Recombinant:Article Title: In vivo imaging in transgenic songbirds reveals superdiffusive neuron migration in the adult brain.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rabbit polyclonal anti-GFP (1:400 dilution) Millipore Sigma RRID: AB_3080 mouse monoclonal anti-NeuN (1:500 dilution) Millipore Sigma MAB377, clone A60; RRID: AB_2298772 mouse monoclonal anti-DCX (1:400 dilution) Santa Cruz Biotechnology sc-271390 (E 6); RRID:AB_10610966 mouse monoclonal anti-Vimentin (40E-C-s) (1:10 dilution) Developmental Studies Hybridoma Bank RRID: AB_528504 a mouse monoclonal anti-HuC/HuD (1:500 dilution) Thermo Fisher Scientific A-21271; RRID:AB_221448 Alexa Fluor 488 conjugated goat anti-rabbit (1:500 or 1:1000 dilution) Abcam AB150077; RRID:AB_2630356 Alexa Fluor 555 conjugated goat anti-mouse (1:1000 dilution) Invitrogen A-21422; RRID:AB_2535844 Chemicals, peptides, and recombinant proteins SR-101 Invitrogen S359 Euthasol Virbac N/A Triton X-100 Sigma CAS: 9036-19-5 Sterilized EBSS Worthington Biochemical LK003188 Hybridization buffer Molecular Instruments N/A Vectashield Antifade Mounting Medium DAPI Vector Laboratories, Inc. H-1200-10 UV-curing Optical Adhesive Norland Products NOA61 Critical commercial assays UBC-GFP Zebra finch genome sequencing (with Illumina NGS) LC Sciences (Houston, TX) N/A Genomic DNA extraction and purification kit New England Biolabs NEB #T3010 Deposited Data Transgenic UBC-GFP Zebra finch genome This study SRA: PRJNA1061303 (https://www.ncbi.nlm.nih.gov/sra/PRJNA1061303) Cell migration data and analysis code This study Zenodo: (https://github.com/naomish1230/Transgenicsongbird-neuron-migration) Experimental models: Organisms/strains UBC-GFP transgenic zebra finches Agate et al.12 (bred in-house at Boston University) N/A Oligonucleotides GAD1 Molecular Instruments (custom probe, RefSeq: XM_002198498) VGLUT2 Molecular Instruments (custom probe, RefSeq: NM_012000.1) PDGFRA Molecular Instruments (custom probe, RefSeq: XM_030271078) CSF1R Molecular Instruments (custom probe, RefSeq: NM_001193260.1) UTS2B Molecular Instruments (custom probe, RefSeq: XM_0308048.3) SLC15A2 Molecular Instruments (custom probe, RefSeq: XM_030277156) Software and algorithms FIJI Schindelin et al.85 (https://github.com/fiji) RRID:SCR_002285 MATLAB Mathworks RRID:SCR_001622 Prairie View Bruker RRID:SCR_017142 (Continued on next page) 18 Cell Reports 43, 113759, February 27, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Other Glass micro-hematocrit capillary tube Thomas Scientific 1202K16 Small bird stereotaxic frame Kopf Instruments Model 940 digital stereotaxic instrument with model 914 and 914T small bird adapter Borosilicate capillary tubes Drummond Scientific N/A (100/VL – 3.500 length) Small diameter round coverglass, #1 thickness, 3 mm diameter Thomas Scientific 1217N66 Stainless steel cannula Ziggy’s Tubes and Wires N/A (custom: 304 S/S Tubing; 12500 OD x .11500 ID x 0.01900) 1.5 mm micro-prism with reflective hypotenuse Tower Optical Corporation Part Number: 4531-0023 (https://www.toweroptical.com/micro-prisms/) Micro-knife Fine Science Tools Item No. 10316-14 Custom kinematic headplate Kim et al.16 N/A Sterile 1.5 mm biopsy punch Royaltek BP15 Vibratome Leica VT1000S Confocal Microscope Zeiss LSM800 2P Microscope system Bruker Corporation N/A Goniometric stage ThorLabs TTR001 7X-45X Binocular Stereo Zoom Microscope with Double Arm Boom Stand AmScope SKU: SM-4B Infrared Camera ELP USB100W05MT-DL36
Hybridization:Article Title: In vivo imaging in transgenic songbirds reveals superdiffusive neuron migration in the adult brain.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rabbit polyclonal anti-GFP (1:400 dilution) Millipore Sigma RRID: AB_3080 mouse monoclonal anti-NeuN (1:500 dilution) Millipore Sigma MAB377, clone A60; RRID: AB_2298772 mouse monoclonal anti-DCX (1:400 dilution) Santa Cruz Biotechnology sc-271390 (E 6); RRID:AB_10610966 mouse monoclonal anti-Vimentin (40E-C-s) (1:10 dilution) Developmental Studies Hybridoma Bank RRID: AB_528504 a mouse monoclonal anti-HuC/HuD (1:500 dilution) Thermo Fisher Scientific A-21271; RRID:AB_221448 Alexa Fluor 488 conjugated goat anti-rabbit (1:500 or 1:1000 dilution) Abcam AB150077; RRID:AB_2630356 Alexa Fluor 555 conjugated goat anti-mouse (1:1000 dilution) Invitrogen A-21422; RRID:AB_2535844 Chemicals, peptides, and recombinant proteins SR-101 Invitrogen S359 Euthasol Virbac N/A Triton X-100 Sigma CAS: 9036-19-5 Sterilized EBSS Worthington Biochemical LK003188 Hybridization buffer Molecular Instruments N/A Vectashield Antifade Mounting Medium DAPI Vector Laboratories, Inc. H-1200-10 UV-curing Optical Adhesive Norland Products NOA61 Critical commercial assays UBC-GFP Zebra finch genome sequencing (with Illumina NGS) LC Sciences (Houston, TX) N/A Genomic DNA extraction and purification kit New England Biolabs NEB #T3010 Deposited Data Transgenic UBC-GFP Zebra finch genome This study SRA: PRJNA1061303 (https://www.ncbi.nlm.nih.gov/sra/PRJNA1061303) Cell migration data and analysis code This study Zenodo: (https://github.com/naomish1230/Transgenicsongbird-neuron-migration) Experimental models: Organisms/strains UBC-GFP transgenic zebra finches Agate et al.12 (bred in-house at Boston University) N/A Oligonucleotides GAD1 Molecular Instruments (custom probe, RefSeq: XM_002198498) VGLUT2 Molecular Instruments (custom probe, RefSeq: NM_012000.1) PDGFRA Molecular Instruments (custom probe, RefSeq: XM_030271078) CSF1R Molecular Instruments (custom probe, RefSeq: NM_001193260.1) UTS2B Molecular Instruments (custom probe, RefSeq: XM_0308048.3) SLC15A2 Molecular Instruments (custom probe, RefSeq: XM_030277156) Software and algorithms FIJI Schindelin et al.85 (https://github.com/fiji) RRID:SCR_002285 MATLAB Mathworks RRID:SCR_001622 Prairie View Bruker RRID:SCR_017142 (Continued on next page) 18 Cell Reports 43, 113759, February 27, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Other Glass micro-hematocrit capillary tube Thomas Scientific 1202K16 Small bird stereotaxic frame Kopf Instruments Model 940 digital stereotaxic instrument with model 914 and 914T small bird adapter Borosilicate capillary tubes Drummond Scientific N/A (100/VL – 3.500 length) Small diameter round coverglass, #1 thickness, 3 mm diameter Thomas Scientific 1217N66 Stainless steel cannula Ziggy’s Tubes and Wires N/A (custom: 304 S/S Tubing; 12500 OD x .11500 ID x 0.01900) 1.5 mm micro-prism with reflective hypotenuse Tower Optical Corporation Part Number: 4531-0023 (https://www.toweroptical.com/micro-prisms/) Micro-knife Fine Science Tools Item No. 10316-14 Custom kinematic headplate Kim et al.16 N/A Sterile 1.5 mm biopsy punch Royaltek BP15 Vibratome Leica VT1000S Confocal Microscope Zeiss LSM800 2P Microscope system Bruker Corporation N/A Goniometric stage ThorLabs TTR001 7X-45X Binocular Stereo Zoom Microscope with Double Arm Boom Stand AmScope SKU: SM-4B Infrared Camera ELP USB100W05MT-DL36
Adhesive:Article Title: In vivo imaging in transgenic songbirds reveals superdiffusive neuron migration in the adult brain.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rabbit polyclonal anti-GFP (1:400 dilution) Millipore Sigma RRID: AB_3080 mouse monoclonal anti-NeuN (1:500 dilution) Millipore Sigma MAB377, clone A60; RRID: AB_2298772 mouse monoclonal anti-DCX (1:400 dilution) Santa Cruz Biotechnology sc-271390 (E 6); RRID:AB_10610966 mouse monoclonal anti-Vimentin (40E-C-s) (1:10 dilution) Developmental Studies Hybridoma Bank RRID: AB_528504 a mouse monoclonal anti-HuC/HuD (1:500 dilution) Thermo Fisher Scientific A-21271; RRID:AB_221448 Alexa Fluor 488 conjugated goat anti-rabbit (1:500 or 1:1000 dilution) Abcam AB150077; RRID:AB_2630356 Alexa Fluor 555 conjugated goat anti-mouse (1:1000 dilution) Invitrogen A-21422; RRID:AB_2535844 Chemicals, peptides, and recombinant proteins SR-101 Invitrogen S359 Euthasol Virbac N/A Triton X-100 Sigma CAS: 9036-19-5 Sterilized EBSS Worthington Biochemical LK003188 Hybridization buffer Molecular Instruments N/A Vectashield Antifade Mounting Medium DAPI Vector Laboratories, Inc. H-1200-10 UV-curing Optical Adhesive Norland Products NOA61 Critical commercial assays UBC-GFP Zebra finch genome sequencing (with Illumina NGS) LC Sciences (Houston, TX) N/A Genomic DNA extraction and purification kit New England Biolabs NEB #T3010 Deposited Data Transgenic UBC-GFP Zebra finch genome This study SRA: PRJNA1061303 (https://www.ncbi.nlm.nih.gov/sra/PRJNA1061303) Cell migration data and analysis code This study Zenodo: (https://github.com/naomish1230/Transgenicsongbird-neuron-migration) Experimental models: Organisms/strains UBC-GFP transgenic zebra finches Agate et al.12 (bred in-house at Boston University) N/A Oligonucleotides GAD1 Molecular Instruments (custom probe, RefSeq: XM_002198498) VGLUT2 Molecular Instruments (custom probe, RefSeq: NM_012000.1) PDGFRA Molecular Instruments (custom probe, RefSeq: XM_030271078) CSF1R Molecular Instruments (custom probe, RefSeq: NM_001193260.1) UTS2B Molecular Instruments (custom probe, RefSeq: XM_0308048.3) SLC15A2 Molecular Instruments (custom probe, RefSeq: XM_030277156) Software and algorithms FIJI Schindelin et al.85 (https://github.com/fiji) RRID:SCR_002285 MATLAB Mathworks RRID:SCR_001622 Prairie View Bruker RRID:SCR_017142 (Continued on next page) 18 Cell Reports 43, 113759, February 27, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Other Glass micro-hematocrit capillary tube Thomas Scientific 1202K16 Small bird stereotaxic frame Kopf Instruments Model 940 digital stereotaxic instrument with model 914 and 914T small bird adapter Borosilicate capillary tubes Drummond Scientific N/A (100/VL – 3.500 length) Small diameter round coverglass, #1 thickness, 3 mm diameter Thomas Scientific 1217N66 Stainless steel cannula Ziggy’s Tubes and Wires N/A (custom: 304 S/S Tubing; 12500 OD x .11500 ID x 0.01900) 1.5 mm micro-prism with reflective hypotenuse Tower Optical Corporation Part Number: 4531-0023 (https://www.toweroptical.com/micro-prisms/) Micro-knife Fine Science Tools Item No. 10316-14 Custom kinematic headplate Kim et al.16 N/A Sterile 1.5 mm biopsy punch Royaltek BP15 Vibratome Leica VT1000S Confocal Microscope Zeiss LSM800 2P Microscope system Bruker Corporation N/A Goniometric stage ThorLabs TTR001 7X-45X Binocular Stereo Zoom Microscope with Double Arm Boom Stand AmScope SKU: SM-4B Infrared Camera ELP USB100W05MT-DL36
Sequencing:Article Title: In vivo imaging in transgenic songbirds reveals superdiffusive neuron migration in the adult brain.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rabbit polyclonal anti-GFP (1:400 dilution) Millipore Sigma RRID: AB_3080 mouse monoclonal anti-NeuN (1:500 dilution) Millipore Sigma MAB377, clone A60; RRID: AB_2298772 mouse monoclonal anti-DCX (1:400 dilution) Santa Cruz Biotechnology sc-271390 (E 6); RRID:AB_10610966 mouse monoclonal anti-Vimentin (40E-C-s) (1:10 dilution) Developmental Studies Hybridoma Bank RRID: AB_528504 a mouse monoclonal anti-HuC/HuD (1:500 dilution) Thermo Fisher Scientific A-21271; RRID:AB_221448 Alexa Fluor 488 conjugated goat anti-rabbit (1:500 or 1:1000 dilution) Abcam AB150077; RRID:AB_2630356 Alexa Fluor 555 conjugated goat anti-mouse (1:1000 dilution) Invitrogen A-21422; RRID:AB_2535844 Chemicals, peptides, and recombinant proteins SR-101 Invitrogen S359 Euthasol Virbac N/A Triton X-100 Sigma CAS: 9036-19-5 Sterilized EBSS Worthington Biochemical LK003188 Hybridization buffer Molecular Instruments N/A Vectashield Antifade Mounting Medium DAPI Vector Laboratories, Inc. H-1200-10 UV-curing Optical Adhesive Norland Products NOA61 Critical commercial assays UBC-GFP Zebra finch genome sequencing (with Illumina NGS) LC Sciences (Houston, TX) N/A Genomic DNA extraction and purification kit New England Biolabs NEB #T3010 Deposited Data Transgenic UBC-GFP Zebra finch genome This study SRA: PRJNA1061303 (https://www.ncbi.nlm.nih.gov/sra/PRJNA1061303) Cell migration data and analysis code This study Zenodo: (https://github.com/naomish1230/Transgenicsongbird-neuron-migration) Experimental models: Organisms/strains UBC-GFP transgenic zebra finches Agate et al.12 (bred in-house at Boston University) N/A Oligonucleotides GAD1 Molecular Instruments (custom probe, RefSeq: XM_002198498) VGLUT2 Molecular Instruments (custom probe, RefSeq: NM_012000.1) PDGFRA Molecular Instruments (custom probe, RefSeq: XM_030271078) CSF1R Molecular Instruments (custom probe, RefSeq: NM_001193260.1) UTS2B Molecular Instruments (custom probe, RefSeq: XM_0308048.3) SLC15A2 Molecular Instruments (custom probe, RefSeq: XM_030277156) Software and algorithms FIJI Schindelin et al.85 (https://github.com/fiji) RRID:SCR_002285 MATLAB Mathworks RRID:SCR_001622 Prairie View Bruker RRID:SCR_017142 (Continued on next page) 18 Cell Reports 43, 113759, February 27, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Other Glass micro-hematocrit capillary tube Thomas Scientific 1202K16 Small bird stereotaxic frame Kopf Instruments Model 940 digital stereotaxic instrument with model 914 and 914T small bird adapter Borosilicate capillary tubes Drummond Scientific N/A (100/VL – 3.500 length) Small diameter round coverglass, #1 thickness, 3 mm diameter Thomas Scientific 1217N66 Stainless steel cannula Ziggy’s Tubes and Wires N/A (custom: 304 S/S Tubing; 12500 OD x .11500 ID x 0.01900) 1.5 mm micro-prism with reflective hypotenuse Tower Optical Corporation Part Number: 4531-0023 (https://www.toweroptical.com/micro-prisms/) Micro-knife Fine Science Tools Item No. 10316-14 Custom kinematic headplate Kim et al.16 N/A Sterile 1.5 mm biopsy punch Royaltek BP15 Vibratome Leica VT1000S Confocal Microscope Zeiss LSM800 2P Microscope system Bruker Corporation N/A Goniometric stage ThorLabs TTR001 7X-45X Binocular Stereo Zoom Microscope with Double Arm Boom Stand AmScope SKU: SM-4B Infrared Camera ELP USB100W05MT-DL36
Next-Generation Sequencing:Article Title: In vivo imaging in transgenic songbirds reveals superdiffusive neuron migration in the adult brain.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rabbit polyclonal anti-GFP (1:400 dilution) Millipore Sigma RRID: AB_3080 mouse monoclonal anti-NeuN (1:500 dilution) Millipore Sigma MAB377, clone A60; RRID: AB_2298772 mouse monoclonal anti-DCX (1:400 dilution) Santa Cruz Biotechnology sc-271390 (E 6); RRID:AB_10610966 mouse monoclonal anti-Vimentin (40E-C-s) (1:10 dilution) Developmental Studies Hybridoma Bank RRID: AB_528504 a mouse monoclonal anti-HuC/HuD (1:500 dilution) Thermo Fisher Scientific A-21271; RRID:AB_221448 Alexa Fluor 488 conjugated goat anti-rabbit (1:500 or 1:1000 dilution) Abcam AB150077; RRID:AB_2630356 Alexa Fluor 555 conjugated goat anti-mouse (1:1000 dilution) Invitrogen A-21422; RRID:AB_2535844 Chemicals, peptides, and recombinant proteins SR-101 Invitrogen S359 Euthasol Virbac N/A Triton X-100 Sigma CAS: 9036-19-5 Sterilized EBSS Worthington Biochemical LK003188 Hybridization buffer Molecular Instruments N/A Vectashield Antifade Mounting Medium DAPI Vector Laboratories, Inc. H-1200-10 UV-curing Optical Adhesive Norland Products NOA61 Critical commercial assays UBC-GFP Zebra finch genome sequencing (with Illumina NGS) LC Sciences (Houston, TX) N/A Genomic DNA extraction and purification kit New England Biolabs NEB #T3010 Deposited Data Transgenic UBC-GFP Zebra finch genome This study SRA: PRJNA1061303 (https://www.ncbi.nlm.nih.gov/sra/PRJNA1061303) Cell migration data and analysis code This study Zenodo: (https://github.com/naomish1230/Transgenicsongbird-neuron-migration) Experimental models: Organisms/strains UBC-GFP transgenic zebra finches Agate et al.12 (bred in-house at Boston University) N/A Oligonucleotides GAD1 Molecular Instruments (custom probe, RefSeq: XM_002198498) VGLUT2 Molecular Instruments (custom probe, RefSeq: NM_012000.1) PDGFRA Molecular Instruments (custom probe, RefSeq: XM_030271078) CSF1R Molecular Instruments (custom probe, RefSeq: NM_001193260.1) UTS2B Molecular Instruments (custom probe, RefSeq: XM_0308048.3) SLC15A2 Molecular Instruments (custom probe, RefSeq: XM_030277156) Software and algorithms FIJI Schindelin et al.85 (https://github.com/fiji) RRID:SCR_002285 MATLAB Mathworks RRID:SCR_001622 Prairie View Bruker RRID:SCR_017142 (Continued on next page) 18 Cell Reports 43, 113759, February 27, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Other Glass micro-hematocrit capillary tube Thomas Scientific 1202K16 Small bird stereotaxic frame Kopf Instruments Model 940 digital stereotaxic instrument with model 914 and 914T small bird adapter Borosilicate capillary tubes Drummond Scientific N/A (100/VL – 3.500 length) Small diameter round coverglass, #1 thickness, 3 mm diameter Thomas Scientific 1217N66 Stainless steel cannula Ziggy’s Tubes and Wires N/A (custom: 304 S/S Tubing; 12500 OD x .11500 ID x 0.01900) 1.5 mm micro-prism with reflective hypotenuse Tower Optical Corporation Part Number: 4531-0023 (https://www.toweroptical.com/micro-prisms/) Micro-knife Fine Science Tools Item No. 10316-14 Custom kinematic headplate Kim et al.16 N/A Sterile 1.5 mm biopsy punch Royaltek BP15 Vibratome Leica VT1000S Confocal Microscope Zeiss LSM800 2P Microscope system Bruker Corporation N/A Goniometric stage ThorLabs TTR001 7X-45X Binocular Stereo Zoom Microscope with Double Arm Boom Stand AmScope SKU: SM-4B Infrared Camera ELP USB100W05MT-DL36
DNA Extraction:Article Title: In vivo imaging in transgenic songbirds reveals superdiffusive neuron migration in the adult brain.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rabbit polyclonal anti-GFP (1:400 dilution) Millipore Sigma RRID: AB_3080 mouse monoclonal anti-NeuN (1:500 dilution) Millipore Sigma MAB377, clone A60; RRID: AB_2298772 mouse monoclonal anti-DCX (1:400 dilution) Santa Cruz Biotechnology sc-271390 (E 6); RRID:AB_10610966 mouse monoclonal anti-Vimentin (40E-C-s) (1:10 dilution) Developmental Studies Hybridoma Bank RRID: AB_528504 a mouse monoclonal anti-HuC/HuD (1:500 dilution) Thermo Fisher Scientific A-21271; RRID:AB_221448 Alexa Fluor 488 conjugated goat anti-rabbit (1:500 or 1:1000 dilution) Abcam AB150077; RRID:AB_2630356 Alexa Fluor 555 conjugated goat anti-mouse (1:1000 dilution) Invitrogen A-21422; RRID:AB_2535844 Chemicals, peptides, and recombinant proteins SR-101 Invitrogen S359 Euthasol Virbac N/A Triton X-100 Sigma CAS: 9036-19-5 Sterilized EBSS Worthington Biochemical LK003188 Hybridization buffer Molecular Instruments N/A Vectashield Antifade Mounting Medium DAPI Vector Laboratories, Inc. H-1200-10 UV-curing Optical Adhesive Norland Products NOA61 Critical commercial assays UBC-GFP Zebra finch genome sequencing (with Illumina NGS) LC Sciences (Houston, TX) N/A Genomic DNA extraction and purification kit New England Biolabs NEB #T3010 Deposited Data Transgenic UBC-GFP Zebra finch genome This study SRA: PRJNA1061303 (https://www.ncbi.nlm.nih.gov/sra/PRJNA1061303) Cell migration data and analysis code This study Zenodo: (https://github.com/naomish1230/Transgenicsongbird-neuron-migration) Experimental models: Organisms/strains UBC-GFP transgenic zebra finches Agate et al.12 (bred in-house at Boston University) N/A Oligonucleotides GAD1 Molecular Instruments (custom probe, RefSeq: XM_002198498) VGLUT2 Molecular Instruments (custom probe, RefSeq: NM_012000.1) PDGFRA Molecular Instruments (custom probe, RefSeq: XM_030271078) CSF1R Molecular Instruments (custom probe, RefSeq: NM_001193260.1) UTS2B Molecular Instruments (custom probe, RefSeq: XM_0308048.3) SLC15A2 Molecular Instruments (custom probe, RefSeq: XM_030277156) Software and algorithms FIJI Schindelin et al.85 (https://github.com/fiji) RRID:SCR_002285 MATLAB Mathworks RRID:SCR_001622 Prairie View Bruker RRID:SCR_017142 (Continued on next page) 18 Cell Reports 43, 113759, February 27, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Other Glass micro-hematocrit capillary tube Thomas Scientific 1202K16 Small bird stereotaxic frame Kopf Instruments Model 940 digital stereotaxic instrument with model 914 and 914T small bird adapter Borosilicate capillary tubes Drummond Scientific N/A (100/VL – 3.500 length) Small diameter round coverglass, #1 thickness, 3 mm diameter Thomas Scientific 1217N66 Stainless steel cannula Ziggy’s Tubes and Wires N/A (custom: 304 S/S Tubing; 12500 OD x .11500 ID x 0.01900) 1.5 mm micro-prism with reflective hypotenuse Tower Optical Corporation Part Number: 4531-0023 (https://www.toweroptical.com/micro-prisms/) Micro-knife Fine Science Tools Item No. 10316-14 Custom kinematic headplate Kim et al.16 N/A Sterile 1.5 mm biopsy punch Royaltek BP15 Vibratome Leica VT1000S Confocal Microscope Zeiss LSM800 2P Microscope system Bruker Corporation N/A Goniometric stage ThorLabs TTR001 7X-45X Binocular Stereo Zoom Microscope with Double Arm Boom Stand AmScope SKU: SM-4B Infrared Camera ELP USB100W05MT-DL36
Purification:Article Title: In vivo imaging in transgenic songbirds reveals superdiffusive neuron migration in the adult brain.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rabbit polyclonal anti-GFP (1:400 dilution) Millipore Sigma RRID: AB_3080 mouse monoclonal anti-NeuN (1:500 dilution) Millipore Sigma MAB377, clone A60; RRID: AB_2298772 mouse monoclonal anti-DCX (1:400 dilution) Santa Cruz Biotechnology sc-271390 (E 6); RRID:AB_10610966 mouse monoclonal anti-Vimentin (40E-C-s) (1:10 dilution) Developmental Studies Hybridoma Bank RRID: AB_528504 a mouse monoclonal anti-HuC/HuD (1:500 dilution) Thermo Fisher Scientific A-21271; RRID:AB_221448 Alexa Fluor 488 conjugated goat anti-rabbit (1:500 or 1:1000 dilution) Abcam AB150077; RRID:AB_2630356 Alexa Fluor 555 conjugated goat anti-mouse (1:1000 dilution) Invitrogen A-21422; RRID:AB_2535844 Chemicals, peptides, and recombinant proteins SR-101 Invitrogen S359 Euthasol Virbac N/A Triton X-100 Sigma CAS: 9036-19-5 Sterilized EBSS Worthington Biochemical LK003188 Hybridization buffer Molecular Instruments N/A Vectashield Antifade Mounting Medium DAPI Vector Laboratories, Inc. H-1200-10 UV-curing Optical Adhesive Norland Products NOA61 Critical commercial assays UBC-GFP Zebra finch genome sequencing (with Illumina NGS) LC Sciences (Houston, TX) N/A Genomic DNA extraction and purification kit New England Biolabs NEB #T3010 Deposited Data Transgenic UBC-GFP Zebra finch genome This study SRA: PRJNA1061303 (https://www.ncbi.nlm.nih.gov/sra/PRJNA1061303) Cell migration data and analysis code This study Zenodo: (https://github.com/naomish1230/Transgenicsongbird-neuron-migration) Experimental models: Organisms/strains UBC-GFP transgenic zebra finches Agate et al.12 (bred in-house at Boston University) N/A Oligonucleotides GAD1 Molecular Instruments (custom probe, RefSeq: XM_002198498) VGLUT2 Molecular Instruments (custom probe, RefSeq: NM_012000.1) PDGFRA Molecular Instruments (custom probe, RefSeq: XM_030271078) CSF1R Molecular Instruments (custom probe, RefSeq: NM_001193260.1) UTS2B Molecular Instruments (custom probe, RefSeq: XM_0308048.3) SLC15A2 Molecular Instruments (custom probe, RefSeq: XM_030277156) Software and algorithms FIJI Schindelin et al.85 (https://github.com/fiji) RRID:SCR_002285 MATLAB Mathworks RRID:SCR_001622 Prairie View Bruker RRID:SCR_017142 (Continued on next page) 18 Cell Reports 43, 113759, February 27, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Other Glass micro-hematocrit capillary tube Thomas Scientific 1202K16 Small bird stereotaxic frame Kopf Instruments Model 940 digital stereotaxic instrument with model 914 and 914T small bird adapter Borosilicate capillary tubes Drummond Scientific N/A (100/VL – 3.500 length) Small diameter round coverglass, #1 thickness, 3 mm diameter Thomas Scientific 1217N66 Stainless steel cannula Ziggy’s Tubes and Wires N/A (custom: 304 S/S Tubing; 12500 OD x .11500 ID x 0.01900) 1.5 mm micro-prism with reflective hypotenuse Tower Optical Corporation Part Number: 4531-0023 (https://www.toweroptical.com/micro-prisms/) Micro-knife Fine Science Tools Item No. 10316-14 Custom kinematic headplate Kim et al.16 N/A Sterile 1.5 mm biopsy punch Royaltek BP15 Vibratome Leica VT1000S Confocal Microscope Zeiss LSM800 2P Microscope system Bruker Corporation N/A Goniometric stage ThorLabs TTR001 7X-45X Binocular Stereo Zoom Microscope with Double Arm Boom Stand AmScope SKU: SM-4B Infrared Camera ELP USB100W05MT-DL36
Transgenic Assay:Article Title: In vivo imaging in transgenic songbirds reveals superdiffusive neuron migration in the adult brain.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rabbit polyclonal anti-GFP (1:400 dilution) Millipore Sigma RRID: AB_3080 mouse monoclonal anti-NeuN (1:500 dilution) Millipore Sigma MAB377, clone A60; RRID: AB_2298772 mouse monoclonal anti-DCX (1:400 dilution) Santa Cruz Biotechnology sc-271390 (E 6); RRID:AB_10610966 mouse monoclonal anti-Vimentin (40E-C-s) (1:10 dilution) Developmental Studies Hybridoma Bank RRID: AB_528504 a mouse monoclonal anti-HuC/HuD (1:500 dilution) Thermo Fisher Scientific A-21271; RRID:AB_221448 Alexa Fluor 488 conjugated goat anti-rabbit (1:500 or 1:1000 dilution) Abcam AB150077; RRID:AB_2630356 Alexa Fluor 555 conjugated goat anti-mouse (1:1000 dilution) Invitrogen A-21422; RRID:AB_2535844 Chemicals, peptides, and recombinant proteins SR-101 Invitrogen S359 Euthasol Virbac N/A Triton X-100 Sigma CAS: 9036-19-5 Sterilized EBSS Worthington Biochemical LK003188 Hybridization buffer Molecular Instruments N/A Vectashield Antifade Mounting Medium DAPI Vector Laboratories, Inc. H-1200-10 UV-curing Optical Adhesive Norland Products NOA61 Critical commercial assays UBC-GFP Zebra finch genome sequencing (with Illumina NGS) LC Sciences (Houston, TX) N/A Genomic DNA extraction and purification kit New England Biolabs NEB #T3010 Deposited Data Transgenic UBC-GFP Zebra finch genome This study SRA: PRJNA1061303 (https://www.ncbi.nlm.nih.gov/sra/PRJNA1061303) Cell migration data and analysis code This study Zenodo: (https://github.com/naomish1230/Transgenicsongbird-neuron-migration) Experimental models: Organisms/strains UBC-GFP transgenic zebra finches Agate et al.12 (bred in-house at Boston University) N/A Oligonucleotides GAD1 Molecular Instruments (custom probe, RefSeq: XM_002198498) VGLUT2 Molecular Instruments (custom probe, RefSeq: NM_012000.1) PDGFRA Molecular Instruments (custom probe, RefSeq: XM_030271078) CSF1R Molecular Instruments (custom probe, RefSeq: NM_001193260.1) UTS2B Molecular Instruments (custom probe, RefSeq: XM_0308048.3) SLC15A2 Molecular Instruments (custom probe, RefSeq: XM_030277156) Software and algorithms FIJI Schindelin et al.85 (https://github.com/fiji) RRID:SCR_002285 MATLAB Mathworks RRID:SCR_001622 Prairie View Bruker RRID:SCR_017142 (Continued on next page) 18 Cell Reports 43, 113759, February 27, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Other Glass micro-hematocrit capillary tube Thomas Scientific 1202K16 Small bird stereotaxic frame Kopf Instruments Model 940 digital stereotaxic instrument with model 914 and 914T small bird adapter Borosilicate capillary tubes Drummond Scientific N/A (100/VL – 3.500 length) Small diameter round coverglass, #1 thickness, 3 mm diameter Thomas Scientific 1217N66 Stainless steel cannula Ziggy’s Tubes and Wires N/A (custom: 304 S/S Tubing; 12500 OD x .11500 ID x 0.01900) 1.5 mm micro-prism with reflective hypotenuse Tower Optical Corporation Part Number: 4531-0023 (https://www.toweroptical.com/micro-prisms/) Micro-knife Fine Science Tools Item No. 10316-14 Custom kinematic headplate Kim et al.16 N/A Sterile 1.5 mm biopsy punch Royaltek BP15 Vibratome Leica VT1000S Confocal Microscope Zeiss LSM800 2P Microscope system Bruker Corporation N/A Goniometric stage ThorLabs TTR001 7X-45X Binocular Stereo Zoom Microscope with Double Arm Boom Stand AmScope SKU: SM-4B Infrared Camera ELP USB100W05MT-DL36
Migration:Article Title: In vivo imaging in transgenic songbirds reveals superdiffusive neuron migration in the adult brain.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rabbit polyclonal anti-GFP (1:400 dilution) Millipore Sigma RRID: AB_3080 mouse monoclonal anti-NeuN (1:500 dilution) Millipore Sigma MAB377, clone A60; RRID: AB_2298772 mouse monoclonal anti-DCX (1:400 dilution) Santa Cruz Biotechnology sc-271390 (E 6); RRID:AB_10610966 mouse monoclonal anti-Vimentin (40E-C-s) (1:10 dilution) Developmental Studies Hybridoma Bank RRID: AB_528504 a mouse monoclonal anti-HuC/HuD (1:500 dilution) Thermo Fisher Scientific A-21271; RRID:AB_221448 Alexa Fluor 488 conjugated goat anti-rabbit (1:500 or 1:1000 dilution) Abcam AB150077; RRID:AB_2630356 Alexa Fluor 555 conjugated goat anti-mouse (1:1000 dilution) Invitrogen A-21422; RRID:AB_2535844 Chemicals, peptides, and recombinant proteins SR-101 Invitrogen S359 Euthasol Virbac N/A Triton X-100 Sigma CAS: 9036-19-5 Sterilized EBSS Worthington Biochemical LK003188 Hybridization buffer Molecular Instruments N/A Vectashield Antifade Mounting Medium DAPI Vector Laboratories, Inc. H-1200-10 UV-curing Optical Adhesive Norland Products NOA61 Critical commercial assays UBC-GFP Zebra finch genome sequencing (with Illumina NGS) LC Sciences (Houston, TX) N/A Genomic DNA extraction and purification kit New England Biolabs NEB #T3010 Deposited Data Transgenic UBC-GFP Zebra finch genome This study SRA: PRJNA1061303 (https://www.ncbi.nlm.nih.gov/sra/PRJNA1061303) Cell migration data and analysis code This study Zenodo: (https://github.com/naomish1230/Transgenicsongbird-neuron-migration) Experimental models: Organisms/strains UBC-GFP transgenic zebra finches Agate et al.12 (bred in-house at Boston University) N/A Oligonucleotides GAD1 Molecular Instruments (custom probe, RefSeq: XM_002198498) VGLUT2 Molecular Instruments (custom probe, RefSeq: NM_012000.1) PDGFRA Molecular Instruments (custom probe, RefSeq: XM_030271078) CSF1R Molecular Instruments (custom probe, RefSeq: NM_001193260.1) UTS2B Molecular Instruments (custom probe, RefSeq: XM_0308048.3) SLC15A2 Molecular Instruments (custom probe, RefSeq: XM_030277156) Software and algorithms FIJI Schindelin et al.85 (https://github.com/fiji) RRID:SCR_002285 MATLAB Mathworks RRID:SCR_001622 Prairie View Bruker RRID:SCR_017142 (Continued on next page) 18 Cell Reports 43, 113759, February 27, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Other Glass micro-hematocrit capillary tube Thomas Scientific 1202K16 Small bird stereotaxic frame Kopf Instruments Model 940 digital stereotaxic instrument with model 914 and 914T small bird adapter Borosilicate capillary tubes Drummond Scientific N/A (100/VL – 3.500 length) Small diameter round coverglass, #1 thickness, 3 mm diameter Thomas Scientific 1217N66 Stainless steel cannula Ziggy’s Tubes and Wires N/A (custom: 304 S/S Tubing; 12500 OD x .11500 ID x 0.01900) 1.5 mm micro-prism with reflective hypotenuse Tower Optical Corporation Part Number: 4531-0023 (https://www.toweroptical.com/micro-prisms/) Micro-knife Fine Science Tools Item No. 10316-14 Custom kinematic headplate Kim et al.16 N/A Sterile 1.5 mm biopsy punch Royaltek BP15 Vibratome Leica VT1000S Confocal Microscope Zeiss LSM800 2P Microscope system Bruker Corporation N/A Goniometric stage ThorLabs TTR001 7X-45X Binocular Stereo Zoom Microscope with Double Arm Boom Stand AmScope SKU: SM-4B Infrared Camera ELP USB100W05MT-DL36
Software:Article Title: In vivo imaging in transgenic songbirds reveals superdiffusive neuron migration in the adult brain.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rabbit polyclonal anti-GFP (1:400 dilution) Millipore Sigma RRID: AB_3080 mouse monoclonal anti-NeuN (1:500 dilution) Millipore Sigma MAB377, clone A60; RRID: AB_2298772 mouse monoclonal anti-DCX (1:400 dilution) Santa Cruz Biotechnology sc-271390 (E 6); RRID:AB_10610966 mouse monoclonal anti-Vimentin (40E-C-s) (1:10 dilution) Developmental Studies Hybridoma Bank RRID: AB_528504 a mouse monoclonal anti-HuC/HuD (1:500 dilution) Thermo Fisher Scientific A-21271; RRID:AB_221448 Alexa Fluor 488 conjugated goat anti-rabbit (1:500 or 1:1000 dilution) Abcam AB150077; RRID:AB_2630356 Alexa Fluor 555 conjugated goat anti-mouse (1:1000 dilution) Invitrogen A-21422; RRID:AB_2535844 Chemicals, peptides, and recombinant proteins SR-101 Invitrogen S359 Euthasol Virbac N/A Triton X-100 Sigma CAS: 9036-19-5 Sterilized EBSS Worthington Biochemical LK003188 Hybridization buffer Molecular Instruments N/A Vectashield Antifade Mounting Medium DAPI Vector Laboratories, Inc. H-1200-10 UV-curing Optical Adhesive Norland Products NOA61 Critical commercial assays UBC-GFP Zebra finch genome sequencing (with Illumina NGS) LC Sciences (Houston, TX) N/A Genomic DNA extraction and purification kit New England Biolabs NEB #T3010 Deposited Data Transgenic UBC-GFP Zebra finch genome This study SRA: PRJNA1061303 (https://www.ncbi.nlm.nih.gov/sra/PRJNA1061303) Cell migration data and analysis code This study Zenodo: (https://github.com/naomish1230/Transgenicsongbird-neuron-migration) Experimental models: Organisms/strains UBC-GFP transgenic zebra finches Agate et al.12 (bred in-house at Boston University) N/A Oligonucleotides GAD1 Molecular Instruments (custom probe, RefSeq: XM_002198498) VGLUT2 Molecular Instruments (custom probe, RefSeq: NM_012000.1) PDGFRA Molecular Instruments (custom probe, RefSeq: XM_030271078) CSF1R Molecular Instruments (custom probe, RefSeq: NM_001193260.1) UTS2B Molecular Instruments (custom probe, RefSeq: XM_0308048.3) SLC15A2 Molecular Instruments (custom probe, RefSeq: XM_030277156) Software and algorithms FIJI Schindelin et al.85 (https://github.com/fiji) RRID:SCR_002285 MATLAB Mathworks RRID:SCR_001622 Prairie View Bruker RRID:SCR_017142 (Continued on next page) 18 Cell Reports 43, 113759, February 27, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Other Glass micro-hematocrit capillary tube Thomas Scientific 1202K16 Small bird stereotaxic frame Kopf Instruments Model 940 digital stereotaxic instrument with model 914 and 914T small bird adapter Borosilicate capillary tubes Drummond Scientific N/A (100/VL – 3.500 length) Small diameter round coverglass, #1 thickness, 3 mm diameter Thomas Scientific 1217N66 Stainless steel cannula Ziggy’s Tubes and Wires N/A (custom: 304 S/S Tubing; 12500 OD x .11500 ID x 0.01900) 1.5 mm micro-prism with reflective hypotenuse Tower Optical Corporation Part Number: 4531-0023 (https://www.toweroptical.com/micro-prisms/) Micro-knife Fine Science Tools Item No. 10316-14 Custom kinematic headplate Kim et al.16 N/A Sterile 1.5 mm biopsy punch Royaltek BP15 Vibratome Leica VT1000S Confocal Microscope Zeiss LSM800 2P Microscope system Bruker Corporation N/A Goniometric stage ThorLabs TTR001 7X-45X Binocular Stereo Zoom Microscope with Double Arm Boom Stand AmScope SKU: SM-4B Infrared Camera ELP USB100W05MT-DL36
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