Microarray:Article Title: Human Huntington's Disease iPSC-Derived Cortical Neurons Display Altered Transcriptomics, Morphology, and Maturation.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER 40,6-diamidino-2-phenylindole (DAPI) molecular probes D3571 1mm OD thin wall glass capillaries Fisher Scientific 22-362566 Trizol Thermo Fischer Scientific 155596026 choloroform Sigma-Aldrich C2432-25ML RNeasy column QIAGEN 74106 RNase-free DNase QIAGEN 79254 reverse transcriptase Invitrogen LS18064022 Agencourt AMPure XP beads Beckman Coulter A63880 Critical Commercial Assays 48 well microarray electrode array (MEA) plates Axion Biosystems M768-KAP-48 96 well microarray electrode array (MEA) plates Axion Biosystems M768-KAP-96 TruSeq Stranded mRNA library preparation kit Illumina 20020594 Deposited Data Raw data and statistical analysis (Mendeley Data) This paper https://doi.org/10.17632/y275mydz78.1 RNA sequencing data This paper GEO: GSE109534 Experimental Models: Cell Lines CS97iHD180n; male, 6 years iPSC Core (CSMC) CS97iHD180n CS09iHD109n; female, age unknown iPSC Core (CSMC) CS09iHD109n CS77iHD77n; male, age unknown iPSC Core (CSMC) CS77iHD77n CS83iCTR33n; female, 21 years iPSC Core (CSMC) CS83iCTR33n CS00iCTR21n; male, 6 years iPSC Core (CSMC) CS00iCTR21n CS25iCTR18n; male, 76 years iPSC Core (CSMC) CS25iCTR18n Experimental Models: Organisms/Strains Qubit fluorometer ThermoFisher Scientific Qubit fluorometer 2100 Bioanalyzer Agilent Technologies 2100 Bioanalyzer Software and Algorithms Neuroleucida 11.07.3 MBF Biosciences v11.07.3 Neuroexplorer 360 11.09 MBF Biosciences v11.09 Maestro Axis software version 2.4.2 Axion Biosystems v2.4.2 Plexon Offline Sorter, v4.3.1 Plexon v4.3.1 STAR (version 2.5.0) / RSEM (version 1.2.25) http://code.google.com/p/rna-star/ Open source DESeq2 Bioconductor package version 1.10.1 in R version 3.2.2 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html Open source Bioconductor g-plots package (version 2.14.2) in R https://www.bioconductor.org/install/ Open source DAVID Bioinformatics database (version 6.8) https://david.ncifcrf.gov/ Open source WGCNA was performed using its package in R https://cran.r-project.org/web/ packages/WGCNA/index.html Open source SAS v9.4 software SAS Institute Inc. v9.4
Microelectrode Array:Article Title: Human Huntington's Disease iPSC-Derived Cortical Neurons Display Altered Transcriptomics, Morphology, and Maturation.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER 40,6-diamidino-2-phenylindole (DAPI) molecular probes D3571 1mm OD thin wall glass capillaries Fisher Scientific 22-362566 Trizol Thermo Fischer Scientific 155596026 choloroform Sigma-Aldrich C2432-25ML RNeasy column QIAGEN 74106 RNase-free DNase QIAGEN 79254 reverse transcriptase Invitrogen LS18064022 Agencourt AMPure XP beads Beckman Coulter A63880 Critical Commercial Assays 48 well microarray electrode array (MEA) plates Axion Biosystems M768-KAP-48 96 well microarray electrode array (MEA) plates Axion Biosystems M768-KAP-96 TruSeq Stranded mRNA library preparation kit Illumina 20020594 Deposited Data Raw data and statistical analysis (Mendeley Data) This paper https://doi.org/10.17632/y275mydz78.1 RNA sequencing data This paper GEO: GSE109534 Experimental Models: Cell Lines CS97iHD180n; male, 6 years iPSC Core (CSMC) CS97iHD180n CS09iHD109n; female, age unknown iPSC Core (CSMC) CS09iHD109n CS77iHD77n; male, age unknown iPSC Core (CSMC) CS77iHD77n CS83iCTR33n; female, 21 years iPSC Core (CSMC) CS83iCTR33n CS00iCTR21n; male, 6 years iPSC Core (CSMC) CS00iCTR21n CS25iCTR18n; male, 76 years iPSC Core (CSMC) CS25iCTR18n Experimental Models: Organisms/Strains Qubit fluorometer ThermoFisher Scientific Qubit fluorometer 2100 Bioanalyzer Agilent Technologies 2100 Bioanalyzer Software and Algorithms Neuroleucida 11.07.3 MBF Biosciences v11.07.3 Neuroexplorer 360 11.09 MBF Biosciences v11.09 Maestro Axis software version 2.4.2 Axion Biosystems v2.4.2 Plexon Offline Sorter, v4.3.1 Plexon v4.3.1 STAR (version 2.5.0) / RSEM (version 1.2.25) http://code.google.com/p/rna-star/ Open source DESeq2 Bioconductor package version 1.10.1 in R version 3.2.2 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html Open source Bioconductor g-plots package (version 2.14.2) in R https://www.bioconductor.org/install/ Open source DAVID Bioinformatics database (version 6.8) https://david.ncifcrf.gov/ Open source WGCNA was performed using its package in R https://cran.r-project.org/web/ packages/WGCNA/index.html Open source SAS v9.4 software SAS Institute Inc. v9.4
RNA Sequencing Assay:Article Title: Human Huntington's Disease iPSC-Derived Cortical Neurons Display Altered Transcriptomics, Morphology, and Maturation.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER 40,6-diamidino-2-phenylindole (DAPI) molecular probes D3571 1mm OD thin wall glass capillaries Fisher Scientific 22-362566 Trizol Thermo Fischer Scientific 155596026 choloroform Sigma-Aldrich C2432-25ML RNeasy column QIAGEN 74106 RNase-free DNase QIAGEN 79254 reverse transcriptase Invitrogen LS18064022 Agencourt AMPure XP beads Beckman Coulter A63880 Critical Commercial Assays 48 well microarray electrode array (MEA) plates Axion Biosystems M768-KAP-48 96 well microarray electrode array (MEA) plates Axion Biosystems M768-KAP-96 TruSeq Stranded mRNA library preparation kit Illumina 20020594 Deposited Data Raw data and statistical analysis (Mendeley Data) This paper https://doi.org/10.17632/y275mydz78.1 RNA sequencing data This paper GEO: GSE109534 Experimental Models: Cell Lines CS97iHD180n; male, 6 years iPSC Core (CSMC) CS97iHD180n CS09iHD109n; female, age unknown iPSC Core (CSMC) CS09iHD109n CS77iHD77n; male, age unknown iPSC Core (CSMC) CS77iHD77n CS83iCTR33n; female, 21 years iPSC Core (CSMC) CS83iCTR33n CS00iCTR21n; male, 6 years iPSC Core (CSMC) CS00iCTR21n CS25iCTR18n; male, 76 years iPSC Core (CSMC) CS25iCTR18n Experimental Models: Organisms/Strains Qubit fluorometer ThermoFisher Scientific Qubit fluorometer 2100 Bioanalyzer Agilent Technologies 2100 Bioanalyzer Software and Algorithms Neuroleucida 11.07.3 MBF Biosciences v11.07.3 Neuroexplorer 360 11.09 MBF Biosciences v11.09 Maestro Axis software version 2.4.2 Axion Biosystems v2.4.2 Plexon Offline Sorter, v4.3.1 Plexon v4.3.1 STAR (version 2.5.0) / RSEM (version 1.2.25) http://code.google.com/p/rna-star/ Open source DESeq2 Bioconductor package version 1.10.1 in R version 3.2.2 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html Open source Bioconductor g-plots package (version 2.14.2) in R https://www.bioconductor.org/install/ Open source DAVID Bioinformatics database (version 6.8) https://david.ncifcrf.gov/ Open source WGCNA was performed using its package in R https://cran.r-project.org/web/ packages/WGCNA/index.html Open source SAS v9.4 software SAS Institute Inc. v9.4
Software:Article Title: Human Huntington's Disease iPSC-Derived Cortical Neurons Display Altered Transcriptomics, Morphology, and Maturation.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER 40,6-diamidino-2-phenylindole (DAPI) molecular probes D3571 1mm OD thin wall glass capillaries Fisher Scientific 22-362566 Trizol Thermo Fischer Scientific 155596026 choloroform Sigma-Aldrich C2432-25ML RNeasy column QIAGEN 74106 RNase-free DNase QIAGEN 79254 reverse transcriptase Invitrogen LS18064022 Agencourt AMPure XP beads Beckman Coulter A63880 Critical Commercial Assays 48 well microarray electrode array (MEA) plates Axion Biosystems M768-KAP-48 96 well microarray electrode array (MEA) plates Axion Biosystems M768-KAP-96 TruSeq Stranded mRNA library preparation kit Illumina 20020594 Deposited Data Raw data and statistical analysis (Mendeley Data) This paper https://doi.org/10.17632/y275mydz78.1 RNA sequencing data This paper GEO: GSE109534 Experimental Models: Cell Lines CS97iHD180n; male, 6 years iPSC Core (CSMC) CS97iHD180n CS09iHD109n; female, age unknown iPSC Core (CSMC) CS09iHD109n CS77iHD77n; male, age unknown iPSC Core (CSMC) CS77iHD77n CS83iCTR33n; female, 21 years iPSC Core (CSMC) CS83iCTR33n CS00iCTR21n; male, 6 years iPSC Core (CSMC) CS00iCTR21n CS25iCTR18n; male, 76 years iPSC Core (CSMC) CS25iCTR18n Experimental Models: Organisms/Strains Qubit fluorometer ThermoFisher Scientific Qubit fluorometer 2100 Bioanalyzer Agilent Technologies 2100 Bioanalyzer Software and Algorithms Neuroleucida 11.07.3 MBF Biosciences v11.07.3 Neuroexplorer 360 11.09 MBF Biosciences v11.09 Maestro Axis software version 2.4.2 Axion Biosystems v2.4.2 Plexon Offline Sorter, v4.3.1 Plexon v4.3.1 STAR (version 2.5.0) / RSEM (version 1.2.25) http://code.google.com/p/rna-star/ Open source DESeq2 Bioconductor package version 1.10.1 in R version 3.2.2 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html Open source Bioconductor g-plots package (version 2.14.2) in R https://www.bioconductor.org/install/ Open source DAVID Bioinformatics database (version 6.8) https://david.ncifcrf.gov/ Open source WGCNA was performed using its package in R https://cran.r-project.org/web/ packages/WGCNA/index.html Open source SAS v9.4 software SAS Institute Inc. v9.4
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