAG-GFP (Addgene plasmid 11150)39, pCAG-YFP (Addgene plasmid 11180)39, pCAG-DsRed (Addgene 11151)39. pRho-GFP-IRES-AP (referred to as Rho-GFP)40. pCAG-nlacZ (Cepko lab, Harvard Medical School), pCAGEN (Addgene plasmid 11160)39. pCALNL-DsRed (Addgene plasmid 13769)39. pCAFNF-DsRed (Addgene plasmid 13771)39. pCALNL-luc28. pRL-TK (Promega, 4E2241).

    Article Title: Polysaccharide-Polyplex Nanofilm Coatings Enhance Nanoneedle-Based Gene Delivery and Transfection Efficiency.
    Article Snippet: Anti-mouse CD44 was purchased from BD Biosciences. pCAG-GFP and pCAG-dsRFP were obtained from Addgene (MA, USA) and developed by Cepko C, et al.[103] Fluc-pcDNA3 was obtained from Addgene (MA, USA) and developed by Safran M, et al.[104] pABOL was obtained in-house and synthesized as previously described.

    Article Title: The mTOR pathway genes mTOR, Rheb, Depdc5, Pten , and Tsc1 have convergent and divergent impacts on cortical neuron development and function
    Article Snippet: pCAG-GFP , Addgene plasmid #11150; deposited by Dr. Connie Cepko.

    Article Title: Caveolin-3 prevents swelling-induced membrane damage via regulation of I Cl,swell activity.
    Article Snippet: Caveola membrane structures harbor mechanosensitive chloride channels (MCCs; including chloride channel 2, chloride channel 3, and SWELL1, also known as LRRC8A) that form a swelling-activated chloride current (ICl,swell) and play an important role in cell volume regulation and mechanoelectrical signal transduction.. However, the role of the muscle-specific caveolar scaffolding protein caveolin-3 (Cav3) in regulation of MCC expression, activity, and contribution to membrane integrity in response to mechanical stress remains unclear.. Here we showed that Cav3-transfected (Cav3-positive) HEK293 cells were significantly resistant to extreme (<20 milliosmole) hypotonic swelling compared with native (Cav3-negative) HEK293 cells; the percentage of cells with membrane damage decreased from 45% in Cav3-negative cells to 17% in Cav3-positive cells (p < 0.05).

    Electroporation:

    Article Title: In situ cell-type-specific cell-surface proteomic profiling in mice.
    Article Snippet: Nelson; Clark et al., 2020 N/A Mouse: MADM6-GT Contreras et al., 2021 N/A Mouse: MADM6-TG Contreras et al., 2021 N/A Oligonucleotides See Table S2 for a complete list of sequences Recombinant DNA See Table S2 for a complete list of gR and miR sequences integrated into plasmids pCAG-GFP Matsuda and Cepko, 2004 RRID:Addgene_11150 pCAG-tdTomato W. Joo, unpublished N/A pX333 Maddalo et al., 2014 RRID:Addgene_64073 pX333-CBh-Cas9-U6-2xsgRNA-LacZ Takeo et al., 2021 N/A pX333-CBh-Cas9-U6-2xsgRNA-Armh4 This paper N/A pCAG-EmGFP-miR Gift from M. Yuzaki N/A pCAG-EmGFP-LacZ-miR This paper N/A pCAG-EmGFP-Armh4-miR This paper N/A pCAG-2xHA-Armh4WT This paper N/A pCAG-V5-Armh4WT This paper N/A pCAG-Armh4WT-2xHA This paper N/A pCAG-2xHA-Armh4DICD This paper N/A pCAG-Armh4Endo6A-2xHA This paper N/A Software and algorithms ZEN Carl Zeiss RRID: SCR_013672 Imaris 9.3 Oxford Instruments RRID:SCR_007370; https://imaris.oxinst.com/ ImageJ (Fiji) NIH https://imagej.net/Fiji/Downloads Prism 9 GraphPad RRID:SCR_002798; https://www.graphpad.com/ Excel Microsoft RRID:SCR_016137 Spectrum Mill Agilent https://proteomics.broadinstitute. org/millhome.htm

    Article Title: Visualizing and manipulating the production and accumulation of hyaluronan for functional assessment in chicken embryos
    Article Snippet: pCAG - GFP , Matsuda and Cepko 4 , pCAG-GFP was a gift from Connie Cepko (Addgene plasmid # 11150; http://n2t.net/addgene:11150 ; RRID:Addgene_11150).

    Article Title: PCSK9 deficiency alters brain lipid composition without affecting brain development and function
    Article Snippet: We transfected the cells with the PCSK9 plasmid or an empty pCAGEN vector and stained with an anti-PCSK9 antibody (Goat-a-PCSK9: AF3985 (anti mouse/rat PCSK9, 0.2 mg/mL), dilution 1:50) and used immunofluorescence to confirm specific PCSK9 expression. pCAG-GFP was purchased from Addgene #11150. pCX::myr-Venus plasmid was a gift from Anna-Katerina Hadjantonalis.

    Article Title: DCX knockout ferret reveals a neurogenic mechanism in cortical development.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains Ferrets: WT This paper N/A Ferrets: DCX knockout mutants This paper N/A Mice: ICR This paper N/A Recombinant DNA pCAG-GFP Addgene Cat#11150 pCAG-DCX-GFP This paper N/A Software and algorithms Spaceranger v 1.0.0 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/ software/downloads/latest R v.4.1.0 R Core Team https://www.R-project.org/ CellRanger v.6.1.2 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/installation Seurat v4.3.0 Stuart et al., 201953 https://satijalab.org/seurat/install.html scrubletR v0.1.0 https://github.com/Moonerss/scrubletR CytoTRACE v0.3.3 Gulati et al., 201934 https://github.com/seqyuan/CytoTRACE SAW-5.4.0 BGIResearch https://github.com/STOmics/SAW stereopy-0.8.0 BGIResearch https://github.com/BGIResearch/stereopy scanpy-1.9.3 the Scanpy development team https://github.com/scverse/scanpy ggplot2 v3.3.2 Wickham, 201654 https://ggplot2.tidyverse.org scran v1.10.2 Lun et al., 201655 https://bioconductor.statistik.tu- dortmund.de/packages/3.8/bioc/ html/scran.html ggtree https://github.com/YuLab- SMU/ggtree V3.0.4 clusterProfiler v4.4.4 Wu et al., 2021.56 http://www.bioconductor.org/packages/ release/bioc/html/clusterProfiler.html ggpubr GitHub - kassambara/ ggpubr: ’ggplot20 V0.5.0 tidyverse https://bioconductor.org/ packages/release/ bioc/html/enrichplot.html V1.14.2 GSEA v4.1.0 Subramanian et al., 200557 http://software.broadinstitute.org/ gsea/index.jsp Cytoscape v3.8.2 Shannon et al. 200358 https://cytoscape.org/ ImageJ (1.5.3a) NIH https://imagej.nih.gov/ij/ Adobe Photoshop CC2020 Adobe Systems http://www.adobe.com GraphPad Prism 8.0 GraphPad Software http://www.graphpad.com/scientific- software/prism/

    Article Title: Sensor systems for target ligands and uses thereof
    Article Snippet: Miscellaneous Plasmids—pCAG-GFP (Addgene plasmid 11150)39, pCAG-YFP (Addgene plasmid 11180)39, pCAG-DsRed (Addgene 11151)39. pRho-GFP-IRES-AP (referred to as Rho-GFP)40. pCAG-nlacZ (Cepko lab, Harvard Medical School), pCAGEN (Addgene plasmid 11160)39. pCALNL-DsRed (Addgene plasmid 13769)39. pCAFNF-DsRed (Addgene plasmid 13771)39. pCALNL-luc28. pRL-TK (Promega, 4E2241).

    Article Title: Polysaccharide-Polyplex Nanofilm Coatings Enhance Nanoneedle-Based Gene Delivery and Transfection Efficiency.
    Article Snippet: Anti-mouse CD44 was purchased from BD Biosciences. pCAG-GFP and pCAG-dsRFP were obtained from Addgene (MA, USA) and developed by Cepko C, et al.[103] Fluc-pcDNA3 was obtained from Addgene (MA, USA) and developed by Safran M, et al.[104] pABOL was obtained in-house and synthesized as previously described.

    Article Title: The mTOR pathway genes mTOR, Rheb, Depdc5, Pten , and Tsc1 have convergent and divergent impacts on cortical neuron development and function
    Article Snippet: pCAG-GFP , Addgene plasmid #11150; deposited by Dr. Connie Cepko.

    Article Title: Caveolin-3 prevents swelling-induced membrane damage via regulation of I Cl,swell activity.
    Article Snippet: Caveola membrane structures harbor mechanosensitive chloride channels (MCCs; including chloride channel 2, chloride channel 3, and SWELL1, also known as LRRC8A) that form a swelling-activated chloride current (ICl,swell) and play an important role in cell volume regulation and mechanoelectrical signal transduction.. However, the role of the muscle-specific caveolar scaffolding protein caveolin-3 (Cav3) in regulation of MCC expression, activity, and contribution to membrane integrity in response to mechanical stress remains unclear.. Here we showed that Cav3-transfected (Cav3-positive) HEK293 cells were significantly resistant to extreme (<20 milliosmole) hypotonic swelling compared with native (Cav3-negative) HEK293 cells; the percentage of cells with membrane damage decreased from 45% in Cav3-negative cells to 17% in Cav3-positive cells (p < 0.05).

    Staining:

    Article Title: In situ cell-type-specific cell-surface proteomic profiling in mice.
    Article Snippet: Nelson; Clark et al., 2020 N/A Mouse: MADM6-GT Contreras et al., 2021 N/A Mouse: MADM6-TG Contreras et al., 2021 N/A Oligonucleotides See Table S2 for a complete list of sequences Recombinant DNA See Table S2 for a complete list of gR and miR sequences integrated into plasmids pCAG-GFP Matsuda and Cepko, 2004 RRID:Addgene_11150 pCAG-tdTomato W. Joo, unpublished N/A pX333 Maddalo et al., 2014 RRID:Addgene_64073 pX333-CBh-Cas9-U6-2xsgRNA-LacZ Takeo et al., 2021 N/A pX333-CBh-Cas9-U6-2xsgRNA-Armh4 This paper N/A pCAG-EmGFP-miR Gift from M. Yuzaki N/A pCAG-EmGFP-LacZ-miR This paper N/A pCAG-EmGFP-Armh4-miR This paper N/A pCAG-2xHA-Armh4WT This paper N/A pCAG-V5-Armh4WT This paper N/A pCAG-Armh4WT-2xHA This paper N/A pCAG-2xHA-Armh4DICD This paper N/A pCAG-Armh4Endo6A-2xHA This paper N/A Software and algorithms ZEN Carl Zeiss RRID: SCR_013672 Imaris 9.3 Oxford Instruments RRID:SCR_007370; https://imaris.oxinst.com/ ImageJ (Fiji) NIH https://imagej.net/Fiji/Downloads Prism 9 GraphPad RRID:SCR_002798; https://www.graphpad.com/ Excel Microsoft RRID:SCR_016137 Spectrum Mill Agilent https://proteomics.broadinstitute. org/millhome.htm

    Article Title: Visualizing and manipulating the production and accumulation of hyaluronan for functional assessment in chicken embryos
    Article Snippet: pCAG - GFP , Matsuda and Cepko 4 , pCAG-GFP was a gift from Connie Cepko (Addgene plasmid # 11150; http://n2t.net/addgene:11150 ; RRID:Addgene_11150).

    Article Title: PCSK9 deficiency alters brain lipid composition without affecting brain development and function
    Article Snippet: We transfected the cells with the PCSK9 plasmid or an empty pCAGEN vector and stained with an anti-PCSK9 antibody (Goat-a-PCSK9: AF3985 (anti mouse/rat PCSK9, 0.2 mg/mL), dilution 1:50) and used immunofluorescence to confirm specific PCSK9 expression. pCAG-GFP was purchased from Addgene #11150. pCX::myr-Venus plasmid was a gift from Anna-Katerina Hadjantonalis.

    Article Title: DCX knockout ferret reveals a neurogenic mechanism in cortical development.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains Ferrets: WT This paper N/A Ferrets: DCX knockout mutants This paper N/A Mice: ICR This paper N/A Recombinant DNA pCAG-GFP Addgene Cat#11150 pCAG-DCX-GFP This paper N/A Software and algorithms Spaceranger v 1.0.0 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/ software/downloads/latest R v.4.1.0 R Core Team https://www.R-project.org/ CellRanger v.6.1.2 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/installation Seurat v4.3.0 Stuart et al., 201953 https://satijalab.org/seurat/install.html scrubletR v0.1.0 https://github.com/Moonerss/scrubletR CytoTRACE v0.3.3 Gulati et al., 201934 https://github.com/seqyuan/CytoTRACE SAW-5.4.0 BGIResearch https://github.com/STOmics/SAW stereopy-0.8.0 BGIResearch https://github.com/BGIResearch/stereopy scanpy-1.9.3 the Scanpy development team https://github.com/scverse/scanpy ggplot2 v3.3.2 Wickham, 201654 https://ggplot2.tidyverse.org scran v1.10.2 Lun et al., 201655 https://bioconductor.statistik.tu- dortmund.de/packages/3.8/bioc/ html/scran.html ggtree https://github.com/YuLab- SMU/ggtree V3.0.4 clusterProfiler v4.4.4 Wu et al., 2021.56 http://www.bioconductor.org/packages/ release/bioc/html/clusterProfiler.html ggpubr GitHub - kassambara/ ggpubr: ’ggplot20 V0.5.0 tidyverse https://bioconductor.org/ packages/release/ bioc/html/enrichplot.html V1.14.2 GSEA v4.1.0 Subramanian et al., 200557 http://software.broadinstitute.org/ gsea/index.jsp Cytoscape v3.8.2 Shannon et al. 200358 https://cytoscape.org/ ImageJ (1.5.3a) NIH https://imagej.nih.gov/ij/ Adobe Photoshop CC2020 Adobe Systems http://www.adobe.com GraphPad Prism 8.0 GraphPad Software http://www.graphpad.com/scientific- software/prism/

    Article Title: Sensor systems for target ligands and uses thereof
    Article Snippet: Miscellaneous Plasmids—pCAG-GFP (Addgene plasmid 11150)39, pCAG-YFP (Addgene plasmid 11180)39, pCAG-DsRed (Addgene 11151)39. pRho-GFP-IRES-AP (referred to as Rho-GFP)40. pCAG-nlacZ (Cepko lab, Harvard Medical School), pCAGEN (Addgene plasmid 11160)39. pCALNL-DsRed (Addgene plasmid 13769)39. pCAFNF-DsRed (Addgene plasmid 13771)39. pCALNL-luc28. pRL-TK (Promega, 4E2241).

    Article Title: Polysaccharide-Polyplex Nanofilm Coatings Enhance Nanoneedle-Based Gene Delivery and Transfection Efficiency.
    Article Snippet: Anti-mouse CD44 was purchased from BD Biosciences. pCAG-GFP and pCAG-dsRFP were obtained from Addgene (MA, USA) and developed by Cepko C, et al.[103] Fluc-pcDNA3 was obtained from Addgene (MA, USA) and developed by Safran M, et al.[104] pABOL was obtained in-house and synthesized as previously described.

    Article Title: The mTOR pathway genes mTOR, Rheb, Depdc5, Pten , and Tsc1 have convergent and divergent impacts on cortical neuron development and function
    Article Snippet: pCAG-GFP , Addgene plasmid #11150; deposited by Dr. Connie Cepko.

    Article Title: Caveolin-3 prevents swelling-induced membrane damage via regulation of I Cl,swell activity.
    Article Snippet: Caveola membrane structures harbor mechanosensitive chloride channels (MCCs; including chloride channel 2, chloride channel 3, and SWELL1, also known as LRRC8A) that form a swelling-activated chloride current (ICl,swell) and play an important role in cell volume regulation and mechanoelectrical signal transduction.. However, the role of the muscle-specific caveolar scaffolding protein caveolin-3 (Cav3) in regulation of MCC expression, activity, and contribution to membrane integrity in response to mechanical stress remains unclear.. Here we showed that Cav3-transfected (Cav3-positive) HEK293 cells were significantly resistant to extreme (<20 milliosmole) hypotonic swelling compared with native (Cav3-negative) HEK293 cells; the percentage of cells with membrane damage decreased from 45% in Cav3-negative cells to 17% in Cav3-positive cells (p < 0.05).

    Transfection:

    Article Title: In situ cell-type-specific cell-surface proteomic profiling in mice.
    Article Snippet: Nelson; Clark et al., 2020 N/A Mouse: MADM6-GT Contreras et al., 2021 N/A Mouse: MADM6-TG Contreras et al., 2021 N/A Oligonucleotides See Table S2 for a complete list of sequences Recombinant DNA See Table S2 for a complete list of gR and miR sequences integrated into plasmids pCAG-GFP Matsuda and Cepko, 2004 RRID:Addgene_11150 pCAG-tdTomato W. Joo, unpublished N/A pX333 Maddalo et al., 2014 RRID:Addgene_64073 pX333-CBh-Cas9-U6-2xsgRNA-LacZ Takeo et al., 2021 N/A pX333-CBh-Cas9-U6-2xsgRNA-Armh4 This paper N/A pCAG-EmGFP-miR Gift from M. Yuzaki N/A pCAG-EmGFP-LacZ-miR This paper N/A pCAG-EmGFP-Armh4-miR This paper N/A pCAG-2xHA-Armh4WT This paper N/A pCAG-V5-Armh4WT This paper N/A pCAG-Armh4WT-2xHA This paper N/A pCAG-2xHA-Armh4DICD This paper N/A pCAG-Armh4Endo6A-2xHA This paper N/A Software and algorithms ZEN Carl Zeiss RRID: SCR_013672 Imaris 9.3 Oxford Instruments RRID:SCR_007370; https://imaris.oxinst.com/ ImageJ (Fiji) NIH https://imagej.net/Fiji/Downloads Prism 9 GraphPad RRID:SCR_002798; https://www.graphpad.com/ Excel Microsoft RRID:SCR_016137 Spectrum Mill Agilent https://proteomics.broadinstitute. org/millhome.htm

    Article Title: Visualizing and manipulating the production and accumulation of hyaluronan for functional assessment in chicken embryos
    Article Snippet: pCAG - GFP , Matsuda and Cepko 4 , pCAG-GFP was a gift from Connie Cepko (Addgene plasmid # 11150; http://n2t.net/addgene:11150 ; RRID:Addgene_11150).

    Article Title: PCSK9 deficiency alters brain lipid composition without affecting brain development and function
    Article Snippet: We transfected the cells with the PCSK9 plasmid or an empty pCAGEN vector and stained with an anti-PCSK9 antibody (Goat-a-PCSK9: AF3985 (anti mouse/rat PCSK9, 0.2 mg/mL), dilution 1:50) and used immunofluorescence to confirm specific PCSK9 expression. pCAG-GFP was purchased from Addgene #11150. pCX::myr-Venus plasmid was a gift from Anna-Katerina Hadjantonalis.

    Article Title: DCX knockout ferret reveals a neurogenic mechanism in cortical development.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains Ferrets: WT This paper N/A Ferrets: DCX knockout mutants This paper N/A Mice: ICR This paper N/A Recombinant DNA pCAG-GFP Addgene Cat#11150 pCAG-DCX-GFP This paper N/A Software and algorithms Spaceranger v 1.0.0 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/ software/downloads/latest R v.4.1.0 R Core Team https://www.R-project.org/ CellRanger v.6.1.2 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/installation Seurat v4.3.0 Stuart et al., 201953 https://satijalab.org/seurat/install.html scrubletR v0.1.0 https://github.com/Moonerss/scrubletR CytoTRACE v0.3.3 Gulati et al., 201934 https://github.com/seqyuan/CytoTRACE SAW-5.4.0 BGIResearch https://github.com/STOmics/SAW stereopy-0.8.0 BGIResearch https://github.com/BGIResearch/stereopy scanpy-1.9.3 the Scanpy development team https://github.com/scverse/scanpy ggplot2 v3.3.2 Wickham, 201654 https://ggplot2.tidyverse.org scran v1.10.2 Lun et al., 201655 https://bioconductor.statistik.tu- dortmund.de/packages/3.8/bioc/ html/scran.html ggtree https://github.com/YuLab- SMU/ggtree V3.0.4 clusterProfiler v4.4.4 Wu et al., 2021.56 http://www.bioconductor.org/packages/ release/bioc/html/clusterProfiler.html ggpubr GitHub - kassambara/ ggpubr: ’ggplot20 V0.5.0 tidyverse https://bioconductor.org/ packages/release/ bioc/html/enrichplot.html V1.14.2 GSEA v4.1.0 Subramanian et al., 200557 http://software.broadinstitute.org/ gsea/index.jsp Cytoscape v3.8.2 Shannon et al. 200358 https://cytoscape.org/ ImageJ (1.5.3a) NIH https://imagej.nih.gov/ij/ Adobe Photoshop CC2020 Adobe Systems http://www.adobe.com GraphPad Prism 8.0 GraphPad Software http://www.graphpad.com/scientific- software/prism/

    Article Title: Sensor systems for target ligands and uses thereof
    Article Snippet: Miscellaneous Plasmids—pCAG-GFP (Addgene plasmid 11150)39, pCAG-YFP (Addgene plasmid 11180)39, pCAG-DsRed (Addgene 11151)39. pRho-GFP-IRES-AP (referred to as Rho-GFP)40. pCAG-nlacZ (Cepko lab, Harvard Medical School), pCAGEN (Addgene plasmid 11160)39. pCALNL-DsRed (Addgene plasmid 13769)39. pCAFNF-DsRed (Addgene plasmid 13771)39. pCALNL-luc28. pRL-TK (Promega, 4E2241).

    Article Title: Polysaccharide-Polyplex Nanofilm Coatings Enhance Nanoneedle-Based Gene Delivery and Transfection Efficiency.
    Article Snippet: Anti-mouse CD44 was purchased from BD Biosciences. pCAG-GFP and pCAG-dsRFP were obtained from Addgene (MA, USA) and developed by Cepko C, et al.[103] Fluc-pcDNA3 was obtained from Addgene (MA, USA) and developed by Safran M, et al.[104] pABOL was obtained in-house and synthesized as previously described.

    Article Title: The mTOR pathway genes mTOR, Rheb, Depdc5, Pten , and Tsc1 have convergent and divergent impacts on cortical neuron development and function
    Article Snippet: pCAG-GFP , Addgene plasmid #11150; deposited by Dr. Connie Cepko.

    Article Title: Caveolin-3 prevents swelling-induced membrane damage via regulation of I Cl,swell activity.
    Article Snippet: Caveola membrane structures harbor mechanosensitive chloride channels (MCCs; including chloride channel 2, chloride channel 3, and SWELL1, also known as LRRC8A) that form a swelling-activated chloride current (ICl,swell) and play an important role in cell volume regulation and mechanoelectrical signal transduction.. However, the role of the muscle-specific caveolar scaffolding protein caveolin-3 (Cav3) in regulation of MCC expression, activity, and contribution to membrane integrity in response to mechanical stress remains unclear.. Here we showed that Cav3-transfected (Cav3-positive) HEK293 cells were significantly resistant to extreme (<20 milliosmole) hypotonic swelling compared with native (Cav3-negative) HEK293 cells; the percentage of cells with membrane damage decreased from 45% in Cav3-negative cells to 17% in Cav3-positive cells (p < 0.05).

    Immunofluorescence:

    Article Title: In situ cell-type-specific cell-surface proteomic profiling in mice.
    Article Snippet: Nelson; Clark et al., 2020 N/A Mouse: MADM6-GT Contreras et al., 2021 N/A Mouse: MADM6-TG Contreras et al., 2021 N/A Oligonucleotides See Table S2 for a complete list of sequences Recombinant DNA See Table S2 for a complete list of gR and miR sequences integrated into plasmids pCAG-GFP Matsuda and Cepko, 2004 RRID:Addgene_11150 pCAG-tdTomato W. Joo, unpublished N/A pX333 Maddalo et al., 2014 RRID:Addgene_64073 pX333-CBh-Cas9-U6-2xsgRNA-LacZ Takeo et al., 2021 N/A pX333-CBh-Cas9-U6-2xsgRNA-Armh4 This paper N/A pCAG-EmGFP-miR Gift from M. Yuzaki N/A pCAG-EmGFP-LacZ-miR This paper N/A pCAG-EmGFP-Armh4-miR This paper N/A pCAG-2xHA-Armh4WT This paper N/A pCAG-V5-Armh4WT This paper N/A pCAG-Armh4WT-2xHA This paper N/A pCAG-2xHA-Armh4DICD This paper N/A pCAG-Armh4Endo6A-2xHA This paper N/A Software and algorithms ZEN Carl Zeiss RRID: SCR_013672 Imaris 9.3 Oxford Instruments RRID:SCR_007370; https://imaris.oxinst.com/ ImageJ (Fiji) NIH https://imagej.net/Fiji/Downloads Prism 9 GraphPad RRID:SCR_002798; https://www.graphpad.com/ Excel Microsoft RRID:SCR_016137 Spectrum Mill Agilent https://proteomics.broadinstitute. org/millhome.htm

    Article Title: Visualizing and manipulating the production and accumulation of hyaluronan for functional assessment in chicken embryos
    Article Snippet: pCAG - GFP , Matsuda and Cepko 4 , pCAG-GFP was a gift from Connie Cepko (Addgene plasmid # 11150; http://n2t.net/addgene:11150 ; RRID:Addgene_11150).

    Article Title: PCSK9 deficiency alters brain lipid composition without affecting brain development and function
    Article Snippet: We transfected the cells with the PCSK9 plasmid or an empty pCAGEN vector and stained with an anti-PCSK9 antibody (Goat-a-PCSK9: AF3985 (anti mouse/rat PCSK9, 0.2 mg/mL), dilution 1:50) and used immunofluorescence to confirm specific PCSK9 expression. pCAG-GFP was purchased from Addgene #11150. pCX::myr-Venus plasmid was a gift from Anna-Katerina Hadjantonalis.

    Article Title: DCX knockout ferret reveals a neurogenic mechanism in cortical development.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains Ferrets: WT This paper N/A Ferrets: DCX knockout mutants This paper N/A Mice: ICR This paper N/A Recombinant DNA pCAG-GFP Addgene Cat#11150 pCAG-DCX-GFP This paper N/A Software and algorithms Spaceranger v 1.0.0 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/ software/downloads/latest R v.4.1.0 R Core Team https://www.R-project.org/ CellRanger v.6.1.2 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/installation Seurat v4.3.0 Stuart et al., 201953 https://satijalab.org/seurat/install.html scrubletR v0.1.0 https://github.com/Moonerss/scrubletR CytoTRACE v0.3.3 Gulati et al., 201934 https://github.com/seqyuan/CytoTRACE SAW-5.4.0 BGIResearch https://github.com/STOmics/SAW stereopy-0.8.0 BGIResearch https://github.com/BGIResearch/stereopy scanpy-1.9.3 the Scanpy development team https://github.com/scverse/scanpy ggplot2 v3.3.2 Wickham, 201654 https://ggplot2.tidyverse.org scran v1.10.2 Lun et al., 201655 https://bioconductor.statistik.tu- dortmund.de/packages/3.8/bioc/ html/scran.html ggtree https://github.com/YuLab- SMU/ggtree V3.0.4 clusterProfiler v4.4.4 Wu et al., 2021.56 http://www.bioconductor.org/packages/ release/bioc/html/clusterProfiler.html ggpubr GitHub - kassambara/ ggpubr: ’ggplot20 V0.5.0 tidyverse https://bioconductor.org/ packages/release/ bioc/html/enrichplot.html V1.14.2 GSEA v4.1.0 Subramanian et al., 200557 http://software.broadinstitute.org/ gsea/index.jsp Cytoscape v3.8.2 Shannon et al. 200358 https://cytoscape.org/ ImageJ (1.5.3a) NIH https://imagej.nih.gov/ij/ Adobe Photoshop CC2020 Adobe Systems http://www.adobe.com GraphPad Prism 8.0 GraphPad Software http://www.graphpad.com/scientific- software/prism/

    Article Title: Sensor systems for target ligands and uses thereof
    Article Snippet: Miscellaneous Plasmids—pCAG-GFP (Addgene plasmid 11150)39, pCAG-YFP (Addgene plasmid 11180)39, pCAG-DsRed (Addgene 11151)39. pRho-GFP-IRES-AP (referred to as Rho-GFP)40. pCAG-nlacZ (Cepko lab, Harvard Medical School), pCAGEN (Addgene plasmid 11160)39. pCALNL-DsRed (Addgene plasmid 13769)39. pCAFNF-DsRed (Addgene plasmid 13771)39. pCALNL-luc28. pRL-TK (Promega, 4E2241).

    Article Title: Polysaccharide-Polyplex Nanofilm Coatings Enhance Nanoneedle-Based Gene Delivery and Transfection Efficiency.
    Article Snippet: Anti-mouse CD44 was purchased from BD Biosciences. pCAG-GFP and pCAG-dsRFP were obtained from Addgene (MA, USA) and developed by Cepko C, et al.[103] Fluc-pcDNA3 was obtained from Addgene (MA, USA) and developed by Safran M, et al.[104] pABOL was obtained in-house and synthesized as previously described.

    Article Title: The mTOR pathway genes mTOR, Rheb, Depdc5, Pten , and Tsc1 have convergent and divergent impacts on cortical neuron development and function
    Article Snippet: pCAG-GFP , Addgene plasmid #11150; deposited by Dr. Connie Cepko.

    Article Title: Caveolin-3 prevents swelling-induced membrane damage via regulation of I Cl,swell activity.
    Article Snippet: Caveola membrane structures harbor mechanosensitive chloride channels (MCCs; including chloride channel 2, chloride channel 3, and SWELL1, also known as LRRC8A) that form a swelling-activated chloride current (ICl,swell) and play an important role in cell volume regulation and mechanoelectrical signal transduction.. However, the role of the muscle-specific caveolar scaffolding protein caveolin-3 (Cav3) in regulation of MCC expression, activity, and contribution to membrane integrity in response to mechanical stress remains unclear.. Here we showed that Cav3-transfected (Cav3-positive) HEK293 cells were significantly resistant to extreme (<20 milliosmole) hypotonic swelling compared with native (Cav3-negative) HEK293 cells; the percentage of cells with membrane damage decreased from 45% in Cav3-negative cells to 17% in Cav3-positive cells (p < 0.05).

    Expressing:

    Article Title: In situ cell-type-specific cell-surface proteomic profiling in mice.
    Article Snippet: Nelson; Clark et al., 2020 N/A Mouse: MADM6-GT Contreras et al., 2021 N/A Mouse: MADM6-TG Contreras et al., 2021 N/A Oligonucleotides See Table S2 for a complete list of sequences Recombinant DNA See Table S2 for a complete list of gR and miR sequences integrated into plasmids pCAG-GFP Matsuda and Cepko, 2004 RRID:Addgene_11150 pCAG-tdTomato W. Joo, unpublished N/A pX333 Maddalo et al., 2014 RRID:Addgene_64073 pX333-CBh-Cas9-U6-2xsgRNA-LacZ Takeo et al., 2021 N/A pX333-CBh-Cas9-U6-2xsgRNA-Armh4 This paper N/A pCAG-EmGFP-miR Gift from M. Yuzaki N/A pCAG-EmGFP-LacZ-miR This paper N/A pCAG-EmGFP-Armh4-miR This paper N/A pCAG-2xHA-Armh4WT This paper N/A pCAG-V5-Armh4WT This paper N/A pCAG-Armh4WT-2xHA This paper N/A pCAG-2xHA-Armh4DICD This paper N/A pCAG-Armh4Endo6A-2xHA This paper N/A Software and algorithms ZEN Carl Zeiss RRID: SCR_013672 Imaris 9.3 Oxford Instruments RRID:SCR_007370; https://imaris.oxinst.com/ ImageJ (Fiji) NIH https://imagej.net/Fiji/Downloads Prism 9 GraphPad RRID:SCR_002798; https://www.graphpad.com/ Excel Microsoft RRID:SCR_016137 Spectrum Mill Agilent https://proteomics.broadinstitute. org/millhome.htm

    Article Title: Visualizing and manipulating the production and accumulation of hyaluronan for functional assessment in chicken embryos
    Article Snippet: pCAG - GFP , Matsuda and Cepko 4 , pCAG-GFP was a gift from Connie Cepko (Addgene plasmid # 11150; http://n2t.net/addgene:11150 ; RRID:Addgene_11150).

    Article Title: PCSK9 deficiency alters brain lipid composition without affecting brain development and function
    Article Snippet: We transfected the cells with the PCSK9 plasmid or an empty pCAGEN vector and stained with an anti-PCSK9 antibody (Goat-a-PCSK9: AF3985 (anti mouse/rat PCSK9, 0.2 mg/mL), dilution 1:50) and used immunofluorescence to confirm specific PCSK9 expression. pCAG-GFP was purchased from Addgene #11150. pCX::myr-Venus plasmid was a gift from Anna-Katerina Hadjantonalis.

    Article Title: DCX knockout ferret reveals a neurogenic mechanism in cortical development.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains Ferrets: WT This paper N/A Ferrets: DCX knockout mutants This paper N/A Mice: ICR This paper N/A Recombinant DNA pCAG-GFP Addgene Cat#11150 pCAG-DCX-GFP This paper N/A Software and algorithms Spaceranger v 1.0.0 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/ software/downloads/latest R v.4.1.0 R Core Team https://www.R-project.org/ CellRanger v.6.1.2 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/installation Seurat v4.3.0 Stuart et al., 201953 https://satijalab.org/seurat/install.html scrubletR v0.1.0 https://github.com/Moonerss/scrubletR CytoTRACE v0.3.3 Gulati et al., 201934 https://github.com/seqyuan/CytoTRACE SAW-5.4.0 BGIResearch https://github.com/STOmics/SAW stereopy-0.8.0 BGIResearch https://github.com/BGIResearch/stereopy scanpy-1.9.3 the Scanpy development team https://github.com/scverse/scanpy ggplot2 v3.3.2 Wickham, 201654 https://ggplot2.tidyverse.org scran v1.10.2 Lun et al., 201655 https://bioconductor.statistik.tu- dortmund.de/packages/3.8/bioc/ html/scran.html ggtree https://github.com/YuLab- SMU/ggtree V3.0.4 clusterProfiler v4.4.4 Wu et al., 2021.56 http://www.bioconductor.org/packages/ release/bioc/html/clusterProfiler.html ggpubr GitHub - kassambara/ ggpubr: ’ggplot20 V0.5.0 tidyverse https://bioconductor.org/ packages/release/ bioc/html/enrichplot.html V1.14.2 GSEA v4.1.0 Subramanian et al., 200557 http://software.broadinstitute.org/ gsea/index.jsp Cytoscape v3.8.2 Shannon et al. 200358 https://cytoscape.org/ ImageJ (1.5.3a) NIH https://imagej.nih.gov/ij/ Adobe Photoshop CC2020 Adobe Systems http://www.adobe.com GraphPad Prism 8.0 GraphPad Software http://www.graphpad.com/scientific- software/prism/

    Article Title: Sensor systems for target ligands and uses thereof
    Article Snippet: Miscellaneous Plasmids—pCAG-GFP (Addgene plasmid 11150)39, pCAG-YFP (Addgene plasmid 11180)39, pCAG-DsRed (Addgene 11151)39. pRho-GFP-IRES-AP (referred to as Rho-GFP)40. pCAG-nlacZ (Cepko lab, Harvard Medical School), pCAGEN (Addgene plasmid 11160)39. pCALNL-DsRed (Addgene plasmid 13769)39. pCAFNF-DsRed (Addgene plasmid 13771)39. pCALNL-luc28. pRL-TK (Promega, 4E2241).

    Article Title: Polysaccharide-Polyplex Nanofilm Coatings Enhance Nanoneedle-Based Gene Delivery and Transfection Efficiency.
    Article Snippet: Anti-mouse CD44 was purchased from BD Biosciences. pCAG-GFP and pCAG-dsRFP were obtained from Addgene (MA, USA) and developed by Cepko C, et al.[103] Fluc-pcDNA3 was obtained from Addgene (MA, USA) and developed by Safran M, et al.[104] pABOL was obtained in-house and synthesized as previously described.

    Article Title: The mTOR pathway genes mTOR, Rheb, Depdc5, Pten , and Tsc1 have convergent and divergent impacts on cortical neuron development and function
    Article Snippet: pCAG-GFP , Addgene plasmid #11150; deposited by Dr. Connie Cepko.

    Article Title: Caveolin-3 prevents swelling-induced membrane damage via regulation of I Cl,swell activity.
    Article Snippet: Caveola membrane structures harbor mechanosensitive chloride channels (MCCs; including chloride channel 2, chloride channel 3, and SWELL1, also known as LRRC8A) that form a swelling-activated chloride current (ICl,swell) and play an important role in cell volume regulation and mechanoelectrical signal transduction.. However, the role of the muscle-specific caveolar scaffolding protein caveolin-3 (Cav3) in regulation of MCC expression, activity, and contribution to membrane integrity in response to mechanical stress remains unclear.. Here we showed that Cav3-transfected (Cav3-positive) HEK293 cells were significantly resistant to extreme (<20 milliosmole) hypotonic swelling compared with native (Cav3-negative) HEK293 cells; the percentage of cells with membrane damage decreased from 45% in Cav3-negative cells to 17% in Cav3-positive cells (p < 0.05).

    Enzyme-linked Immunosorbent Assay:

    Article Title: In situ cell-type-specific cell-surface proteomic profiling in mice.
    Article Snippet: Nelson; Clark et al., 2020 N/A Mouse: MADM6-GT Contreras et al., 2021 N/A Mouse: MADM6-TG Contreras et al., 2021 N/A Oligonucleotides See Table S2 for a complete list of sequences Recombinant DNA See Table S2 for a complete list of gR and miR sequences integrated into plasmids pCAG-GFP Matsuda and Cepko, 2004 RRID:Addgene_11150 pCAG-tdTomato W. Joo, unpublished N/A pX333 Maddalo et al., 2014 RRID:Addgene_64073 pX333-CBh-Cas9-U6-2xsgRNA-LacZ Takeo et al., 2021 N/A pX333-CBh-Cas9-U6-2xsgRNA-Armh4 This paper N/A pCAG-EmGFP-miR Gift from M. Yuzaki N/A pCAG-EmGFP-LacZ-miR This paper N/A pCAG-EmGFP-Armh4-miR This paper N/A pCAG-2xHA-Armh4WT This paper N/A pCAG-V5-Armh4WT This paper N/A pCAG-Armh4WT-2xHA This paper N/A pCAG-2xHA-Armh4DICD This paper N/A pCAG-Armh4Endo6A-2xHA This paper N/A Software and algorithms ZEN Carl Zeiss RRID: SCR_013672 Imaris 9.3 Oxford Instruments RRID:SCR_007370; https://imaris.oxinst.com/ ImageJ (Fiji) NIH https://imagej.net/Fiji/Downloads Prism 9 GraphPad RRID:SCR_002798; https://www.graphpad.com/ Excel Microsoft RRID:SCR_016137 Spectrum Mill Agilent https://proteomics.broadinstitute. org/millhome.htm

    Article Title: Visualizing and manipulating the production and accumulation of hyaluronan for functional assessment in chicken embryos
    Article Snippet: pCAG - GFP , Matsuda and Cepko 4 , pCAG-GFP was a gift from Connie Cepko (Addgene plasmid # 11150; http://n2t.net/addgene:11150 ; RRID:Addgene_11150).

    Article Title: PCSK9 deficiency alters brain lipid composition without affecting brain development and function
    Article Snippet: We transfected the cells with the PCSK9 plasmid or an empty pCAGEN vector and stained with an anti-PCSK9 antibody (Goat-a-PCSK9: AF3985 (anti mouse/rat PCSK9, 0.2 mg/mL), dilution 1:50) and used immunofluorescence to confirm specific PCSK9 expression. pCAG-GFP was purchased from Addgene #11150. pCX::myr-Venus plasmid was a gift from Anna-Katerina Hadjantonalis.

    Article Title: DCX knockout ferret reveals a neurogenic mechanism in cortical development.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains Ferrets: WT This paper N/A Ferrets: DCX knockout mutants This paper N/A Mice: ICR This paper N/A Recombinant DNA pCAG-GFP Addgene Cat#11150 pCAG-DCX-GFP This paper N/A Software and algorithms Spaceranger v 1.0.0 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/ software/downloads/latest R v.4.1.0 R Core Team https://www.R-project.org/ CellRanger v.6.1.2 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/installation Seurat v4.3.0 Stuart et al., 201953 https://satijalab.org/seurat/install.html scrubletR v0.1.0 https://github.com/Moonerss/scrubletR CytoTRACE v0.3.3 Gulati et al., 201934 https://github.com/seqyuan/CytoTRACE SAW-5.4.0 BGIResearch https://github.com/STOmics/SAW stereopy-0.8.0 BGIResearch https://github.com/BGIResearch/stereopy scanpy-1.9.3 the Scanpy development team https://github.com/scverse/scanpy ggplot2 v3.3.2 Wickham, 201654 https://ggplot2.tidyverse.org scran v1.10.2 Lun et al., 201655 https://bioconductor.statistik.tu- dortmund.de/packages/3.8/bioc/ html/scran.html ggtree https://github.com/YuLab- SMU/ggtree V3.0.4 clusterProfiler v4.4.4 Wu et al., 2021.56 http://www.bioconductor.org/packages/ release/bioc/html/clusterProfiler.html ggpubr GitHub - kassambara/ ggpubr: ’ggplot20 V0.5.0 tidyverse https://bioconductor.org/ packages/release/ bioc/html/enrichplot.html V1.14.2 GSEA v4.1.0 Subramanian et al., 200557 http://software.broadinstitute.org/ gsea/index.jsp Cytoscape v3.8.2 Shannon et al. 200358 https://cytoscape.org/ ImageJ (1.5.3a) NIH https://imagej.nih.gov/ij/ Adobe Photoshop CC2020 Adobe Systems http://www.adobe.com GraphPad Prism 8.0 GraphPad Software http://www.graphpad.com/scientific- software/prism/

    Article Title: Sensor systems for target ligands and uses thereof
    Article Snippet: Miscellaneous Plasmids—pCAG-GFP (Addgene plasmid 11150)39, pCAG-YFP (Addgene plasmid 11180)39, pCAG-DsRed (Addgene 11151)39. pRho-GFP-IRES-AP (referred to as Rho-GFP)40. pCAG-nlacZ (Cepko lab, Harvard Medical School), pCAGEN (Addgene plasmid 11160)39. pCALNL-DsRed (Addgene plasmid 13769)39. pCAFNF-DsRed (Addgene plasmid 13771)39. pCALNL-luc28. pRL-TK (Promega, 4E2241).

    Article Title: Polysaccharide-Polyplex Nanofilm Coatings Enhance Nanoneedle-Based Gene Delivery and Transfection Efficiency.
    Article Snippet: Anti-mouse CD44 was purchased from BD Biosciences. pCAG-GFP and pCAG-dsRFP were obtained from Addgene (MA, USA) and developed by Cepko C, et al.[103] Fluc-pcDNA3 was obtained from Addgene (MA, USA) and developed by Safran M, et al.[104] pABOL was obtained in-house and synthesized as previously described.

    Article Title: The mTOR pathway genes mTOR, Rheb, Depdc5, Pten , and Tsc1 have convergent and divergent impacts on cortical neuron development and function
    Article Snippet: pCAG-GFP , Addgene plasmid #11150; deposited by Dr. Connie Cepko.

    Article Title: Caveolin-3 prevents swelling-induced membrane damage via regulation of I Cl,swell activity.
    Article Snippet: Caveola membrane structures harbor mechanosensitive chloride channels (MCCs; including chloride channel 2, chloride channel 3, and SWELL1, also known as LRRC8A) that form a swelling-activated chloride current (ICl,swell) and play an important role in cell volume regulation and mechanoelectrical signal transduction.. However, the role of the muscle-specific caveolar scaffolding protein caveolin-3 (Cav3) in regulation of MCC expression, activity, and contribution to membrane integrity in response to mechanical stress remains unclear.. Here we showed that Cav3-transfected (Cav3-positive) HEK293 cells were significantly resistant to extreme (<20 milliosmole) hypotonic swelling compared with native (Cav3-negative) HEK293 cells; the percentage of cells with membrane damage decreased from 45% in Cav3-negative cells to 17% in Cav3-positive cells (p < 0.05).

    Western Blot:

    Article Title: In situ cell-type-specific cell-surface proteomic profiling in mice.
    Article Snippet: Nelson; Clark et al., 2020 N/A Mouse: MADM6-GT Contreras et al., 2021 N/A Mouse: MADM6-TG Contreras et al., 2021 N/A Oligonucleotides See Table S2 for a complete list of sequences Recombinant DNA See Table S2 for a complete list of gR and miR sequences integrated into plasmids pCAG-GFP Matsuda and Cepko, 2004 RRID:Addgene_11150 pCAG-tdTomato W. Joo, unpublished N/A pX333 Maddalo et al., 2014 RRID:Addgene_64073 pX333-CBh-Cas9-U6-2xsgRNA-LacZ Takeo et al., 2021 N/A pX333-CBh-Cas9-U6-2xsgRNA-Armh4 This paper N/A pCAG-EmGFP-miR Gift from M. Yuzaki N/A pCAG-EmGFP-LacZ-miR This paper N/A pCAG-EmGFP-Armh4-miR This paper N/A pCAG-2xHA-Armh4WT This paper N/A pCAG-V5-Armh4WT This paper N/A pCAG-Armh4WT-2xHA This paper N/A pCAG-2xHA-Armh4DICD This paper N/A pCAG-Armh4Endo6A-2xHA This paper N/A Software and algorithms ZEN Carl Zeiss RRID: SCR_013672 Imaris 9.3 Oxford Instruments RRID:SCR_007370; https://imaris.oxinst.com/ ImageJ (Fiji) NIH https://imagej.net/Fiji/Downloads Prism 9 GraphPad RRID:SCR_002798; https://www.graphpad.com/ Excel Microsoft RRID:SCR_016137 Spectrum Mill Agilent https://proteomics.broadinstitute. org/millhome.htm

    Article Title: Visualizing and manipulating the production and accumulation of hyaluronan for functional assessment in chicken embryos
    Article Snippet: pCAG - GFP , Matsuda and Cepko 4 , pCAG-GFP was a gift from Connie Cepko (Addgene plasmid # 11150; http://n2t.net/addgene:11150 ; RRID:Addgene_11150).

    Article Title: PCSK9 deficiency alters brain lipid composition without affecting brain development and function
    Article Snippet: We transfected the cells with the PCSK9 plasmid or an empty pCAGEN vector and stained with an anti-PCSK9 antibody (Goat-a-PCSK9: AF3985 (anti mouse/rat PCSK9, 0.2 mg/mL), dilution 1:50) and used immunofluorescence to confirm specific PCSK9 expression. pCAG-GFP was purchased from Addgene #11150. pCX::myr-Venus plasmid was a gift from Anna-Katerina Hadjantonalis.

    Article Title: DCX knockout ferret reveals a neurogenic mechanism in cortical development.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains Ferrets: WT This paper N/A Ferrets: DCX knockout mutants This paper N/A Mice: ICR This paper N/A Recombinant DNA pCAG-GFP Addgene Cat#11150 pCAG-DCX-GFP This paper N/A Software and algorithms Spaceranger v 1.0.0 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/ software/downloads/latest R v.4.1.0 R Core Team https://www.R-project.org/ CellRanger v.6.1.2 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/installation Seurat v4.3.0 Stuart et al., 201953 https://satijalab.org/seurat/install.html scrubletR v0.1.0 https://github.com/Moonerss/scrubletR CytoTRACE v0.3.3 Gulati et al., 201934 https://github.com/seqyuan/CytoTRACE SAW-5.4.0 BGIResearch https://github.com/STOmics/SAW stereopy-0.8.0 BGIResearch https://github.com/BGIResearch/stereopy scanpy-1.9.3 the Scanpy development team https://github.com/scverse/scanpy ggplot2 v3.3.2 Wickham, 201654 https://ggplot2.tidyverse.org scran v1.10.2 Lun et al., 201655 https://bioconductor.statistik.tu- dortmund.de/packages/3.8/bioc/ html/scran.html ggtree https://github.com/YuLab- SMU/ggtree V3.0.4 clusterProfiler v4.4.4 Wu et al., 2021.56 http://www.bioconductor.org/packages/ release/bioc/html/clusterProfiler.html ggpubr GitHub - kassambara/ ggpubr: ’ggplot20 V0.5.0 tidyverse https://bioconductor.org/ packages/release/ bioc/html/enrichplot.html V1.14.2 GSEA v4.1.0 Subramanian et al., 200557 http://software.broadinstitute.org/ gsea/index.jsp Cytoscape v3.8.2 Shannon et al. 200358 https://cytoscape.org/ ImageJ (1.5.3a) NIH https://imagej.nih.gov/ij/ Adobe Photoshop CC2020 Adobe Systems http://www.adobe.com GraphPad Prism 8.0 GraphPad Software http://www.graphpad.com/scientific- software/prism/

    Article Title: Sensor systems for target ligands and uses thereof
    Article Snippet: Miscellaneous Plasmids—pCAG-GFP (Addgene plasmid 11150)39, pCAG-YFP (Addgene plasmid 11180)39, pCAG-DsRed (Addgene 11151)39. pRho-GFP-IRES-AP (referred to as Rho-GFP)40. pCAG-nlacZ (Cepko lab, Harvard Medical School), pCAGEN (Addgene plasmid 11160)39. pCALNL-DsRed (Addgene plasmid 13769)39. pCAFNF-DsRed (Addgene plasmid 13771)39. pCALNL-luc28. pRL-TK (Promega, 4E2241).

    Article Title: Polysaccharide-Polyplex Nanofilm Coatings Enhance Nanoneedle-Based Gene Delivery and Transfection Efficiency.
    Article Snippet: Anti-mouse CD44 was purchased from BD Biosciences. pCAG-GFP and pCAG-dsRFP were obtained from Addgene (MA, USA) and developed by Cepko C, et al.[103] Fluc-pcDNA3 was obtained from Addgene (MA, USA) and developed by Safran M, et al.[104] pABOL was obtained in-house and synthesized as previously described.

    Article Title: The mTOR pathway genes mTOR, Rheb, Depdc5, Pten , and Tsc1 have convergent and divergent impacts on cortical neuron development and function
    Article Snippet: pCAG-GFP , Addgene plasmid #11150; deposited by Dr. Connie Cepko.

    Article Title: Caveolin-3 prevents swelling-induced membrane damage via regulation of I Cl,swell activity.
    Article Snippet: Caveola membrane structures harbor mechanosensitive chloride channels (MCCs; including chloride channel 2, chloride channel 3, and SWELL1, also known as LRRC8A) that form a swelling-activated chloride current (ICl,swell) and play an important role in cell volume regulation and mechanoelectrical signal transduction.. However, the role of the muscle-specific caveolar scaffolding protein caveolin-3 (Cav3) in regulation of MCC expression, activity, and contribution to membrane integrity in response to mechanical stress remains unclear.. Here we showed that Cav3-transfected (Cav3-positive) HEK293 cells were significantly resistant to extreme (<20 milliosmole) hypotonic swelling compared with native (Cav3-negative) HEK293 cells; the percentage of cells with membrane damage decreased from 45% in Cav3-negative cells to 17% in Cav3-positive cells (p < 0.05).

    Concentration Assay:

    Article Title: In situ cell-type-specific cell-surface proteomic profiling in mice.
    Article Snippet: Nelson; Clark et al., 2020 N/A Mouse: MADM6-GT Contreras et al., 2021 N/A Mouse: MADM6-TG Contreras et al., 2021 N/A Oligonucleotides See Table S2 for a complete list of sequences Recombinant DNA See Table S2 for a complete list of gR and miR sequences integrated into plasmids pCAG-GFP Matsuda and Cepko, 2004 RRID:Addgene_11150 pCAG-tdTomato W. Joo, unpublished N/A pX333 Maddalo et al., 2014 RRID:Addgene_64073 pX333-CBh-Cas9-U6-2xsgRNA-LacZ Takeo et al., 2021 N/A pX333-CBh-Cas9-U6-2xsgRNA-Armh4 This paper N/A pCAG-EmGFP-miR Gift from M. Yuzaki N/A pCAG-EmGFP-LacZ-miR This paper N/A pCAG-EmGFP-Armh4-miR This paper N/A pCAG-2xHA-Armh4WT This paper N/A pCAG-V5-Armh4WT This paper N/A pCAG-Armh4WT-2xHA This paper N/A pCAG-2xHA-Armh4DICD This paper N/A pCAG-Armh4Endo6A-2xHA This paper N/A Software and algorithms ZEN Carl Zeiss RRID: SCR_013672 Imaris 9.3 Oxford Instruments RRID:SCR_007370; https://imaris.oxinst.com/ ImageJ (Fiji) NIH https://imagej.net/Fiji/Downloads Prism 9 GraphPad RRID:SCR_002798; https://www.graphpad.com/ Excel Microsoft RRID:SCR_016137 Spectrum Mill Agilent https://proteomics.broadinstitute. org/millhome.htm

    Article Title: Visualizing and manipulating the production and accumulation of hyaluronan for functional assessment in chicken embryos
    Article Snippet: pCAG - GFP , Matsuda and Cepko 4 , pCAG-GFP was a gift from Connie Cepko (Addgene plasmid # 11150; http://n2t.net/addgene:11150 ; RRID:Addgene_11150).

    Article Title: PCSK9 deficiency alters brain lipid composition without affecting brain development and function
    Article Snippet: We transfected the cells with the PCSK9 plasmid or an empty pCAGEN vector and stained with an anti-PCSK9 antibody (Goat-a-PCSK9: AF3985 (anti mouse/rat PCSK9, 0.2 mg/mL), dilution 1:50) and used immunofluorescence to confirm specific PCSK9 expression. pCAG-GFP was purchased from Addgene #11150. pCX::myr-Venus plasmid was a gift from Anna-Katerina Hadjantonalis.

    Article Title: DCX knockout ferret reveals a neurogenic mechanism in cortical development.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains Ferrets: WT This paper N/A Ferrets: DCX knockout mutants This paper N/A Mice: ICR This paper N/A Recombinant DNA pCAG-GFP Addgene Cat#11150 pCAG-DCX-GFP This paper N/A Software and algorithms Spaceranger v 1.0.0 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/ software/downloads/latest R v.4.1.0 R Core Team https://www.R-project.org/ CellRanger v.6.1.2 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/installation Seurat v4.3.0 Stuart et al., 201953 https://satijalab.org/seurat/install.html scrubletR v0.1.0 https://github.com/Moonerss/scrubletR CytoTRACE v0.3.3 Gulati et al., 201934 https://github.com/seqyuan/CytoTRACE SAW-5.4.0 BGIResearch https://github.com/STOmics/SAW stereopy-0.8.0 BGIResearch https://github.com/BGIResearch/stereopy scanpy-1.9.3 the Scanpy development team https://github.com/scverse/scanpy ggplot2 v3.3.2 Wickham, 201654 https://ggplot2.tidyverse.org scran v1.10.2 Lun et al., 201655 https://bioconductor.statistik.tu- dortmund.de/packages/3.8/bioc/ html/scran.html ggtree https://github.com/YuLab- SMU/ggtree V3.0.4 clusterProfiler v4.4.4 Wu et al., 2021.56 http://www.bioconductor.org/packages/ release/bioc/html/clusterProfiler.html ggpubr GitHub - kassambara/ ggpubr: ’ggplot20 V0.5.0 tidyverse https://bioconductor.org/ packages/release/ bioc/html/enrichplot.html V1.14.2 GSEA v4.1.0 Subramanian et al., 200557 http://software.broadinstitute.org/ gsea/index.jsp Cytoscape v3.8.2 Shannon et al. 200358 https://cytoscape.org/ ImageJ (1.5.3a) NIH https://imagej.nih.gov/ij/ Adobe Photoshop CC2020 Adobe Systems http://www.adobe.com GraphPad Prism 8.0 GraphPad Software http://www.graphpad.com/scientific- software/prism/

    Article Title: Sensor systems for target ligands and uses thereof
    Article Snippet: Miscellaneous Plasmids—pCAG-GFP (Addgene plasmid 11150)39, pCAG-YFP (Addgene plasmid 11180)39, pCAG-DsRed (Addgene 11151)39. pRho-GFP-IRES-AP (referred to as Rho-GFP)40. pCAG-nlacZ (Cepko lab, Harvard Medical School), pCAGEN (Addgene plasmid 11160)39. pCALNL-DsRed (Addgene plasmid 13769)39. pCAFNF-DsRed (Addgene plasmid 13771)39. pCALNL-luc28. pRL-TK (Promega, 4E2241).

    Article Title: Polysaccharide-Polyplex Nanofilm Coatings Enhance Nanoneedle-Based Gene Delivery and Transfection Efficiency.
    Article Snippet: Anti-mouse CD44 was purchased from BD Biosciences. pCAG-GFP and pCAG-dsRFP were obtained from Addgene (MA, USA) and developed by Cepko C, et al.[103] Fluc-pcDNA3 was obtained from Addgene (MA, USA) and developed by Safran M, et al.[104] pABOL was obtained in-house and synthesized as previously described.

    Article Title: The mTOR pathway genes mTOR, Rheb, Depdc5, Pten , and Tsc1 have convergent and divergent impacts on cortical neuron development and function
    Article Snippet: pCAG-GFP , Addgene plasmid #11150; deposited by Dr. Connie Cepko.

    Article Title: Caveolin-3 prevents swelling-induced membrane damage via regulation of I Cl,swell activity.
    Article Snippet: Caveola membrane structures harbor mechanosensitive chloride channels (MCCs; including chloride channel 2, chloride channel 3, and SWELL1, also known as LRRC8A) that form a swelling-activated chloride current (ICl,swell) and play an important role in cell volume regulation and mechanoelectrical signal transduction.. However, the role of the muscle-specific caveolar scaffolding protein caveolin-3 (Cav3) in regulation of MCC expression, activity, and contribution to membrane integrity in response to mechanical stress remains unclear.. Here we showed that Cav3-transfected (Cav3-positive) HEK293 cells were significantly resistant to extreme (<20 milliosmole) hypotonic swelling compared with native (Cav3-negative) HEK293 cells; the percentage of cells with membrane damage decreased from 45% in Cav3-negative cells to 17% in Cav3-positive cells (p < 0.05).

    In Vitro:

    Article Title: In situ cell-type-specific cell-surface proteomic profiling in mice.
    Article Snippet: Nelson; Clark et al., 2020 N/A Mouse: MADM6-GT Contreras et al., 2021 N/A Mouse: MADM6-TG Contreras et al., 2021 N/A Oligonucleotides See Table S2 for a complete list of sequences Recombinant DNA See Table S2 for a complete list of gR and miR sequences integrated into plasmids pCAG-GFP Matsuda and Cepko, 2004 RRID:Addgene_11150 pCAG-tdTomato W. Joo, unpublished N/A pX333 Maddalo et al., 2014 RRID:Addgene_64073 pX333-CBh-Cas9-U6-2xsgRNA-LacZ Takeo et al., 2021 N/A pX333-CBh-Cas9-U6-2xsgRNA-Armh4 This paper N/A pCAG-EmGFP-miR Gift from M. Yuzaki N/A pCAG-EmGFP-LacZ-miR This paper N/A pCAG-EmGFP-Armh4-miR This paper N/A pCAG-2xHA-Armh4WT This paper N/A pCAG-V5-Armh4WT This paper N/A pCAG-Armh4WT-2xHA This paper N/A pCAG-2xHA-Armh4DICD This paper N/A pCAG-Armh4Endo6A-2xHA This paper N/A Software and algorithms ZEN Carl Zeiss RRID: SCR_013672 Imaris 9.3 Oxford Instruments RRID:SCR_007370; https://imaris.oxinst.com/ ImageJ (Fiji) NIH https://imagej.net/Fiji/Downloads Prism 9 GraphPad RRID:SCR_002798; https://www.graphpad.com/ Excel Microsoft RRID:SCR_016137 Spectrum Mill Agilent https://proteomics.broadinstitute. org/millhome.htm

    Article Title: Visualizing and manipulating the production and accumulation of hyaluronan for functional assessment in chicken embryos
    Article Snippet: pCAG - GFP , Matsuda and Cepko 4 , pCAG-GFP was a gift from Connie Cepko (Addgene plasmid # 11150; http://n2t.net/addgene:11150 ; RRID:Addgene_11150).

    Article Title: PCSK9 deficiency alters brain lipid composition without affecting brain development and function
    Article Snippet: We transfected the cells with the PCSK9 plasmid or an empty pCAGEN vector and stained with an anti-PCSK9 antibody (Goat-a-PCSK9: AF3985 (anti mouse/rat PCSK9, 0.2 mg/mL), dilution 1:50) and used immunofluorescence to confirm specific PCSK9 expression. pCAG-GFP was purchased from Addgene #11150. pCX::myr-Venus plasmid was a gift from Anna-Katerina Hadjantonalis.

    Article Title: DCX knockout ferret reveals a neurogenic mechanism in cortical development.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains Ferrets: WT This paper N/A Ferrets: DCX knockout mutants This paper N/A Mice: ICR This paper N/A Recombinant DNA pCAG-GFP Addgene Cat#11150 pCAG-DCX-GFP This paper N/A Software and algorithms Spaceranger v 1.0.0 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/ software/downloads/latest R v.4.1.0 R Core Team https://www.R-project.org/ CellRanger v.6.1.2 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/installation Seurat v4.3.0 Stuart et al., 201953 https://satijalab.org/seurat/install.html scrubletR v0.1.0 https://github.com/Moonerss/scrubletR CytoTRACE v0.3.3 Gulati et al., 201934 https://github.com/seqyuan/CytoTRACE SAW-5.4.0 BGIResearch https://github.com/STOmics/SAW stereopy-0.8.0 BGIResearch https://github.com/BGIResearch/stereopy scanpy-1.9.3 the Scanpy development team https://github.com/scverse/scanpy ggplot2 v3.3.2 Wickham, 201654 https://ggplot2.tidyverse.org scran v1.10.2 Lun et al., 201655 https://bioconductor.statistik.tu- dortmund.de/packages/3.8/bioc/ html/scran.html ggtree https://github.com/YuLab- SMU/ggtree V3.0.4 clusterProfiler v4.4.4 Wu et al., 2021.56 http://www.bioconductor.org/packages/ release/bioc/html/clusterProfiler.html ggpubr GitHub - kassambara/ ggpubr: ’ggplot20 V0.5.0 tidyverse https://bioconductor.org/ packages/release/ bioc/html/enrichplot.html V1.14.2 GSEA v4.1.0 Subramanian et al., 200557 http://software.broadinstitute.org/ gsea/index.jsp Cytoscape v3.8.2 Shannon et al. 200358 https://cytoscape.org/ ImageJ (1.5.3a) NIH https://imagej.nih.gov/ij/ Adobe Photoshop CC2020 Adobe Systems http://www.adobe.com GraphPad Prism 8.0 GraphPad Software http://www.graphpad.com/scientific- software/prism/

    Article Title: Sensor systems for target ligands and uses thereof
    Article Snippet: Miscellaneous Plasmids—pCAG-GFP (Addgene plasmid 11150)39, pCAG-YFP (Addgene plasmid 11180)39, pCAG-DsRed (Addgene 11151)39. pRho-GFP-IRES-AP (referred to as Rho-GFP)40. pCAG-nlacZ (Cepko lab, Harvard Medical School), pCAGEN (Addgene plasmid 11160)39. pCALNL-DsRed (Addgene plasmid 13769)39. pCAFNF-DsRed (Addgene plasmid 13771)39. pCALNL-luc28. pRL-TK (Promega, 4E2241).

    Article Title: Polysaccharide-Polyplex Nanofilm Coatings Enhance Nanoneedle-Based Gene Delivery and Transfection Efficiency.
    Article Snippet: Anti-mouse CD44 was purchased from BD Biosciences. pCAG-GFP and pCAG-dsRFP were obtained from Addgene (MA, USA) and developed by Cepko C, et al.[103] Fluc-pcDNA3 was obtained from Addgene (MA, USA) and developed by Safran M, et al.[104] pABOL was obtained in-house and synthesized as previously described.

    Article Title: The mTOR pathway genes mTOR, Rheb, Depdc5, Pten , and Tsc1 have convergent and divergent impacts on cortical neuron development and function
    Article Snippet: pCAG-GFP , Addgene plasmid #11150; deposited by Dr. Connie Cepko.

    Article Title: Caveolin-3 prevents swelling-induced membrane damage via regulation of I Cl,swell activity.
    Article Snippet: Caveola membrane structures harbor mechanosensitive chloride channels (MCCs; including chloride channel 2, chloride channel 3, and SWELL1, also known as LRRC8A) that form a swelling-activated chloride current (ICl,swell) and play an important role in cell volume regulation and mechanoelectrical signal transduction.. However, the role of the muscle-specific caveolar scaffolding protein caveolin-3 (Cav3) in regulation of MCC expression, activity, and contribution to membrane integrity in response to mechanical stress remains unclear.. Here we showed that Cav3-transfected (Cav3-positive) HEK293 cells were significantly resistant to extreme (<20 milliosmole) hypotonic swelling compared with native (Cav3-negative) HEK293 cells; the percentage of cells with membrane damage decreased from 45% in Cav3-negative cells to 17% in Cav3-positive cells (p < 0.05).

    Control:

    Article Title: In situ cell-type-specific cell-surface proteomic profiling in mice.
    Article Snippet: Nelson; Clark et al., 2020 N/A Mouse: MADM6-GT Contreras et al., 2021 N/A Mouse: MADM6-TG Contreras et al., 2021 N/A Oligonucleotides See Table S2 for a complete list of sequences Recombinant DNA See Table S2 for a complete list of gR and miR sequences integrated into plasmids pCAG-GFP Matsuda and Cepko, 2004 RRID:Addgene_11150 pCAG-tdTomato W. Joo, unpublished N/A pX333 Maddalo et al., 2014 RRID:Addgene_64073 pX333-CBh-Cas9-U6-2xsgRNA-LacZ Takeo et al., 2021 N/A pX333-CBh-Cas9-U6-2xsgRNA-Armh4 This paper N/A pCAG-EmGFP-miR Gift from M. Yuzaki N/A pCAG-EmGFP-LacZ-miR This paper N/A pCAG-EmGFP-Armh4-miR This paper N/A pCAG-2xHA-Armh4WT This paper N/A pCAG-V5-Armh4WT This paper N/A pCAG-Armh4WT-2xHA This paper N/A pCAG-2xHA-Armh4DICD This paper N/A pCAG-Armh4Endo6A-2xHA This paper N/A Software and algorithms ZEN Carl Zeiss RRID: SCR_013672 Imaris 9.3 Oxford Instruments RRID:SCR_007370; https://imaris.oxinst.com/ ImageJ (Fiji) NIH https://imagej.net/Fiji/Downloads Prism 9 GraphPad RRID:SCR_002798; https://www.graphpad.com/ Excel Microsoft RRID:SCR_016137 Spectrum Mill Agilent https://proteomics.broadinstitute. org/millhome.htm

    Article Title: Visualizing and manipulating the production and accumulation of hyaluronan for functional assessment in chicken embryos
    Article Snippet: pCAG - GFP , Matsuda and Cepko 4 , pCAG-GFP was a gift from Connie Cepko (Addgene plasmid # 11150; http://n2t.net/addgene:11150 ; RRID:Addgene_11150).

    Article Title: PCSK9 deficiency alters brain lipid composition without affecting brain development and function
    Article Snippet: We transfected the cells with the PCSK9 plasmid or an empty pCAGEN vector and stained with an anti-PCSK9 antibody (Goat-a-PCSK9: AF3985 (anti mouse/rat PCSK9, 0.2 mg/mL), dilution 1:50) and used immunofluorescence to confirm specific PCSK9 expression. pCAG-GFP was purchased from Addgene #11150. pCX::myr-Venus plasmid was a gift from Anna-Katerina Hadjantonalis.

    Article Title: DCX knockout ferret reveals a neurogenic mechanism in cortical development.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains Ferrets: WT This paper N/A Ferrets: DCX knockout mutants This paper N/A Mice: ICR This paper N/A Recombinant DNA pCAG-GFP Addgene Cat#11150 pCAG-DCX-GFP This paper N/A Software and algorithms Spaceranger v 1.0.0 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/ software/downloads/latest R v.4.1.0 R Core Team https://www.R-project.org/ CellRanger v.6.1.2 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/installation Seurat v4.3.0 Stuart et al., 201953 https://satijalab.org/seurat/install.html scrubletR v0.1.0 https://github.com/Moonerss/scrubletR CytoTRACE v0.3.3 Gulati et al., 201934 https://github.com/seqyuan/CytoTRACE SAW-5.4.0 BGIResearch https://github.com/STOmics/SAW stereopy-0.8.0 BGIResearch https://github.com/BGIResearch/stereopy scanpy-1.9.3 the Scanpy development team https://github.com/scverse/scanpy ggplot2 v3.3.2 Wickham, 201654 https://ggplot2.tidyverse.org scran v1.10.2 Lun et al., 201655 https://bioconductor.statistik.tu- dortmund.de/packages/3.8/bioc/ html/scran.html ggtree https://github.com/YuLab- SMU/ggtree V3.0.4 clusterProfiler v4.4.4 Wu et al., 2021.56 http://www.bioconductor.org/packages/ release/bioc/html/clusterProfiler.html ggpubr GitHub - kassambara/ ggpubr: ’ggplot20 V0.5.0 tidyverse https://bioconductor.org/ packages/release/ bioc/html/enrichplot.html V1.14.2 GSEA v4.1.0 Subramanian et al., 200557 http://software.broadinstitute.org/ gsea/index.jsp Cytoscape v3.8.2 Shannon et al. 200358 https://cytoscape.org/ ImageJ (1.5.3a) NIH https://imagej.nih.gov/ij/ Adobe Photoshop CC2020 Adobe Systems http://www.adobe.com GraphPad Prism 8.0 GraphPad Software http://www.graphpad.com/scientific- software/prism/

    Article Title: Sensor systems for target ligands and uses thereof
    Article Snippet: Miscellaneous Plasmids—pCAG-GFP (Addgene plasmid 11150)39, pCAG-YFP (Addgene plasmid 11180)39, pCAG-DsRed (Addgene 11151)39. pRho-GFP-IRES-AP (referred to as Rho-GFP)40. pCAG-nlacZ (Cepko lab, Harvard Medical School), pCAGEN (Addgene plasmid 11160)39. pCALNL-DsRed (Addgene plasmid 13769)39. pCAFNF-DsRed (Addgene plasmid 13771)39. pCALNL-luc28. pRL-TK (Promega, 4E2241).

    Article Title: Polysaccharide-Polyplex Nanofilm Coatings Enhance Nanoneedle-Based Gene Delivery and Transfection Efficiency.
    Article Snippet: Anti-mouse CD44 was purchased from BD Biosciences. pCAG-GFP and pCAG-dsRFP were obtained from Addgene (MA, USA) and developed by Cepko C, et al.[103] Fluc-pcDNA3 was obtained from Addgene (MA, USA) and developed by Safran M, et al.[104] pABOL was obtained in-house and synthesized as previously described.

    Article Title: The mTOR pathway genes mTOR, Rheb, Depdc5, Pten , and Tsc1 have convergent and divergent impacts on cortical neuron development and function
    Article Snippet: pCAG-GFP , Addgene plasmid #11150; deposited by Dr. Connie Cepko.

    Article Title: Caveolin-3 prevents swelling-induced membrane damage via regulation of I Cl,swell activity.
    Article Snippet: Caveola membrane structures harbor mechanosensitive chloride channels (MCCs; including chloride channel 2, chloride channel 3, and SWELL1, also known as LRRC8A) that form a swelling-activated chloride current (ICl,swell) and play an important role in cell volume regulation and mechanoelectrical signal transduction.. However, the role of the muscle-specific caveolar scaffolding protein caveolin-3 (Cav3) in regulation of MCC expression, activity, and contribution to membrane integrity in response to mechanical stress remains unclear.. Here we showed that Cav3-transfected (Cav3-positive) HEK293 cells were significantly resistant to extreme (<20 milliosmole) hypotonic swelling compared with native (Cav3-negative) HEK293 cells; the percentage of cells with membrane damage decreased from 45% in Cav3-negative cells to 17% in Cav3-positive cells (p < 0.05).

    Two Tailed Test:

    Article Title: In situ cell-type-specific cell-surface proteomic profiling in mice.
    Article Snippet: Nelson; Clark et al., 2020 N/A Mouse: MADM6-GT Contreras et al., 2021 N/A Mouse: MADM6-TG Contreras et al., 2021 N/A Oligonucleotides See Table S2 for a complete list of sequences Recombinant DNA See Table S2 for a complete list of gR and miR sequences integrated into plasmids pCAG-GFP Matsuda and Cepko, 2004 RRID:Addgene_11150 pCAG-tdTomato W. Joo, unpublished N/A pX333 Maddalo et al., 2014 RRID:Addgene_64073 pX333-CBh-Cas9-U6-2xsgRNA-LacZ Takeo et al., 2021 N/A pX333-CBh-Cas9-U6-2xsgRNA-Armh4 This paper N/A pCAG-EmGFP-miR Gift from M. Yuzaki N/A pCAG-EmGFP-LacZ-miR This paper N/A pCAG-EmGFP-Armh4-miR This paper N/A pCAG-2xHA-Armh4WT This paper N/A pCAG-V5-Armh4WT This paper N/A pCAG-Armh4WT-2xHA This paper N/A pCAG-2xHA-Armh4DICD This paper N/A pCAG-Armh4Endo6A-2xHA This paper N/A Software and algorithms ZEN Carl Zeiss RRID: SCR_013672 Imaris 9.3 Oxford Instruments RRID:SCR_007370; https://imaris.oxinst.com/ ImageJ (Fiji) NIH https://imagej.net/Fiji/Downloads Prism 9 GraphPad RRID:SCR_002798; https://www.graphpad.com/ Excel Microsoft RRID:SCR_016137 Spectrum Mill Agilent https://proteomics.broadinstitute. org/millhome.htm

    Article Title: Visualizing and manipulating the production and accumulation of hyaluronan for functional assessment in chicken embryos
    Article Snippet: pCAG - GFP , Matsuda and Cepko 4 , pCAG-GFP was a gift from Connie Cepko (Addgene plasmid # 11150; http://n2t.net/addgene:11150 ; RRID:Addgene_11150).

    Article Title: PCSK9 deficiency alters brain lipid composition without affecting brain development and function
    Article Snippet: We transfected the cells with the PCSK9 plasmid or an empty pCAGEN vector and stained with an anti-PCSK9 antibody (Goat-a-PCSK9: AF3985 (anti mouse/rat PCSK9, 0.2 mg/mL), dilution 1:50) and used immunofluorescence to confirm specific PCSK9 expression. pCAG-GFP was purchased from Addgene #11150. pCX::myr-Venus plasmid was a gift from Anna-Katerina Hadjantonalis.

    Article Title: DCX knockout ferret reveals a neurogenic mechanism in cortical development.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains Ferrets: WT This paper N/A Ferrets: DCX knockout mutants This paper N/A Mice: ICR This paper N/A Recombinant DNA pCAG-GFP Addgene Cat#11150 pCAG-DCX-GFP This paper N/A Software and algorithms Spaceranger v 1.0.0 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/ software/downloads/latest R v.4.1.0 R Core Team https://www.R-project.org/ CellRanger v.6.1.2 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/installation Seurat v4.3.0 Stuart et al., 201953 https://satijalab.org/seurat/install.html scrubletR v0.1.0 https://github.com/Moonerss/scrubletR CytoTRACE v0.3.3 Gulati et al., 201934 https://github.com/seqyuan/CytoTRACE SAW-5.4.0 BGIResearch https://github.com/STOmics/SAW stereopy-0.8.0 BGIResearch https://github.com/BGIResearch/stereopy scanpy-1.9.3 the Scanpy development team https://github.com/scverse/scanpy ggplot2 v3.3.2 Wickham, 201654 https://ggplot2.tidyverse.org scran v1.10.2 Lun et al., 201655 https://bioconductor.statistik.tu- dortmund.de/packages/3.8/bioc/ html/scran.html ggtree https://github.com/YuLab- SMU/ggtree V3.0.4 clusterProfiler v4.4.4 Wu et al., 2021.56 http://www.bioconductor.org/packages/ release/bioc/html/clusterProfiler.html ggpubr GitHub - kassambara/ ggpubr: ’ggplot20 V0.5.0 tidyverse https://bioconductor.org/ packages/release/ bioc/html/enrichplot.html V1.14.2 GSEA v4.1.0 Subramanian et al., 200557 http://software.broadinstitute.org/ gsea/index.jsp Cytoscape v3.8.2 Shannon et al. 200358 https://cytoscape.org/ ImageJ (1.5.3a) NIH https://imagej.nih.gov/ij/ Adobe Photoshop CC2020 Adobe Systems http://www.adobe.com GraphPad Prism 8.0 GraphPad Software http://www.graphpad.com/scientific- software/prism/

    Article Title: Sensor systems for target ligands and uses thereof
    Article Snippet: Miscellaneous Plasmids—pCAG-GFP (Addgene plasmid 11150)39, pCAG-YFP (Addgene plasmid 11180)39, pCAG-DsRed (Addgene 11151)39. pRho-GFP-IRES-AP (referred to as Rho-GFP)40. pCAG-nlacZ (Cepko lab, Harvard Medical School), pCAGEN (Addgene plasmid 11160)39. pCALNL-DsRed (Addgene plasmid 13769)39. pCAFNF-DsRed (Addgene plasmid 13771)39. pCALNL-luc28. pRL-TK (Promega, 4E2241).

    Article Title: Polysaccharide-Polyplex Nanofilm Coatings Enhance Nanoneedle-Based Gene Delivery and Transfection Efficiency.
    Article Snippet: Anti-mouse CD44 was purchased from BD Biosciences. pCAG-GFP and pCAG-dsRFP were obtained from Addgene (MA, USA) and developed by Cepko C, et al.[103] Fluc-pcDNA3 was obtained from Addgene (MA, USA) and developed by Safran M, et al.[104] pABOL was obtained in-house and synthesized as previously described.

    Article Title: The mTOR pathway genes mTOR, Rheb, Depdc5, Pten , and Tsc1 have convergent and divergent impacts on cortical neuron development and function
    Article Snippet: pCAG-GFP , Addgene plasmid #11150; deposited by Dr. Connie Cepko.

    Article Title: Caveolin-3 prevents swelling-induced membrane damage via regulation of I Cl,swell activity.
    Article Snippet: Caveola membrane structures harbor mechanosensitive chloride channels (MCCs; including chloride channel 2, chloride channel 3, and SWELL1, also known as LRRC8A) that form a swelling-activated chloride current (ICl,swell) and play an important role in cell volume regulation and mechanoelectrical signal transduction.. However, the role of the muscle-specific caveolar scaffolding protein caveolin-3 (Cav3) in regulation of MCC expression, activity, and contribution to membrane integrity in response to mechanical stress remains unclear.. Here we showed that Cav3-transfected (Cav3-positive) HEK293 cells were significantly resistant to extreme (<20 milliosmole) hypotonic swelling compared with native (Cav3-negative) HEK293 cells; the percentage of cells with membrane damage decreased from 45% in Cav3-negative cells to 17% in Cav3-positive cells (p < 0.05).

    Immunostaining:

    Article Title: In situ cell-type-specific cell-surface proteomic profiling in mice.
    Article Snippet: Nelson; Clark et al., 2020 N/A Mouse: MADM6-GT Contreras et al., 2021 N/A Mouse: MADM6-TG Contreras et al., 2021 N/A Oligonucleotides See Table S2 for a complete list of sequences Recombinant DNA See Table S2 for a complete list of gR and miR sequences integrated into plasmids pCAG-GFP Matsuda and Cepko, 2004 RRID:Addgene_11150 pCAG-tdTomato W. Joo, unpublished N/A pX333 Maddalo et al., 2014 RRID:Addgene_64073 pX333-CBh-Cas9-U6-2xsgRNA-LacZ Takeo et al., 2021 N/A pX333-CBh-Cas9-U6-2xsgRNA-Armh4 This paper N/A pCAG-EmGFP-miR Gift from M. Yuzaki N/A pCAG-EmGFP-LacZ-miR This paper N/A pCAG-EmGFP-Armh4-miR This paper N/A pCAG-2xHA-Armh4WT This paper N/A pCAG-V5-Armh4WT This paper N/A pCAG-Armh4WT-2xHA This paper N/A pCAG-2xHA-Armh4DICD This paper N/A pCAG-Armh4Endo6A-2xHA This paper N/A Software and algorithms ZEN Carl Zeiss RRID: SCR_013672 Imaris 9.3 Oxford Instruments RRID:SCR_007370; https://imaris.oxinst.com/ ImageJ (Fiji) NIH https://imagej.net/Fiji/Downloads Prism 9 GraphPad RRID:SCR_002798; https://www.graphpad.com/ Excel Microsoft RRID:SCR_016137 Spectrum Mill Agilent https://proteomics.broadinstitute. org/millhome.htm

    Article Title: Visualizing and manipulating the production and accumulation of hyaluronan for functional assessment in chicken embryos
    Article Snippet: pCAG - GFP , Matsuda and Cepko 4 , pCAG-GFP was a gift from Connie Cepko (Addgene plasmid # 11150; http://n2t.net/addgene:11150 ; RRID:Addgene_11150).

    Article Title: PCSK9 deficiency alters brain lipid composition without affecting brain development and function
    Article Snippet: We transfected the cells with the PCSK9 plasmid or an empty pCAGEN vector and stained with an anti-PCSK9 antibody (Goat-a-PCSK9: AF3985 (anti mouse/rat PCSK9, 0.2 mg/mL), dilution 1:50) and used immunofluorescence to confirm specific PCSK9 expression. pCAG-GFP was purchased from Addgene #11150. pCX::myr-Venus plasmid was a gift from Anna-Katerina Hadjantonalis.

    Article Title: DCX knockout ferret reveals a neurogenic mechanism in cortical development.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains Ferrets: WT This paper N/A Ferrets: DCX knockout mutants This paper N/A Mice: ICR This paper N/A Recombinant DNA pCAG-GFP Addgene Cat#11150 pCAG-DCX-GFP This paper N/A Software and algorithms Spaceranger v 1.0.0 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/ software/downloads/latest R v.4.1.0 R Core Team https://www.R-project.org/ CellRanger v.6.1.2 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/installation Seurat v4.3.0 Stuart et al., 201953 https://satijalab.org/seurat/install.html scrubletR v0.1.0 https://github.com/Moonerss/scrubletR CytoTRACE v0.3.3 Gulati et al., 201934 https://github.com/seqyuan/CytoTRACE SAW-5.4.0 BGIResearch https://github.com/STOmics/SAW stereopy-0.8.0 BGIResearch https://github.com/BGIResearch/stereopy scanpy-1.9.3 the Scanpy development team https://github.com/scverse/scanpy ggplot2 v3.3.2 Wickham, 201654 https://ggplot2.tidyverse.org scran v1.10.2 Lun et al., 201655 https://bioconductor.statistik.tu- dortmund.de/packages/3.8/bioc/ html/scran.html ggtree https://github.com/YuLab- SMU/ggtree V3.0.4 clusterProfiler v4.4.4 Wu et al., 2021.56 http://www.bioconductor.org/packages/ release/bioc/html/clusterProfiler.html ggpubr GitHub - kassambara/ ggpubr: ’ggplot20 V0.5.0 tidyverse https://bioconductor.org/ packages/release/ bioc/html/enrichplot.html V1.14.2 GSEA v4.1.0 Subramanian et al., 200557 http://software.broadinstitute.org/ gsea/index.jsp Cytoscape v3.8.2 Shannon et al. 200358 https://cytoscape.org/ ImageJ (1.5.3a) NIH https://imagej.nih.gov/ij/ Adobe Photoshop CC2020 Adobe Systems http://www.adobe.com GraphPad Prism 8.0 GraphPad Software http://www.graphpad.com/scientific- software/prism/

    Article Title: Sensor systems for target ligands and uses thereof
    Article Snippet: Miscellaneous Plasmids—pCAG-GFP (Addgene plasmid 11150)39, pCAG-YFP (Addgene plasmid 11180)39, pCAG-DsRed (Addgene 11151)39. pRho-GFP-IRES-AP (referred to as Rho-GFP)40. pCAG-nlacZ (Cepko lab, Harvard Medical School), pCAGEN (Addgene plasmid 11160)39. pCALNL-DsRed (Addgene plasmid 13769)39. pCAFNF-DsRed (Addgene plasmid 13771)39. pCALNL-luc28. pRL-TK (Promega, 4E2241).

    Article Title: Polysaccharide-Polyplex Nanofilm Coatings Enhance Nanoneedle-Based Gene Delivery and Transfection Efficiency.
    Article Snippet: Anti-mouse CD44 was purchased from BD Biosciences. pCAG-GFP and pCAG-dsRFP were obtained from Addgene (MA, USA) and developed by Cepko C, et al.[103] Fluc-pcDNA3 was obtained from Addgene (MA, USA) and developed by Safran M, et al.[104] pABOL was obtained in-house and synthesized as previously described.

    Article Title: The mTOR pathway genes mTOR, Rheb, Depdc5, Pten , and Tsc1 have convergent and divergent impacts on cortical neuron development and function
    Article Snippet: pCAG-GFP , Addgene plasmid #11150; deposited by Dr. Connie Cepko.

    Article Title: Caveolin-3 prevents swelling-induced membrane damage via regulation of I Cl,swell activity.
    Article Snippet: Caveola membrane structures harbor mechanosensitive chloride channels (MCCs; including chloride channel 2, chloride channel 3, and SWELL1, also known as LRRC8A) that form a swelling-activated chloride current (ICl,swell) and play an important role in cell volume regulation and mechanoelectrical signal transduction.. However, the role of the muscle-specific caveolar scaffolding protein caveolin-3 (Cav3) in regulation of MCC expression, activity, and contribution to membrane integrity in response to mechanical stress remains unclear.. Here we showed that Cav3-transfected (Cav3-positive) HEK293 cells were significantly resistant to extreme (<20 milliosmole) hypotonic swelling compared with native (Cav3-negative) HEK293 cells; the percentage of cells with membrane damage decreased from 45% in Cav3-negative cells to 17% in Cav3-positive cells (p < 0.05).

    Comparison:

    Article Title: In situ cell-type-specific cell-surface proteomic profiling in mice.
    Article Snippet: Nelson; Clark et al., 2020 N/A Mouse: MADM6-GT Contreras et al., 2021 N/A Mouse: MADM6-TG Contreras et al., 2021 N/A Oligonucleotides See Table S2 for a complete list of sequences Recombinant DNA See Table S2 for a complete list of gR and miR sequences integrated into plasmids pCAG-GFP Matsuda and Cepko, 2004 RRID:Addgene_11150 pCAG-tdTomato W. Joo, unpublished N/A pX333 Maddalo et al., 2014 RRID:Addgene_64073 pX333-CBh-Cas9-U6-2xsgRNA-LacZ Takeo et al., 2021 N/A pX333-CBh-Cas9-U6-2xsgRNA-Armh4 This paper N/A pCAG-EmGFP-miR Gift from M. Yuzaki N/A pCAG-EmGFP-LacZ-miR This paper N/A pCAG-EmGFP-Armh4-miR This paper N/A pCAG-2xHA-Armh4WT This paper N/A pCAG-V5-Armh4WT This paper N/A pCAG-Armh4WT-2xHA This paper N/A pCAG-2xHA-Armh4DICD This paper N/A pCAG-Armh4Endo6A-2xHA This paper N/A Software and algorithms ZEN Carl Zeiss RRID: SCR_013672 Imaris 9.3 Oxford Instruments RRID:SCR_007370; https://imaris.oxinst.com/ ImageJ (Fiji) NIH https://imagej.net/Fiji/Downloads Prism 9 GraphPad RRID:SCR_002798; https://www.graphpad.com/ Excel Microsoft RRID:SCR_016137 Spectrum Mill Agilent https://proteomics.broadinstitute. org/millhome.htm

    Article Title: Visualizing and manipulating the production and accumulation of hyaluronan for functional assessment in chicken embryos
    Article Snippet: pCAG - GFP , Matsuda and Cepko 4 , pCAG-GFP was a gift from Connie Cepko (Addgene plasmid # 11150; http://n2t.net/addgene:11150 ; RRID:Addgene_11150).

    Article Title: PCSK9 deficiency alters brain lipid composition without affecting brain development and function
    Article Snippet: We transfected the cells with the PCSK9 plasmid or an empty pCAGEN vector and stained with an anti-PCSK9 antibody (Goat-a-PCSK9: AF3985 (anti mouse/rat PCSK9, 0.2 mg/mL), dilution 1:50) and used immunofluorescence to confirm specific PCSK9 expression. pCAG-GFP was purchased from Addgene #11150. pCX::myr-Venus plasmid was a gift from Anna-Katerina Hadjantonalis.

    Article Title: DCX knockout ferret reveals a neurogenic mechanism in cortical development.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains Ferrets: WT This paper N/A Ferrets: DCX knockout mutants This paper N/A Mice: ICR This paper N/A Recombinant DNA pCAG-GFP Addgene Cat#11150 pCAG-DCX-GFP This paper N/A Software and algorithms Spaceranger v 1.0.0 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/ software/downloads/latest R v.4.1.0 R Core Team https://www.R-project.org/ CellRanger v.6.1.2 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/installation Seurat v4.3.0 Stuart et al., 201953 https://satijalab.org/seurat/install.html scrubletR v0.1.0 https://github.com/Moonerss/scrubletR CytoTRACE v0.3.3 Gulati et al., 201934 https://github.com/seqyuan/CytoTRACE SAW-5.4.0 BGIResearch https://github.com/STOmics/SAW stereopy-0.8.0 BGIResearch https://github.com/BGIResearch/stereopy scanpy-1.9.3 the Scanpy development team https://github.com/scverse/scanpy ggplot2 v3.3.2 Wickham, 201654 https://ggplot2.tidyverse.org scran v1.10.2 Lun et al., 201655 https://bioconductor.statistik.tu- dortmund.de/packages/3.8/bioc/ html/scran.html ggtree https://github.com/YuLab- SMU/ggtree V3.0.4 clusterProfiler v4.4.4 Wu et al., 2021.56 http://www.bioconductor.org/packages/ release/bioc/html/clusterProfiler.html ggpubr GitHub - kassambara/ ggpubr: ’ggplot20 V0.5.0 tidyverse https://bioconductor.org/ packages/release/ bioc/html/enrichplot.html V1.14.2 GSEA v4.1.0 Subramanian et al., 200557 http://software.broadinstitute.org/ gsea/index.jsp Cytoscape v3.8.2 Shannon et al. 200358 https://cytoscape.org/ ImageJ (1.5.3a) NIH https://imagej.nih.gov/ij/ Adobe Photoshop CC2020 Adobe Systems http://www.adobe.com GraphPad Prism 8.0 GraphPad Software http://www.graphpad.com/scientific- software/prism/

    Article Title: Sensor systems for target ligands and uses thereof
    Article Snippet: Miscellaneous Plasmids—pCAG-GFP (Addgene plasmid 11150)39, pCAG-YFP (Addgene plasmid 11180)39, pCAG-DsRed (Addgene 11151)39. pRho-GFP-IRES-AP (referred to as Rho-GFP)40. pCAG-nlacZ (Cepko lab, Harvard Medical School), pCAGEN (Addgene plasmid 11160)39. pCALNL-DsRed (Addgene plasmid 13769)39. pCAFNF-DsRed (Addgene plasmid 13771)39. pCALNL-luc28. pRL-TK (Promega, 4E2241).

    Article Title: Polysaccharide-Polyplex Nanofilm Coatings Enhance Nanoneedle-Based Gene Delivery and Transfection Efficiency.
    Article Snippet: Anti-mouse CD44 was purchased from BD Biosciences. pCAG-GFP and pCAG-dsRFP were obtained from Addgene (MA, USA) and developed by Cepko C, et al.[103] Fluc-pcDNA3 was obtained from Addgene (MA, USA) and developed by Safran M, et al.[104] pABOL was obtained in-house and synthesized as previously described.

    Article Title: The mTOR pathway genes mTOR, Rheb, Depdc5, Pten , and Tsc1 have convergent and divergent impacts on cortical neuron development and function
    Article Snippet: pCAG-GFP , Addgene plasmid #11150; deposited by Dr. Connie Cepko.

    Article Title: Caveolin-3 prevents swelling-induced membrane damage via regulation of I Cl,swell activity.
    Article Snippet: Caveola membrane structures harbor mechanosensitive chloride channels (MCCs; including chloride channel 2, chloride channel 3, and SWELL1, also known as LRRC8A) that form a swelling-activated chloride current (ICl,swell) and play an important role in cell volume regulation and mechanoelectrical signal transduction.. However, the role of the muscle-specific caveolar scaffolding protein caveolin-3 (Cav3) in regulation of MCC expression, activity, and contribution to membrane integrity in response to mechanical stress remains unclear.. Here we showed that Cav3-transfected (Cav3-positive) HEK293 cells were significantly resistant to extreme (<20 milliosmole) hypotonic swelling compared with native (Cav3-negative) HEK293 cells; the percentage of cells with membrane damage decreased from 45% in Cav3-negative cells to 17% in Cav3-positive cells (p < 0.05).

    Mass Spectrometry:

    Article Title: In situ cell-type-specific cell-surface proteomic profiling in mice.
    Article Snippet: Nelson; Clark et al., 2020 N/A Mouse: MADM6-GT Contreras et al., 2021 N/A Mouse: MADM6-TG Contreras et al., 2021 N/A Oligonucleotides See Table S2 for a complete list of sequences Recombinant DNA See Table S2 for a complete list of gR and miR sequences integrated into plasmids pCAG-GFP Matsuda and Cepko, 2004 RRID:Addgene_11150 pCAG-tdTomato W. Joo, unpublished N/A pX333 Maddalo et al., 2014 RRID:Addgene_64073 pX333-CBh-Cas9-U6-2xsgRNA-LacZ Takeo et al., 2021 N/A pX333-CBh-Cas9-U6-2xsgRNA-Armh4 This paper N/A pCAG-EmGFP-miR Gift from M. Yuzaki N/A pCAG-EmGFP-LacZ-miR This paper N/A pCAG-EmGFP-Armh4-miR This paper N/A pCAG-2xHA-Armh4WT This paper N/A pCAG-V5-Armh4WT This paper N/A pCAG-Armh4WT-2xHA This paper N/A pCAG-2xHA-Armh4DICD This paper N/A pCAG-Armh4Endo6A-2xHA This paper N/A Software and algorithms ZEN Carl Zeiss RRID: SCR_013672 Imaris 9.3 Oxford Instruments RRID:SCR_007370; https://imaris.oxinst.com/ ImageJ (Fiji) NIH https://imagej.net/Fiji/Downloads Prism 9 GraphPad RRID:SCR_002798; https://www.graphpad.com/ Excel Microsoft RRID:SCR_016137 Spectrum Mill Agilent https://proteomics.broadinstitute. org/millhome.htm

    Article Title: Visualizing and manipulating the production and accumulation of hyaluronan for functional assessment in chicken embryos
    Article Snippet: pCAG - GFP , Matsuda and Cepko 4 , pCAG-GFP was a gift from Connie Cepko (Addgene plasmid # 11150; http://n2t.net/addgene:11150 ; RRID:Addgene_11150).

    Article Title: PCSK9 deficiency alters brain lipid composition without affecting brain development and function
    Article Snippet: We transfected the cells with the PCSK9 plasmid or an empty pCAGEN vector and stained with an anti-PCSK9 antibody (Goat-a-PCSK9: AF3985 (anti mouse/rat PCSK9, 0.2 mg/mL), dilution 1:50) and used immunofluorescence to confirm specific PCSK9 expression. pCAG-GFP was purchased from Addgene #11150. pCX::myr-Venus plasmid was a gift from Anna-Katerina Hadjantonalis.

    Article Title: DCX knockout ferret reveals a neurogenic mechanism in cortical development.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains Ferrets: WT This paper N/A Ferrets: DCX knockout mutants This paper N/A Mice: ICR This paper N/A Recombinant DNA pCAG-GFP Addgene Cat#11150 pCAG-DCX-GFP This paper N/A Software and algorithms Spaceranger v 1.0.0 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/ software/downloads/latest R v.4.1.0 R Core Team https://www.R-project.org/ CellRanger v.6.1.2 10X genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/installation Seurat v4.3.0 Stuart et al., 201953 https://satijalab.org/seurat/install.html scrubletR v0.1.0 https://github.com/Moonerss/scrubletR CytoTRACE v0.3.3 Gulati et al., 201934 https://github.com/seqyuan/CytoTRACE SAW-5.4.0 BGIResearch https://github.com/STOmics/SAW stereopy-0.8.0 BGIResearch https://github.com/BGIResearch/stereopy scanpy-1.9.3 the Scanpy development team https://github.com/scverse/scanpy ggplot2 v3.3.2 Wickham, 201654 https://ggplot2.tidyverse.org scran v1.10.2 Lun et al., 201655 https://bioconductor.statistik.tu- dortmund.de/packages/3.8/bioc/ html/scran.html ggtree https://github.com/YuLab- SMU/ggtree V3.0.4 clusterProfiler v4.4.4 Wu et al., 2021.56 http://www.bioconductor.org/packages/ release/bioc/html/clusterProfiler.html ggpubr GitHub - kassambara/ ggpubr: ’ggplot20 V0.5.0 tidyverse https://bioconductor.org/ packages/release/ bioc/html/enrichplot.html V1.14.2 GSEA v4.1.0 Subramanian et al., 200557 http://software.broadinstitute.org/ gsea/index.jsp Cytoscape v3.8.2 Shannon et al. 200358 https://cytoscape.org/ ImageJ (1.5.3a) NIH https://imagej.nih.gov/ij/ Adobe Photoshop CC2020 Adobe Systems http://www.adobe.com GraphPad Prism 8.0 GraphPad Software http://www.graphpad.com/scientific- software/prism/

    Article Title: Sensor systems for target ligands and uses thereof
    Article Snippet: Miscellaneous Plasmids—pCAG-GFP (Addgene plasmid 11150)39, pCAG-YFP (Addgene plasmid 11180)39, pCAG-DsRed (Addgene 11151)39. pRho-GFP-IRES-AP (referred to as Rho-GFP)40. pCAG-nlacZ (Cepko lab, Harvard Medical School), pCAGEN (Addgene plasmid 11160)39. pCALNL-DsRed (Addgene plasmid 13769)39. pCAFNF-DsRed (Addgene plasmid 13771)39. pCALNL-luc28. pRL-TK (Promega, 4E2241).

    Article Title: Polysaccharide-Polyplex Nanofilm Coatings Enhance Nanoneedle-Based Gene Delivery and Transfection Efficiency.
    Article Snippet: Anti-mouse CD44 was purchased from BD Biosciences. pCAG-GFP and pCAG-dsRFP were obtained from Addgene (MA, USA) and developed by Cepko C, et al.[103] Fluc-pcDNA3 was obtained from Addgene (MA, USA) and developed by Safran M, et al.[104] pABOL was obtained in-house and synthesized as previously described.

    Article Title: The mTOR pathway genes mTOR, Rheb, Depdc5, Pten , and Tsc1 have convergent and divergent impacts on cortical neuron development and function
    Article Snippet: pCAG-GFP , Addgene plasmid #11150; deposited by Dr. Connie Cepko.

    Article Title: Caveolin-3 prevents swelling-induced membrane damage via regulation of I Cl,swell activity.
    Article Snippet: Caveola membrane structures harbor mechanosensitive chloride channels (MCCs; including chloride channel 2, chloride channel 3, and SWELL1, also known as LRRC8A) that form a swelling-activated chloride current (ICl,swell) and play an important role in cell volume regulation and mechanoelectrical signal transduction.. However, the role of the muscle-specific caveolar scaffolding protein caveolin-3 (Cav3) in regulation of MCC expression, activity, and contribution to membrane integrity in response to mechanical stress remains unclear.. Here we showed that Cav3-transfected (Cav3-positive) HEK293 cells were significantly resistant to extreme (<20 milliosmole) hypotonic swelling compared with native (Cav3-negative) HEK293 cells; the percentage of cells with membrane damage decreased from 45% in Cav3-negative cells to 17% in Cav3-positive cells (p < 0.05).



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    (A) Neurospheres were formed by mixing non-electroporated and electroporated cells before being plated in U-bottom ULA wells. (B) Maximum intensity projection image of a confocal stack of a DIV14 neurosphere in which neurons were separately electroporated with RFP (red) and Xph20-GFP (green). (C) Zoomed images on primary dendrites from neurons expressing intrabodies to PSD-95 (Xph20-GFP), or gephyrin (GPHN.FingR-GFP), revealing excitatory or inhibitory post-synapses, respectively. (D) Numbers of PSD-95 and gephyrin-positive puncta per electroporated neuron. Data represent the mean ± SEM of 14 and 10 neurospheres, respectively, and were compared by non-parametric Mann-Whitney test. Dots show individual neurospheres. (E) Maximum intensity projection of a confocal stack of a DIV14 neurosphere in which neurons were co-electroporated with GPHN.FingR-GFP (green) and Xph20-mRuby2 (magenta), allowing the detection of both excitatory and inhibitory post-synapses in the same cells. (F) Zoom on a dendritic segment corresponding to the rectangular area highlighted in (E). (G) Confocal image of a primary dendrite from a neuron expressing GFP-actin, further immunolabeled for GFP, showing numerous dendritic spines bulging out of the shaft.

    Journal: bioRxiv

    Article Title: Neurospheres from primary rodent brain cells to probe the 3D organization and function of synapses

    doi: 10.64898/2026.03.19.712855

    Figure Lengend Snippet: (A) Neurospheres were formed by mixing non-electroporated and electroporated cells before being plated in U-bottom ULA wells. (B) Maximum intensity projection image of a confocal stack of a DIV14 neurosphere in which neurons were separately electroporated with RFP (red) and Xph20-GFP (green). (C) Zoomed images on primary dendrites from neurons expressing intrabodies to PSD-95 (Xph20-GFP), or gephyrin (GPHN.FingR-GFP), revealing excitatory or inhibitory post-synapses, respectively. (D) Numbers of PSD-95 and gephyrin-positive puncta per electroporated neuron. Data represent the mean ± SEM of 14 and 10 neurospheres, respectively, and were compared by non-parametric Mann-Whitney test. Dots show individual neurospheres. (E) Maximum intensity projection of a confocal stack of a DIV14 neurosphere in which neurons were co-electroporated with GPHN.FingR-GFP (green) and Xph20-mRuby2 (magenta), allowing the detection of both excitatory and inhibitory post-synapses in the same cells. (F) Zoom on a dendritic segment corresponding to the rectangular area highlighted in (E). (G) Confocal image of a primary dendrite from a neuron expressing GFP-actin, further immunolabeled for GFP, showing numerous dendritic spines bulging out of the shaft.

    Article Snippet: The intrabody to gephyrin, GPHN.FingR-GFP (Addgene # 46296 pCAG_GPHN.FingR-eGFP-CCR5TC), was a gift from D. Arnold (University of Southern California, Los Angeles, CA, USA) ( ).

    Techniques: Expressing, MANN-WHITNEY, Immunolabeling

    (A) Neurospheres were formed by mixing non-electroporated and electroporated cells before being plated in U-bottom ULA wells. (B) Maximum intensity projection image of a confocal stack of a DIV14 neurosphere in which neurons were separately electroporated with RFP (red) and Xph20-GFP (green). (C) Zoomed images on primary dendrites from neurons expressing intrabodies to PSD-95 (Xph20-GFP), or gephyrin (GPHN.FingR-GFP), revealing excitatory or inhibitory post-synapses, respectively. (D) Numbers of PSD-95 and gephyrin-positive puncta per electroporated neuron. Data represent the mean ± SEM of 14 and 10 neurospheres, respectively, and were compared by non-parametric Mann-Whitney test. Dots show individual neurospheres. (E) Maximum intensity projection of a confocal stack of a DIV14 neurosphere in which neurons were co-electroporated with GPHN.FingR-GFP (green) and Xph20-mRuby2 (magenta), allowing the detection of both excitatory and inhibitory post-synapses in the same cells. (F) Zoom on a dendritic segment corresponding to the rectangular area highlighted in (E). (G) Confocal image of a primary dendrite from a neuron expressing GFP-actin, further immunolabeled for GFP, showing numerous dendritic spines bulging out of the shaft.

    Journal: bioRxiv

    Article Title: Neurospheres from primary rodent brain cells to probe the 3D organization and function of synapses

    doi: 10.64898/2026.03.19.712855

    Figure Lengend Snippet: (A) Neurospheres were formed by mixing non-electroporated and electroporated cells before being plated in U-bottom ULA wells. (B) Maximum intensity projection image of a confocal stack of a DIV14 neurosphere in which neurons were separately electroporated with RFP (red) and Xph20-GFP (green). (C) Zoomed images on primary dendrites from neurons expressing intrabodies to PSD-95 (Xph20-GFP), or gephyrin (GPHN.FingR-GFP), revealing excitatory or inhibitory post-synapses, respectively. (D) Numbers of PSD-95 and gephyrin-positive puncta per electroporated neuron. Data represent the mean ± SEM of 14 and 10 neurospheres, respectively, and were compared by non-parametric Mann-Whitney test. Dots show individual neurospheres. (E) Maximum intensity projection of a confocal stack of a DIV14 neurosphere in which neurons were co-electroporated with GPHN.FingR-GFP (green) and Xph20-mRuby2 (magenta), allowing the detection of both excitatory and inhibitory post-synapses in the same cells. (F) Zoom on a dendritic segment corresponding to the rectangular area highlighted in (E). (G) Confocal image of a primary dendrite from a neuron expressing GFP-actin, further immunolabeled for GFP, showing numerous dendritic spines bulging out of the shaft.

    Article Snippet: The intrabody to PSD-95, Xph20-GFP (Addgene #135,530 pCAG_Xph20-eGFP-CCR5TC), was a gift from M. Sainlos (IINS, University of Bordeaux) ( ).

    Techniques: Expressing, MANN-WHITNEY, Immunolabeling