Derivative Assay:Article Title: Sliced Human Cortical Organoids for Modeling Distinct Cortical Layer Formation
Article Snippet: Johns Hopkins University School of Medicine ( Wen et al., 2014 ) D3–2 Isogenic human iPSC line derived from “D3–2,” with the DISC1 mutation corrected using transcription activator-like effector nuclease (TALEN) Johns Hopkins University School of Medicine ( Wen et al., 2014 ) D3-R Software and Algorithms Zeiss Zen (Blue edition) Zeiss https://www.zeiss.com/microscopy/us/products/microscope-software/zen.html NextSeq System Suite v2.0 Illumine https://support.illumina.com/downloads/nextseq-system-suite-v2–0.html Neuralynx Cheetah Neuralynx https://neuralynx.com/software/cheetah Axon AxoScope 10.4 Molecular Devices http://mdc.custhelp.com/app/answers/detail/a_id/18779/~/axon%E2%84%A2pclamp%E2%84%A2-10-electrophysiology-data-acquisition-%26-analysis-software-download ImageJ (Fiji) NIH https://imagej.nih.gov/ij/docs/guide/146–2.html GraphPad Prism (8.0) GraphPad https://www.graphpad.com/scientific-software/prism/ Microsoft Excel Microsoft https://www.microsoft.com/en-us/p/excel/cfq7ttc0k7dx?activetab=pivot%3aoverviewtab Adobe Photoshop(CC) Adobe https://www.adobe.com/products/photoshop.html Adobe Illustrator (CC) Adobe https://www.adobe.com/products/illustrator.html TopHat (2.0) Johns Hopkins University https://ccb.jhu.edu/software/tophat/index.shtml R, R studio with R package Seurat (v 2.3.4) RStudio https://cran.r-project.org/web/packages/Seurat/index.html R studio with edgeR (v2.15) package RStudio https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4023662/ R package ClustifyR RStudio https://github.com/rnabioco/clustifyr Axon CLAMPfit Molecular Devices http://mdc.custhelp.com/app/answers/detail/a_id/18779/~/axon%E2%84%A2pclamp%E2%84%A2–10-electrophysiology-data-acquisition-%26-analysis-software-download KlustaKwik (1.5) Klusta http://klustakwik.sourceforge.net/ Neuralynx SpikeSort3D Neuralynx https://neuralynx.com/software/spikesort-3d MathWorks MATLAB MathWorks https://www.mathworks.com/ SpinU 12-well Spinning Bioreactor ( Qian et al., 2016 ), ( Qian et al., 2018 ) N/A Bulk RNA sequencing data of mutant DISC1 neurons ( Wen et al., 2014 ) {"type":"entrez-geo","attrs":{"text":"GSE57821","term_id":"57821"}} GSE57821 Open in a separate window KEY RESOURCES TABLE Analysis of hypoxia Detection of hypoxic cells in unsliced organoids and SNOs was performed using Hypoxyprobe Kit (HPI).
Mutagenesis:Article Title: Sliced Human Cortical Organoids for Modeling Distinct Cortical Layer Formation
Article Snippet: Johns Hopkins University School of Medicine ( Wen et al., 2014 ) D3–2 Isogenic human iPSC line derived from “D3–2,” with the DISC1 mutation corrected using transcription activator-like effector nuclease (TALEN) Johns Hopkins University School of Medicine ( Wen et al., 2014 ) D3-R Software and Algorithms Zeiss Zen (Blue edition) Zeiss https://www.zeiss.com/microscopy/us/products/microscope-software/zen.html NextSeq System Suite v2.0 Illumine https://support.illumina.com/downloads/nextseq-system-suite-v2–0.html Neuralynx Cheetah Neuralynx https://neuralynx.com/software/cheetah Axon AxoScope 10.4 Molecular Devices http://mdc.custhelp.com/app/answers/detail/a_id/18779/~/axon%E2%84%A2pclamp%E2%84%A2-10-electrophysiology-data-acquisition-%26-analysis-software-download ImageJ (Fiji) NIH https://imagej.nih.gov/ij/docs/guide/146–2.html GraphPad Prism (8.0) GraphPad https://www.graphpad.com/scientific-software/prism/ Microsoft Excel Microsoft https://www.microsoft.com/en-us/p/excel/cfq7ttc0k7dx?activetab=pivot%3aoverviewtab Adobe Photoshop(CC) Adobe https://www.adobe.com/products/photoshop.html Adobe Illustrator (CC) Adobe https://www.adobe.com/products/illustrator.html TopHat (2.0) Johns Hopkins University https://ccb.jhu.edu/software/tophat/index.shtml R, R studio with R package Seurat (v 2.3.4) RStudio https://cran.r-project.org/web/packages/Seurat/index.html R studio with edgeR (v2.15) package RStudio https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4023662/ R package ClustifyR RStudio https://github.com/rnabioco/clustifyr Axon CLAMPfit Molecular Devices http://mdc.custhelp.com/app/answers/detail/a_id/18779/~/axon%E2%84%A2pclamp%E2%84%A2–10-electrophysiology-data-acquisition-%26-analysis-software-download KlustaKwik (1.5) Klusta http://klustakwik.sourceforge.net/ Neuralynx SpikeSort3D Neuralynx https://neuralynx.com/software/spikesort-3d MathWorks MATLAB MathWorks https://www.mathworks.com/ SpinU 12-well Spinning Bioreactor ( Qian et al., 2016 ), ( Qian et al., 2018 ) N/A Bulk RNA sequencing data of mutant DISC1 neurons ( Wen et al., 2014 ) {"type":"entrez-geo","attrs":{"text":"GSE57821","term_id":"57821"}} GSE57821 Open in a separate window KEY RESOURCES TABLE Analysis of hypoxia Detection of hypoxic cells in unsliced organoids and SNOs was performed using Hypoxyprobe Kit (HPI).
TALENs:Article Title: Sliced Human Cortical Organoids for Modeling Distinct Cortical Layer Formation
Article Snippet: Johns Hopkins University School of Medicine ( Wen et al., 2014 ) D3–2 Isogenic human iPSC line derived from “D3–2,” with the DISC1 mutation corrected using transcription activator-like effector nuclease (TALEN) Johns Hopkins University School of Medicine ( Wen et al., 2014 ) D3-R Software and Algorithms Zeiss Zen (Blue edition) Zeiss https://www.zeiss.com/microscopy/us/products/microscope-software/zen.html NextSeq System Suite v2.0 Illumine https://support.illumina.com/downloads/nextseq-system-suite-v2–0.html Neuralynx Cheetah Neuralynx https://neuralynx.com/software/cheetah Axon AxoScope 10.4 Molecular Devices http://mdc.custhelp.com/app/answers/detail/a_id/18779/~/axon%E2%84%A2pclamp%E2%84%A2-10-electrophysiology-data-acquisition-%26-analysis-software-download ImageJ (Fiji) NIH https://imagej.nih.gov/ij/docs/guide/146–2.html GraphPad Prism (8.0) GraphPad https://www.graphpad.com/scientific-software/prism/ Microsoft Excel Microsoft https://www.microsoft.com/en-us/p/excel/cfq7ttc0k7dx?activetab=pivot%3aoverviewtab Adobe Photoshop(CC) Adobe https://www.adobe.com/products/photoshop.html Adobe Illustrator (CC) Adobe https://www.adobe.com/products/illustrator.html TopHat (2.0) Johns Hopkins University https://ccb.jhu.edu/software/tophat/index.shtml R, R studio with R package Seurat (v 2.3.4) RStudio https://cran.r-project.org/web/packages/Seurat/index.html R studio with edgeR (v2.15) package RStudio https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4023662/ R package ClustifyR RStudio https://github.com/rnabioco/clustifyr Axon CLAMPfit Molecular Devices http://mdc.custhelp.com/app/answers/detail/a_id/18779/~/axon%E2%84%A2pclamp%E2%84%A2–10-electrophysiology-data-acquisition-%26-analysis-software-download KlustaKwik (1.5) Klusta http://klustakwik.sourceforge.net/ Neuralynx SpikeSort3D Neuralynx https://neuralynx.com/software/spikesort-3d MathWorks MATLAB MathWorks https://www.mathworks.com/ SpinU 12-well Spinning Bioreactor ( Qian et al., 2016 ), ( Qian et al., 2018 ) N/A Bulk RNA sequencing data of mutant DISC1 neurons ( Wen et al., 2014 ) {"type":"entrez-geo","attrs":{"text":"GSE57821","term_id":"57821"}} GSE57821 Open in a separate window KEY RESOURCES TABLE Analysis of hypoxia Detection of hypoxic cells in unsliced organoids and SNOs was performed using Hypoxyprobe Kit (HPI).
Software:Article Title: Sliced Human Cortical Organoids for Modeling Distinct Cortical Layer Formation
Article Snippet: Johns Hopkins University School of Medicine ( Wen et al., 2014 ) D3–2 Isogenic human iPSC line derived from “D3–2,” with the DISC1 mutation corrected using transcription activator-like effector nuclease (TALEN) Johns Hopkins University School of Medicine ( Wen et al., 2014 ) D3-R Software and Algorithms Zeiss Zen (Blue edition) Zeiss https://www.zeiss.com/microscopy/us/products/microscope-software/zen.html NextSeq System Suite v2.0 Illumine https://support.illumina.com/downloads/nextseq-system-suite-v2–0.html Neuralynx Cheetah Neuralynx https://neuralynx.com/software/cheetah Axon AxoScope 10.4 Molecular Devices http://mdc.custhelp.com/app/answers/detail/a_id/18779/~/axon%E2%84%A2pclamp%E2%84%A2-10-electrophysiology-data-acquisition-%26-analysis-software-download ImageJ (Fiji) NIH https://imagej.nih.gov/ij/docs/guide/146–2.html GraphPad Prism (8.0) GraphPad https://www.graphpad.com/scientific-software/prism/ Microsoft Excel Microsoft https://www.microsoft.com/en-us/p/excel/cfq7ttc0k7dx?activetab=pivot%3aoverviewtab Adobe Photoshop(CC) Adobe https://www.adobe.com/products/photoshop.html Adobe Illustrator (CC) Adobe https://www.adobe.com/products/illustrator.html TopHat (2.0) Johns Hopkins University https://ccb.jhu.edu/software/tophat/index.shtml R, R studio with R package Seurat (v 2.3.4) RStudio https://cran.r-project.org/web/packages/Seurat/index.html R studio with edgeR (v2.15) package RStudio https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4023662/ R package ClustifyR RStudio https://github.com/rnabioco/clustifyr Axon CLAMPfit Molecular Devices http://mdc.custhelp.com/app/answers/detail/a_id/18779/~/axon%E2%84%A2pclamp%E2%84%A2–10-electrophysiology-data-acquisition-%26-analysis-software-download KlustaKwik (1.5) Klusta http://klustakwik.sourceforge.net/ Neuralynx SpikeSort3D Neuralynx https://neuralynx.com/software/spikesort-3d MathWorks MATLAB MathWorks https://www.mathworks.com/ SpinU 12-well Spinning Bioreactor ( Qian et al., 2016 ), ( Qian et al., 2018 ) N/A Bulk RNA sequencing data of mutant DISC1 neurons ( Wen et al., 2014 ) {"type":"entrez-geo","attrs":{"text":"GSE57821","term_id":"57821"}} GSE57821 Open in a separate window KEY RESOURCES TABLE Analysis of hypoxia Detection of hypoxic cells in unsliced organoids and SNOs was performed using Hypoxyprobe Kit (HPI).
RNA Sequencing:Article Title: Sliced Human Cortical Organoids for Modeling Distinct Cortical Layer Formation
Article Snippet: Johns Hopkins University School of Medicine ( Wen et al., 2014 ) D3–2 Isogenic human iPSC line derived from “D3–2,” with the DISC1 mutation corrected using transcription activator-like effector nuclease (TALEN) Johns Hopkins University School of Medicine ( Wen et al., 2014 ) D3-R Software and Algorithms Zeiss Zen (Blue edition) Zeiss https://www.zeiss.com/microscopy/us/products/microscope-software/zen.html NextSeq System Suite v2.0 Illumine https://support.illumina.com/downloads/nextseq-system-suite-v2–0.html Neuralynx Cheetah Neuralynx https://neuralynx.com/software/cheetah Axon AxoScope 10.4 Molecular Devices http://mdc.custhelp.com/app/answers/detail/a_id/18779/~/axon%E2%84%A2pclamp%E2%84%A2-10-electrophysiology-data-acquisition-%26-analysis-software-download ImageJ (Fiji) NIH https://imagej.nih.gov/ij/docs/guide/146–2.html GraphPad Prism (8.0) GraphPad https://www.graphpad.com/scientific-software/prism/ Microsoft Excel Microsoft https://www.microsoft.com/en-us/p/excel/cfq7ttc0k7dx?activetab=pivot%3aoverviewtab Adobe Photoshop(CC) Adobe https://www.adobe.com/products/photoshop.html Adobe Illustrator (CC) Adobe https://www.adobe.com/products/illustrator.html TopHat (2.0) Johns Hopkins University https://ccb.jhu.edu/software/tophat/index.shtml R, R studio with R package Seurat (v 2.3.4) RStudio https://cran.r-project.org/web/packages/Seurat/index.html R studio with edgeR (v2.15) package RStudio https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4023662/ R package ClustifyR RStudio https://github.com/rnabioco/clustifyr Axon CLAMPfit Molecular Devices http://mdc.custhelp.com/app/answers/detail/a_id/18779/~/axon%E2%84%A2pclamp%E2%84%A2–10-electrophysiology-data-acquisition-%26-analysis-software-download KlustaKwik (1.5) Klusta http://klustakwik.sourceforge.net/ Neuralynx SpikeSort3D Neuralynx https://neuralynx.com/software/spikesort-3d MathWorks MATLAB MathWorks https://www.mathworks.com/ SpinU 12-well Spinning Bioreactor ( Qian et al., 2016 ), ( Qian et al., 2018 ) N/A Bulk RNA sequencing data of mutant DISC1 neurons ( Wen et al., 2014 ) {"type":"entrez-geo","attrs":{"text":"GSE57821","term_id":"57821"}} GSE57821 Open in a separate window KEY RESOURCES TABLE Analysis of hypoxia Detection of hypoxic cells in unsliced organoids and SNOs was performed using Hypoxyprobe Kit (HPI).
Recombinant:Article Title: Sliced Human Cortical Organoids for Modeling Distinct Cortical Layer Formation
Article Snippet: Johns Hopkins University School of Medicine ( Wen et al., 2014 ) D3–2 Isogenic human iPSC line derived from “D3–2,” with the DISC1 mutation corrected using transcription activator-like effector nuclease (TALEN) Johns Hopkins University School of Medicine ( Wen et al., 2014 ) D3-R Software and Algorithms Zeiss Zen (Blue edition) Zeiss https://www.zeiss.com/microscopy/us/products/microscope-software/zen.html NextSeq System Suite v2.0 Illumine https://support.illumina.com/downloads/nextseq-system-suite-v2–0.html Neuralynx Cheetah Neuralynx https://neuralynx.com/software/cheetah Axon AxoScope 10.4 Molecular Devices http://mdc.custhelp.com/app/answers/detail/a_id/18779/~/axon%E2%84%A2pclamp%E2%84%A2-10-electrophysiology-data-acquisition-%26-analysis-software-download ImageJ (Fiji) NIH https://imagej.nih.gov/ij/docs/guide/146–2.html GraphPad Prism (8.0) GraphPad https://www.graphpad.com/scientific-software/prism/ Microsoft Excel Microsoft https://www.microsoft.com/en-us/p/excel/cfq7ttc0k7dx?activetab=pivot%3aoverviewtab Adobe Photoshop(CC) Adobe https://www.adobe.com/products/photoshop.html Adobe Illustrator (CC) Adobe https://www.adobe.com/products/illustrator.html TopHat (2.0) Johns Hopkins University https://ccb.jhu.edu/software/tophat/index.shtml R, R studio with R package Seurat (v 2.3.4) RStudio https://cran.r-project.org/web/packages/Seurat/index.html R studio with edgeR (v2.15) package RStudio https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4023662/ R package ClustifyR RStudio https://github.com/rnabioco/clustifyr Axon CLAMPfit Molecular Devices http://mdc.custhelp.com/app/answers/detail/a_id/18779/~/axon%E2%84%A2pclamp%E2%84%A2–10-electrophysiology-data-acquisition-%26-analysis-software-download KlustaKwik (1.5) Klusta http://klustakwik.sourceforge.net/ Neuralynx SpikeSort3D Neuralynx https://neuralynx.com/software/spikesort-3d MathWorks MATLAB MathWorks https://www.mathworks.com/ SpinU 12-well Spinning Bioreactor ( Qian et al., 2016 ), ( Qian et al., 2018 ) N/A Bulk RNA sequencing data of mutant DISC1 neurons ( Wen et al., 2014 ) {"type":"entrez-geo","attrs":{"text":"GSE57821","term_id":"57821"}} GSE57821 Open in a separate window KEY RESOURCES TABLE Analysis of hypoxia Detection of hypoxic cells in unsliced organoids and SNOs was performed using Hypoxyprobe Kit (HPI).
Saline:Article Title: Sliced Human Cortical Organoids for Modeling Distinct Cortical Layer Formation
Article Snippet: Johns Hopkins University School of Medicine ( Wen et al., 2014 ) D3–2 Isogenic human iPSC line derived from “D3–2,” with the DISC1 mutation corrected using transcription activator-like effector nuclease (TALEN) Johns Hopkins University School of Medicine ( Wen et al., 2014 ) D3-R Software and Algorithms Zeiss Zen (Blue edition) Zeiss https://www.zeiss.com/microscopy/us/products/microscope-software/zen.html NextSeq System Suite v2.0 Illumine https://support.illumina.com/downloads/nextseq-system-suite-v2–0.html Neuralynx Cheetah Neuralynx https://neuralynx.com/software/cheetah Axon AxoScope 10.4 Molecular Devices http://mdc.custhelp.com/app/answers/detail/a_id/18779/~/axon%E2%84%A2pclamp%E2%84%A2-10-electrophysiology-data-acquisition-%26-analysis-software-download ImageJ (Fiji) NIH https://imagej.nih.gov/ij/docs/guide/146–2.html GraphPad Prism (8.0) GraphPad https://www.graphpad.com/scientific-software/prism/ Microsoft Excel Microsoft https://www.microsoft.com/en-us/p/excel/cfq7ttc0k7dx?activetab=pivot%3aoverviewtab Adobe Photoshop(CC) Adobe https://www.adobe.com/products/photoshop.html Adobe Illustrator (CC) Adobe https://www.adobe.com/products/illustrator.html TopHat (2.0) Johns Hopkins University https://ccb.jhu.edu/software/tophat/index.shtml R, R studio with R package Seurat (v 2.3.4) RStudio https://cran.r-project.org/web/packages/Seurat/index.html R studio with edgeR (v2.15) package RStudio https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4023662/ R package ClustifyR RStudio https://github.com/rnabioco/clustifyr Axon CLAMPfit Molecular Devices http://mdc.custhelp.com/app/answers/detail/a_id/18779/~/axon%E2%84%A2pclamp%E2%84%A2–10-electrophysiology-data-acquisition-%26-analysis-software-download KlustaKwik (1.5) Klusta http://klustakwik.sourceforge.net/ Neuralynx SpikeSort3D Neuralynx https://neuralynx.com/software/spikesort-3d MathWorks MATLAB MathWorks https://www.mathworks.com/ SpinU 12-well Spinning Bioreactor ( Qian et al., 2016 ), ( Qian et al., 2018 ) N/A Bulk RNA sequencing data of mutant DISC1 neurons ( Wen et al., 2014 ) {"type":"entrez-geo","attrs":{"text":"GSE57821","term_id":"57821"}} GSE57821 Open in a separate window KEY RESOURCES TABLE Analysis of hypoxia Detection of hypoxic cells in unsliced organoids and SNOs was performed using Hypoxyprobe Kit (HPI).
Knock-Out:Article Title: Sliced Human Cortical Organoids for Modeling Distinct Cortical Layer Formation
Article Snippet: Johns Hopkins University School of Medicine ( Wen et al., 2014 ) D3–2 Isogenic human iPSC line derived from “D3–2,” with the DISC1 mutation corrected using transcription activator-like effector nuclease (TALEN) Johns Hopkins University School of Medicine ( Wen et al., 2014 ) D3-R Software and Algorithms Zeiss Zen (Blue edition) Zeiss https://www.zeiss.com/microscopy/us/products/microscope-software/zen.html NextSeq System Suite v2.0 Illumine https://support.illumina.com/downloads/nextseq-system-suite-v2–0.html Neuralynx Cheetah Neuralynx https://neuralynx.com/software/cheetah Axon AxoScope 10.4 Molecular Devices http://mdc.custhelp.com/app/answers/detail/a_id/18779/~/axon%E2%84%A2pclamp%E2%84%A2-10-electrophysiology-data-acquisition-%26-analysis-software-download ImageJ (Fiji) NIH https://imagej.nih.gov/ij/docs/guide/146–2.html GraphPad Prism (8.0) GraphPad https://www.graphpad.com/scientific-software/prism/ Microsoft Excel Microsoft https://www.microsoft.com/en-us/p/excel/cfq7ttc0k7dx?activetab=pivot%3aoverviewtab Adobe Photoshop(CC) Adobe https://www.adobe.com/products/photoshop.html Adobe Illustrator (CC) Adobe https://www.adobe.com/products/illustrator.html TopHat (2.0) Johns Hopkins University https://ccb.jhu.edu/software/tophat/index.shtml R, R studio with R package Seurat (v 2.3.4) RStudio https://cran.r-project.org/web/packages/Seurat/index.html R studio with edgeR (v2.15) package RStudio https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4023662/ R package ClustifyR RStudio https://github.com/rnabioco/clustifyr Axon CLAMPfit Molecular Devices http://mdc.custhelp.com/app/answers/detail/a_id/18779/~/axon%E2%84%A2pclamp%E2%84%A2–10-electrophysiology-data-acquisition-%26-analysis-software-download KlustaKwik (1.5) Klusta http://klustakwik.sourceforge.net/ Neuralynx SpikeSort3D Neuralynx https://neuralynx.com/software/spikesort-3d MathWorks MATLAB MathWorks https://www.mathworks.com/ SpinU 12-well Spinning Bioreactor ( Qian et al., 2016 ), ( Qian et al., 2018 ) N/A Bulk RNA sequencing data of mutant DISC1 neurons ( Wen et al., 2014 ) {"type":"entrez-geo","attrs":{"text":"GSE57821","term_id":"57821"}} GSE57821 Open in a separate window KEY RESOURCES TABLE Analysis of hypoxia Detection of hypoxic cells in unsliced organoids and SNOs was performed using Hypoxyprobe Kit (HPI).
Protease Inhibitor:Article Title: Sliced Human Cortical Organoids for Modeling Distinct Cortical Layer Formation
Article Snippet: Johns Hopkins University School of Medicine ( Wen et al., 2014 ) D3–2 Isogenic human iPSC line derived from “D3–2,” with the DISC1 mutation corrected using transcription activator-like effector nuclease (TALEN) Johns Hopkins University School of Medicine ( Wen et al., 2014 ) D3-R Software and Algorithms Zeiss Zen (Blue edition) Zeiss https://www.zeiss.com/microscopy/us/products/microscope-software/zen.html NextSeq System Suite v2.0 Illumine https://support.illumina.com/downloads/nextseq-system-suite-v2–0.html Neuralynx Cheetah Neuralynx https://neuralynx.com/software/cheetah Axon AxoScope 10.4 Molecular Devices http://mdc.custhelp.com/app/answers/detail/a_id/18779/~/axon%E2%84%A2pclamp%E2%84%A2-10-electrophysiology-data-acquisition-%26-analysis-software-download ImageJ (Fiji) NIH https://imagej.nih.gov/ij/docs/guide/146–2.html GraphPad Prism (8.0) GraphPad https://www.graphpad.com/scientific-software/prism/ Microsoft Excel Microsoft https://www.microsoft.com/en-us/p/excel/cfq7ttc0k7dx?activetab=pivot%3aoverviewtab Adobe Photoshop(CC) Adobe https://www.adobe.com/products/photoshop.html Adobe Illustrator (CC) Adobe https://www.adobe.com/products/illustrator.html TopHat (2.0) Johns Hopkins University https://ccb.jhu.edu/software/tophat/index.shtml R, R studio with R package Seurat (v 2.3.4) RStudio https://cran.r-project.org/web/packages/Seurat/index.html R studio with edgeR (v2.15) package RStudio https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4023662/ R package ClustifyR RStudio https://github.com/rnabioco/clustifyr Axon CLAMPfit Molecular Devices http://mdc.custhelp.com/app/answers/detail/a_id/18779/~/axon%E2%84%A2pclamp%E2%84%A2–10-electrophysiology-data-acquisition-%26-analysis-software-download KlustaKwik (1.5) Klusta http://klustakwik.sourceforge.net/ Neuralynx SpikeSort3D Neuralynx https://neuralynx.com/software/spikesort-3d MathWorks MATLAB MathWorks https://www.mathworks.com/ SpinU 12-well Spinning Bioreactor ( Qian et al., 2016 ), ( Qian et al., 2018 ) N/A Bulk RNA sequencing data of mutant DISC1 neurons ( Wen et al., 2014 ) {"type":"entrez-geo","attrs":{"text":"GSE57821","term_id":"57821"}} GSE57821 Open in a separate window KEY RESOURCES TABLE Analysis of hypoxia Detection of hypoxic cells in unsliced organoids and SNOs was performed using Hypoxyprobe Kit (HPI).
Imaging:Article Title: Sliced Human Cortical Organoids for Modeling Distinct Cortical Layer Formation
Article Snippet: Johns Hopkins University School of Medicine ( Wen et al., 2014 ) D3–2 Isogenic human iPSC line derived from “D3–2,” with the DISC1 mutation corrected using transcription activator-like effector nuclease (TALEN) Johns Hopkins University School of Medicine ( Wen et al., 2014 ) D3-R Software and Algorithms Zeiss Zen (Blue edition) Zeiss https://www.zeiss.com/microscopy/us/products/microscope-software/zen.html NextSeq System Suite v2.0 Illumine https://support.illumina.com/downloads/nextseq-system-suite-v2–0.html Neuralynx Cheetah Neuralynx https://neuralynx.com/software/cheetah Axon AxoScope 10.4 Molecular Devices http://mdc.custhelp.com/app/answers/detail/a_id/18779/~/axon%E2%84%A2pclamp%E2%84%A2-10-electrophysiology-data-acquisition-%26-analysis-software-download ImageJ (Fiji) NIH https://imagej.nih.gov/ij/docs/guide/146–2.html GraphPad Prism (8.0) GraphPad https://www.graphpad.com/scientific-software/prism/ Microsoft Excel Microsoft https://www.microsoft.com/en-us/p/excel/cfq7ttc0k7dx?activetab=pivot%3aoverviewtab Adobe Photoshop(CC) Adobe https://www.adobe.com/products/photoshop.html Adobe Illustrator (CC) Adobe https://www.adobe.com/products/illustrator.html TopHat (2.0) Johns Hopkins University https://ccb.jhu.edu/software/tophat/index.shtml R, R studio with R package Seurat (v 2.3.4) RStudio https://cran.r-project.org/web/packages/Seurat/index.html R studio with edgeR (v2.15) package RStudio https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4023662/ R package ClustifyR RStudio https://github.com/rnabioco/clustifyr Axon CLAMPfit Molecular Devices http://mdc.custhelp.com/app/answers/detail/a_id/18779/~/axon%E2%84%A2pclamp%E2%84%A2–10-electrophysiology-data-acquisition-%26-analysis-software-download KlustaKwik (1.5) Klusta http://klustakwik.sourceforge.net/ Neuralynx SpikeSort3D Neuralynx https://neuralynx.com/software/spikesort-3d MathWorks MATLAB MathWorks https://www.mathworks.com/ SpinU 12-well Spinning Bioreactor ( Qian et al., 2016 ), ( Qian et al., 2018 ) N/A Bulk RNA sequencing data of mutant DISC1 neurons ( Wen et al., 2014 ) {"type":"entrez-geo","attrs":{"text":"GSE57821","term_id":"57821"}} GSE57821 Open in a separate window KEY RESOURCES TABLE Analysis of hypoxia Detection of hypoxic cells in unsliced organoids and SNOs was performed using Hypoxyprobe Kit (HPI).
DNA Library Preparation:Article Title: Sliced Human Cortical Organoids for Modeling Distinct Cortical Layer Formation
Article Snippet: Johns Hopkins University School of Medicine ( Wen et al., 2014 ) D3–2 Isogenic human iPSC line derived from “D3–2,” with the DISC1 mutation corrected using transcription activator-like effector nuclease (TALEN) Johns Hopkins University School of Medicine ( Wen et al., 2014 ) D3-R Software and Algorithms Zeiss Zen (Blue edition) Zeiss https://www.zeiss.com/microscopy/us/products/microscope-software/zen.html NextSeq System Suite v2.0 Illumine https://support.illumina.com/downloads/nextseq-system-suite-v2–0.html Neuralynx Cheetah Neuralynx https://neuralynx.com/software/cheetah Axon AxoScope 10.4 Molecular Devices http://mdc.custhelp.com/app/answers/detail/a_id/18779/~/axon%E2%84%A2pclamp%E2%84%A2-10-electrophysiology-data-acquisition-%26-analysis-software-download ImageJ (Fiji) NIH https://imagej.nih.gov/ij/docs/guide/146–2.html GraphPad Prism (8.0) GraphPad https://www.graphpad.com/scientific-software/prism/ Microsoft Excel Microsoft https://www.microsoft.com/en-us/p/excel/cfq7ttc0k7dx?activetab=pivot%3aoverviewtab Adobe Photoshop(CC) Adobe https://www.adobe.com/products/photoshop.html Adobe Illustrator (CC) Adobe https://www.adobe.com/products/illustrator.html TopHat (2.0) Johns Hopkins University https://ccb.jhu.edu/software/tophat/index.shtml R, R studio with R package Seurat (v 2.3.4) RStudio https://cran.r-project.org/web/packages/Seurat/index.html R studio with edgeR (v2.15) package RStudio https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4023662/ R package ClustifyR RStudio https://github.com/rnabioco/clustifyr Axon CLAMPfit Molecular Devices http://mdc.custhelp.com/app/answers/detail/a_id/18779/~/axon%E2%84%A2pclamp%E2%84%A2–10-electrophysiology-data-acquisition-%26-analysis-software-download KlustaKwik (1.5) Klusta http://klustakwik.sourceforge.net/ Neuralynx SpikeSort3D Neuralynx https://neuralynx.com/software/spikesort-3d MathWorks MATLAB MathWorks https://www.mathworks.com/ SpinU 12-well Spinning Bioreactor ( Qian et al., 2016 ), ( Qian et al., 2018 ) N/A Bulk RNA sequencing data of mutant DISC1 neurons ( Wen et al., 2014 ) {"type":"entrez-geo","attrs":{"text":"GSE57821","term_id":"57821"}} GSE57821 Open in a separate window KEY RESOURCES TABLE Analysis of hypoxia Detection of hypoxic cells in unsliced organoids and SNOs was performed using Hypoxyprobe Kit (HPI).
Plasmid Preparation:Article Title: Sliced Human Cortical Organoids for Modeling Distinct Cortical Layer Formation
Article Snippet: Johns Hopkins University School of Medicine ( Wen et al., 2014 ) D3–2 Isogenic human iPSC line derived from “D3–2,” with the DISC1 mutation corrected using transcription activator-like effector nuclease (TALEN) Johns Hopkins University School of Medicine ( Wen et al., 2014 ) D3-R Software and Algorithms Zeiss Zen (Blue edition) Zeiss https://www.zeiss.com/microscopy/us/products/microscope-software/zen.html NextSeq System Suite v2.0 Illumine https://support.illumina.com/downloads/nextseq-system-suite-v2–0.html Neuralynx Cheetah Neuralynx https://neuralynx.com/software/cheetah Axon AxoScope 10.4 Molecular Devices http://mdc.custhelp.com/app/answers/detail/a_id/18779/~/axon%E2%84%A2pclamp%E2%84%A2-10-electrophysiology-data-acquisition-%26-analysis-software-download ImageJ (Fiji) NIH https://imagej.nih.gov/ij/docs/guide/146–2.html GraphPad Prism (8.0) GraphPad https://www.graphpad.com/scientific-software/prism/ Microsoft Excel Microsoft https://www.microsoft.com/en-us/p/excel/cfq7ttc0k7dx?activetab=pivot%3aoverviewtab Adobe Photoshop(CC) Adobe https://www.adobe.com/products/photoshop.html Adobe Illustrator (CC) Adobe https://www.adobe.com/products/illustrator.html TopHat (2.0) Johns Hopkins University https://ccb.jhu.edu/software/tophat/index.shtml R, R studio with R package Seurat (v 2.3.4) RStudio https://cran.r-project.org/web/packages/Seurat/index.html R studio with edgeR (v2.15) package RStudio https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4023662/ R package ClustifyR RStudio https://github.com/rnabioco/clustifyr Axon CLAMPfit Molecular Devices http://mdc.custhelp.com/app/answers/detail/a_id/18779/~/axon%E2%84%A2pclamp%E2%84%A2–10-electrophysiology-data-acquisition-%26-analysis-software-download KlustaKwik (1.5) Klusta http://klustakwik.sourceforge.net/ Neuralynx SpikeSort3D Neuralynx https://neuralynx.com/software/spikesort-3d MathWorks MATLAB MathWorks https://www.mathworks.com/ SpinU 12-well Spinning Bioreactor ( Qian et al., 2016 ), ( Qian et al., 2018 ) N/A Bulk RNA sequencing data of mutant DISC1 neurons ( Wen et al., 2014 ) {"type":"entrez-geo","attrs":{"text":"GSE57821","term_id":"57821"}} GSE57821 Open in a separate window KEY RESOURCES TABLE Analysis of hypoxia Detection of hypoxic cells in unsliced organoids and SNOs was performed using Hypoxyprobe Kit (HPI).
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