Recombinant:Article Title: Continuous and Discrete Neuron Types of the Adult Murine Striatum.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, Peptides, and Recombinant Proteins Hibernate-A Medium ThermoFisher Cat#A1247501 Trypsin inhibitor from chicken egg white Sigma Cat#T9253-500MG Percoll Sigma Cat#P1644 DAPI (4’,6-Diamidine-20-phenylindole dihydrochloride) Sigma Cat#10236276001 Triton X-100 Sigma Cat#T8787 Betaine Sigma-Aldrich Cat#61962 Recombinant RNase inhibitor Clontech Cat2313A dNTP NEB Cat#N0447 SMARTScribe Reverse Transcriptase Clontech Cat#639538 DTT (dithiothreitol) ThermoFisher Cat#R0861 Lambda Exonuclease NEB Cat#M0262L RNase-away ThermoFisher Cat#10328011 Critical Commercial Assays RNAscope Fluorescent Multiplex Reagent Kit ACDBio Cat#320850 Papain Dissociation System Worthington Cat#LK003150 Nextera XT DNA Library Prep Kit Illumina Cat#FC-131-1024 KAPA Hifi HotStart ReadyMix Kapa Biosystems Cat#KK2602 Ampure XP beads Ampure XP beads Cat#A63880 BioAnalyzer High Sensitivity Chips Agilent Cat#5067-4626 Falcon Cell Strainers Fisher Cat#08-771-2 ERCC RNA Spike-In Mix Invitrogen Cat#4456740 Cryomold VWR Cat#15160-215 Deposited Data Mouse Brain Atlas Allen Institute http://mouse.brain-map.org/ Mouse Reference Genome GRCm38/mm10 UCSC Genome Browser http://genome.ucsc.edu/cgi-bin/ hgGateway?db=mm10 Raw and analyzed data This paper GEO: GSE139412 Experimental Models: Organisms/Strains Mouse: FVB.Cg-Tg(Drd1-tdTomato)5Calak/ Mmnc Mus musculus Malenka Laboratory RRID:MMRRC_030512-UNC Mouse: Wildtype: C57BL/6J Jackson Laboratory JAX: #000664 Mouse: Tg(Drd2-EGFP)S118Gsat/Mmnc Malenka Laboratory RRID:MMRRC_000230-UNC Oligonucleotides Template Switch Oligo (AAGCAGTGGTATCAACG CAGAGTGAATrGrG+G) IDT Picelli et al., 2014 IS_PCR primer (AAGCAGTGGTATCAACGCAGAGT) IDT Picelli et al., 2014 Oligo dT: (50-AAGCAGTGGTATCAACGC AGAGTACT30VN-30) IDT Picelli et al., 2014 RNAscope Mm-Tac1 probe ACD Biosciences Cat#410351 RNAscope Mm-Penk probe ACD Biosciences Cat#318761 RNAscope Mm-Tac2 probe ACD Biosciences Cat#446391 RNAscope Mm-Nxph4 probe ACD Biosciences Cat#489641 (Continued on next page) Neuron 105, 1–12.e1–e8, February 19, 2020 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER RNAscope Mm-Cnr1 probe ACD Biosciences Cat#420721 RNAscope Mm-Crym probe ACD Biosciences Cat#466131 RNAscope Mm-Sema5b probe ACD Biosciences N/A RNAscope Mm-Id4 probe ACD Biosciences Cat#447861 RNAscope Mm-Nts probe ACD Biosciences Cat#420441 RNAscope Mm-Synpr probe ACD Biosciences Cat#500961 RNAscope Mm-Dner probe ACD Biosciences Cat#413951 RNAscope Mm-Tnnt1 probe ACD Biosciences Cat#466911 RNAscope Mm-Cxcl14 probe ACD Biosciences Cat#459741 RNAscope Mm-Th probe ACD Biosciences Cat#317621 RNAscope Mm-Htr7 probe ACD Biosciences Cat#401321 RNAscope Mm-Kremen1 probe ACD Biosciences Cat#425771 Software and Algorithms Star v2.4.0, https://github.com/alexdobin/STAR HTSeq v0.11.1, https://htseq.readthedocs.io/ en/release_0.11.1/ R v3.5.1, http://www.r-project.org; RRID:SCR_001905 Python v3.6.6, https://www.python.org Scanpy v1.3.7, https://icb-scanpy.readthedocs- hosted.com/en/stable/ CellProfiler v2.2.1, https://cellprofiler.org/releases/ Seurat v2.3.4, https://satijalab.org/seurat/ spdep v1.1-3, https://cran.r-project.org/web/ packages/spdep/index.html Fiji ImageJ Open source https://fiji.sc/ N/A Samtools N/A v1.3, http://samtools.sourceforge.net/; RRID:SCR_002105 Integrative Genomics Viewer (IGV) N/A http://software.broadinstitute.org/ software/igv; RRID:SCR_011793 Other FACS (Aria II) BD Biosciences N/A NextSeq 500 Illumina N/A Leica CM 3050 S cryostat Leica N/A HybEZ II Hybridization System for Manual Assays ACDBio N/A
Reverse Transcription:Article Title: Continuous and Discrete Neuron Types of the Adult Murine Striatum.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, Peptides, and Recombinant Proteins Hibernate-A Medium ThermoFisher Cat#A1247501 Trypsin inhibitor from chicken egg white Sigma Cat#T9253-500MG Percoll Sigma Cat#P1644 DAPI (4’,6-Diamidine-20-phenylindole dihydrochloride) Sigma Cat#10236276001 Triton X-100 Sigma Cat#T8787 Betaine Sigma-Aldrich Cat#61962 Recombinant RNase inhibitor Clontech Cat2313A dNTP NEB Cat#N0447 SMARTScribe Reverse Transcriptase Clontech Cat#639538 DTT (dithiothreitol) ThermoFisher Cat#R0861 Lambda Exonuclease NEB Cat#M0262L RNase-away ThermoFisher Cat#10328011 Critical Commercial Assays RNAscope Fluorescent Multiplex Reagent Kit ACDBio Cat#320850 Papain Dissociation System Worthington Cat#LK003150 Nextera XT DNA Library Prep Kit Illumina Cat#FC-131-1024 KAPA Hifi HotStart ReadyMix Kapa Biosystems Cat#KK2602 Ampure XP beads Ampure XP beads Cat#A63880 BioAnalyzer High Sensitivity Chips Agilent Cat#5067-4626 Falcon Cell Strainers Fisher Cat#08-771-2 ERCC RNA Spike-In Mix Invitrogen Cat#4456740 Cryomold VWR Cat#15160-215 Deposited Data Mouse Brain Atlas Allen Institute http://mouse.brain-map.org/ Mouse Reference Genome GRCm38/mm10 UCSC Genome Browser http://genome.ucsc.edu/cgi-bin/ hgGateway?db=mm10 Raw and analyzed data This paper GEO: GSE139412 Experimental Models: Organisms/Strains Mouse: FVB.Cg-Tg(Drd1-tdTomato)5Calak/ Mmnc Mus musculus Malenka Laboratory RRID:MMRRC_030512-UNC Mouse: Wildtype: C57BL/6J Jackson Laboratory JAX: #000664 Mouse: Tg(Drd2-EGFP)S118Gsat/Mmnc Malenka Laboratory RRID:MMRRC_000230-UNC Oligonucleotides Template Switch Oligo (AAGCAGTGGTATCAACG CAGAGTGAATrGrG+G) IDT Picelli et al., 2014 IS_PCR primer (AAGCAGTGGTATCAACGCAGAGT) IDT Picelli et al., 2014 Oligo dT: (50-AAGCAGTGGTATCAACGC AGAGTACT30VN-30) IDT Picelli et al., 2014 RNAscope Mm-Tac1 probe ACD Biosciences Cat#410351 RNAscope Mm-Penk probe ACD Biosciences Cat#318761 RNAscope Mm-Tac2 probe ACD Biosciences Cat#446391 RNAscope Mm-Nxph4 probe ACD Biosciences Cat#489641 (Continued on next page) Neuron 105, 1–12.e1–e8, February 19, 2020 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER RNAscope Mm-Cnr1 probe ACD Biosciences Cat#420721 RNAscope Mm-Crym probe ACD Biosciences Cat#466131 RNAscope Mm-Sema5b probe ACD Biosciences N/A RNAscope Mm-Id4 probe ACD Biosciences Cat#447861 RNAscope Mm-Nts probe ACD Biosciences Cat#420441 RNAscope Mm-Synpr probe ACD Biosciences Cat#500961 RNAscope Mm-Dner probe ACD Biosciences Cat#413951 RNAscope Mm-Tnnt1 probe ACD Biosciences Cat#466911 RNAscope Mm-Cxcl14 probe ACD Biosciences Cat#459741 RNAscope Mm-Th probe ACD Biosciences Cat#317621 RNAscope Mm-Htr7 probe ACD Biosciences Cat#401321 RNAscope Mm-Kremen1 probe ACD Biosciences Cat#425771 Software and Algorithms Star v2.4.0, https://github.com/alexdobin/STAR HTSeq v0.11.1, https://htseq.readthedocs.io/ en/release_0.11.1/ R v3.5.1, http://www.r-project.org; RRID:SCR_001905 Python v3.6.6, https://www.python.org Scanpy v1.3.7, https://icb-scanpy.readthedocs- hosted.com/en/stable/ CellProfiler v2.2.1, https://cellprofiler.org/releases/ Seurat v2.3.4, https://satijalab.org/seurat/ spdep v1.1-3, https://cran.r-project.org/web/ packages/spdep/index.html Fiji ImageJ Open source https://fiji.sc/ N/A Samtools N/A v1.3, http://samtools.sourceforge.net/; RRID:SCR_002105 Integrative Genomics Viewer (IGV) N/A http://software.broadinstitute.org/ software/igv; RRID:SCR_011793 Other FACS (Aria II) BD Biosciences N/A NextSeq 500 Illumina N/A Leica CM 3050 S cryostat Leica N/A HybEZ II Hybridization System for Manual Assays ACDBio N/A
RNAscope:Article Title: Continuous and Discrete Neuron Types of the Adult Murine Striatum.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, Peptides, and Recombinant Proteins Hibernate-A Medium ThermoFisher Cat#A1247501 Trypsin inhibitor from chicken egg white Sigma Cat#T9253-500MG Percoll Sigma Cat#P1644 DAPI (4’,6-Diamidine-20-phenylindole dihydrochloride) Sigma Cat#10236276001 Triton X-100 Sigma Cat#T8787 Betaine Sigma-Aldrich Cat#61962 Recombinant RNase inhibitor Clontech Cat2313A dNTP NEB Cat#N0447 SMARTScribe Reverse Transcriptase Clontech Cat#639538 DTT (dithiothreitol) ThermoFisher Cat#R0861 Lambda Exonuclease NEB Cat#M0262L RNase-away ThermoFisher Cat#10328011 Critical Commercial Assays RNAscope Fluorescent Multiplex Reagent Kit ACDBio Cat#320850 Papain Dissociation System Worthington Cat#LK003150 Nextera XT DNA Library Prep Kit Illumina Cat#FC-131-1024 KAPA Hifi HotStart ReadyMix Kapa Biosystems Cat#KK2602 Ampure XP beads Ampure XP beads Cat#A63880 BioAnalyzer High Sensitivity Chips Agilent Cat#5067-4626 Falcon Cell Strainers Fisher Cat#08-771-2 ERCC RNA Spike-In Mix Invitrogen Cat#4456740 Cryomold VWR Cat#15160-215 Deposited Data Mouse Brain Atlas Allen Institute http://mouse.brain-map.org/ Mouse Reference Genome GRCm38/mm10 UCSC Genome Browser http://genome.ucsc.edu/cgi-bin/ hgGateway?db=mm10 Raw and analyzed data This paper GEO: GSE139412 Experimental Models: Organisms/Strains Mouse: FVB.Cg-Tg(Drd1-tdTomato)5Calak/ Mmnc Mus musculus Malenka Laboratory RRID:MMRRC_030512-UNC Mouse: Wildtype: C57BL/6J Jackson Laboratory JAX: #000664 Mouse: Tg(Drd2-EGFP)S118Gsat/Mmnc Malenka Laboratory RRID:MMRRC_000230-UNC Oligonucleotides Template Switch Oligo (AAGCAGTGGTATCAACG CAGAGTGAATrGrG+G) IDT Picelli et al., 2014 IS_PCR primer (AAGCAGTGGTATCAACGCAGAGT) IDT Picelli et al., 2014 Oligo dT: (50-AAGCAGTGGTATCAACGC AGAGTACT30VN-30) IDT Picelli et al., 2014 RNAscope Mm-Tac1 probe ACD Biosciences Cat#410351 RNAscope Mm-Penk probe ACD Biosciences Cat#318761 RNAscope Mm-Tac2 probe ACD Biosciences Cat#446391 RNAscope Mm-Nxph4 probe ACD Biosciences Cat#489641 (Continued on next page) Neuron 105, 1–12.e1–e8, February 19, 2020 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER RNAscope Mm-Cnr1 probe ACD Biosciences Cat#420721 RNAscope Mm-Crym probe ACD Biosciences Cat#466131 RNAscope Mm-Sema5b probe ACD Biosciences N/A RNAscope Mm-Id4 probe ACD Biosciences Cat#447861 RNAscope Mm-Nts probe ACD Biosciences Cat#420441 RNAscope Mm-Synpr probe ACD Biosciences Cat#500961 RNAscope Mm-Dner probe ACD Biosciences Cat#413951 RNAscope Mm-Tnnt1 probe ACD Biosciences Cat#466911 RNAscope Mm-Cxcl14 probe ACD Biosciences Cat#459741 RNAscope Mm-Th probe ACD Biosciences Cat#317621 RNAscope Mm-Htr7 probe ACD Biosciences Cat#401321 RNAscope Mm-Kremen1 probe ACD Biosciences Cat#425771 Software and Algorithms Star v2.4.0, https://github.com/alexdobin/STAR HTSeq v0.11.1, https://htseq.readthedocs.io/ en/release_0.11.1/ R v3.5.1, http://www.r-project.org; RRID:SCR_001905 Python v3.6.6, https://www.python.org Scanpy v1.3.7, https://icb-scanpy.readthedocs- hosted.com/en/stable/ CellProfiler v2.2.1, https://cellprofiler.org/releases/ Seurat v2.3.4, https://satijalab.org/seurat/ spdep v1.1-3, https://cran.r-project.org/web/ packages/spdep/index.html Fiji ImageJ Open source https://fiji.sc/ N/A Samtools N/A v1.3, http://samtools.sourceforge.net/; RRID:SCR_002105 Integrative Genomics Viewer (IGV) N/A http://software.broadinstitute.org/ software/igv; RRID:SCR_011793 Other FACS (Aria II) BD Biosciences N/A NextSeq 500 Illumina N/A Leica CM 3050 S cryostat Leica N/A HybEZ II Hybridization System for Manual Assays ACDBio N/A
Multiplex Assay:Article Title: Continuous and Discrete Neuron Types of the Adult Murine Striatum.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, Peptides, and Recombinant Proteins Hibernate-A Medium ThermoFisher Cat#A1247501 Trypsin inhibitor from chicken egg white Sigma Cat#T9253-500MG Percoll Sigma Cat#P1644 DAPI (4’,6-Diamidine-20-phenylindole dihydrochloride) Sigma Cat#10236276001 Triton X-100 Sigma Cat#T8787 Betaine Sigma-Aldrich Cat#61962 Recombinant RNase inhibitor Clontech Cat2313A dNTP NEB Cat#N0447 SMARTScribe Reverse Transcriptase Clontech Cat#639538 DTT (dithiothreitol) ThermoFisher Cat#R0861 Lambda Exonuclease NEB Cat#M0262L RNase-away ThermoFisher Cat#10328011 Critical Commercial Assays RNAscope Fluorescent Multiplex Reagent Kit ACDBio Cat#320850 Papain Dissociation System Worthington Cat#LK003150 Nextera XT DNA Library Prep Kit Illumina Cat#FC-131-1024 KAPA Hifi HotStart ReadyMix Kapa Biosystems Cat#KK2602 Ampure XP beads Ampure XP beads Cat#A63880 BioAnalyzer High Sensitivity Chips Agilent Cat#5067-4626 Falcon Cell Strainers Fisher Cat#08-771-2 ERCC RNA Spike-In Mix Invitrogen Cat#4456740 Cryomold VWR Cat#15160-215 Deposited Data Mouse Brain Atlas Allen Institute http://mouse.brain-map.org/ Mouse Reference Genome GRCm38/mm10 UCSC Genome Browser http://genome.ucsc.edu/cgi-bin/ hgGateway?db=mm10 Raw and analyzed data This paper GEO: GSE139412 Experimental Models: Organisms/Strains Mouse: FVB.Cg-Tg(Drd1-tdTomato)5Calak/ Mmnc Mus musculus Malenka Laboratory RRID:MMRRC_030512-UNC Mouse: Wildtype: C57BL/6J Jackson Laboratory JAX: #000664 Mouse: Tg(Drd2-EGFP)S118Gsat/Mmnc Malenka Laboratory RRID:MMRRC_000230-UNC Oligonucleotides Template Switch Oligo (AAGCAGTGGTATCAACG CAGAGTGAATrGrG+G) IDT Picelli et al., 2014 IS_PCR primer (AAGCAGTGGTATCAACGCAGAGT) IDT Picelli et al., 2014 Oligo dT: (50-AAGCAGTGGTATCAACGC AGAGTACT30VN-30) IDT Picelli et al., 2014 RNAscope Mm-Tac1 probe ACD Biosciences Cat#410351 RNAscope Mm-Penk probe ACD Biosciences Cat#318761 RNAscope Mm-Tac2 probe ACD Biosciences Cat#446391 RNAscope Mm-Nxph4 probe ACD Biosciences Cat#489641 (Continued on next page) Neuron 105, 1–12.e1–e8, February 19, 2020 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER RNAscope Mm-Cnr1 probe ACD Biosciences Cat#420721 RNAscope Mm-Crym probe ACD Biosciences Cat#466131 RNAscope Mm-Sema5b probe ACD Biosciences N/A RNAscope Mm-Id4 probe ACD Biosciences Cat#447861 RNAscope Mm-Nts probe ACD Biosciences Cat#420441 RNAscope Mm-Synpr probe ACD Biosciences Cat#500961 RNAscope Mm-Dner probe ACD Biosciences Cat#413951 RNAscope Mm-Tnnt1 probe ACD Biosciences Cat#466911 RNAscope Mm-Cxcl14 probe ACD Biosciences Cat#459741 RNAscope Mm-Th probe ACD Biosciences Cat#317621 RNAscope Mm-Htr7 probe ACD Biosciences Cat#401321 RNAscope Mm-Kremen1 probe ACD Biosciences Cat#425771 Software and Algorithms Star v2.4.0, https://github.com/alexdobin/STAR HTSeq v0.11.1, https://htseq.readthedocs.io/ en/release_0.11.1/ R v3.5.1, http://www.r-project.org; RRID:SCR_001905 Python v3.6.6, https://www.python.org Scanpy v1.3.7, https://icb-scanpy.readthedocs- hosted.com/en/stable/ CellProfiler v2.2.1, https://cellprofiler.org/releases/ Seurat v2.3.4, https://satijalab.org/seurat/ spdep v1.1-3, https://cran.r-project.org/web/ packages/spdep/index.html Fiji ImageJ Open source https://fiji.sc/ N/A Samtools N/A v1.3, http://samtools.sourceforge.net/; RRID:SCR_002105 Integrative Genomics Viewer (IGV) N/A http://software.broadinstitute.org/ software/igv; RRID:SCR_011793 Other FACS (Aria II) BD Biosciences N/A NextSeq 500 Illumina N/A Leica CM 3050 S cryostat Leica N/A HybEZ II Hybridization System for Manual Assays ACDBio N/A
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