Virus:Article Title: Angiogenesis in the mature mouse cortex is governed in a regional- and Notch1-dependent manner.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rat anti-CD31 BD Biosciences Cat #553370 sheep anti-CD93 R&D Systems Cat #AF1696 donkey anti-rat (Cy5) Invitrogen Cat #A10523 donkey anti-sheep (Alexa 488) Thermo Fisher Cat #A-11015 Bacterial and virus strains AAV-BR1-iCre Dr. J.Körbelin’s laboratory48 N/A AAV-BR1-eGFP Dr. J.Körbelin’s laboratory48 N/A Chemicals, peptides, and recombinant proteins dexamethasone Vetoquinol DIN: 00617210 lidocaine Hikma Canada Limited DIN: 02422026 FITC-dextran Sigma Aldrich Cat #46945 Texas Red dextran Thermo Fisher Cat #D1830 euthanyl Bimedia-MTC Animal Health Inc. DIN: 00141704 DNase treatment Qiagen Cat #79254 HBSS Thermo Fisher Cat #14175095 Auto-MACS Rinsing Solution Miltenyi Biotec Cat #130-091-222 BSA Miltenyi Biotec Cat #130-091-376 Critical commercial assays RNeasy Mini Kit Qiagen Cat #73104 High-Capacity cDNA synthesis kit Applied Biosystems Cat #4368814 SYBR Green Master Mix Applied Biosystems Cat #4309155 Adult Brain Dissociation Kit Miltenyi Biotec Cat #130-107-677 Myelin Removal Kit Miltenyi Biotec Cat #130-042-401 Deposited data Primer-Blast National Library of Medicine Primer designing tool (nih.gov) Primer Bank Harvard University PrimerBank (harvard.edu) Genome Browser University of California Santa Cruz UCSC Genome Browser Gateway Bulk endothelial RNA seq dataset This paper SRA data: PRJNA1179510 Experimental models: Organisms/strains mouse: C57BL/6J Jackson Laboratories RRID:IMSR_JAX:000664 mouse: Vegfr2/Flk1 Dr. Jane Rossant N/A mouse: Notch1flox Jackson Laboratories RRID:IMSR_JAX:007181 mouse: Ai9 Jackson Laboratories RRID:IMSR_JAX:007909 Oligonucleotides Primers for RT-qPCR are listed in Table S1 – – Software and algorithms Fiji software (ImageJ 1.53q) National Institute of Health Fiji Downloads (imagej.net) BrainVision SciMedia BV Workbench | Data Acquisition/Analysis Software for Neuro/Cardiac Imaging (scimedia.com) Fluoview FV10-ASW software Olympus Corp. – Python 3.9.12 Python Software Foundation Python Release Python 3.9.12 | Python.org Seaborn KDE package Seaborn seaborn.kdeplot — seaborn 0.13.2 documentation (pydata.org) (Continued on next page) Cell Reports 43, 115029, December 24, 2024 13 .. REAGENT or RESOURCE SOURCE IDENTIFIER Jupyter notebook Project Jupyter https://jupyter.org/ Prism (v7 & 8) GraphPad Software RRID:SCR_002798 featureCounts v1.5.0-p3 featureCounts – DESeq2R package (1.20.0) Bioconductor – Other CD31 microbeads Miltenyi Biotech Cat #130-097-418 CD45 microbeads Miltenyi Biotech Cat #130-052-301
Bioprocessing:Article Title: Angiogenesis in the mature mouse cortex is governed in a regional- and Notch1-dependent manner.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rat anti-CD31 BD Biosciences Cat #553370 sheep anti-CD93 R&D Systems Cat #AF1696 donkey anti-rat (Cy5) Invitrogen Cat #A10523 donkey anti-sheep (Alexa 488) Thermo Fisher Cat #A-11015 Bacterial and virus strains AAV-BR1-iCre Dr. J.Körbelin’s laboratory48 N/A AAV-BR1-eGFP Dr. J.Körbelin’s laboratory48 N/A Chemicals, peptides, and recombinant proteins dexamethasone Vetoquinol DIN: 00617210 lidocaine Hikma Canada Limited DIN: 02422026 FITC-dextran Sigma Aldrich Cat #46945 Texas Red dextran Thermo Fisher Cat #D1830 euthanyl Bimedia-MTC Animal Health Inc. DIN: 00141704 DNase treatment Qiagen Cat #79254 HBSS Thermo Fisher Cat #14175095 Auto-MACS Rinsing Solution Miltenyi Biotec Cat #130-091-222 BSA Miltenyi Biotec Cat #130-091-376 Critical commercial assays RNeasy Mini Kit Qiagen Cat #73104 High-Capacity cDNA synthesis kit Applied Biosystems Cat #4368814 SYBR Green Master Mix Applied Biosystems Cat #4309155 Adult Brain Dissociation Kit Miltenyi Biotec Cat #130-107-677 Myelin Removal Kit Miltenyi Biotec Cat #130-042-401 Deposited data Primer-Blast National Library of Medicine Primer designing tool (nih.gov) Primer Bank Harvard University PrimerBank (harvard.edu) Genome Browser University of California Santa Cruz UCSC Genome Browser Gateway Bulk endothelial RNA seq dataset This paper SRA data: PRJNA1179510 Experimental models: Organisms/strains mouse: C57BL/6J Jackson Laboratories RRID:IMSR_JAX:000664 mouse: Vegfr2/Flk1 Dr. Jane Rossant N/A mouse: Notch1flox Jackson Laboratories RRID:IMSR_JAX:007181 mouse: Ai9 Jackson Laboratories RRID:IMSR_JAX:007909 Oligonucleotides Primers for RT-qPCR are listed in Table S1 – – Software and algorithms Fiji software (ImageJ 1.53q) National Institute of Health Fiji Downloads (imagej.net) BrainVision SciMedia BV Workbench | Data Acquisition/Analysis Software for Neuro/Cardiac Imaging (scimedia.com) Fluoview FV10-ASW software Olympus Corp. – Python 3.9.12 Python Software Foundation Python Release Python 3.9.12 | Python.org Seaborn KDE package Seaborn seaborn.kdeplot — seaborn 0.13.2 documentation (pydata.org) (Continued on next page) Cell Reports 43, 115029, December 24, 2024 13 .. REAGENT or RESOURCE SOURCE IDENTIFIER Jupyter notebook Project Jupyter https://jupyter.org/ Prism (v7 & 8) GraphPad Software RRID:SCR_002798 featureCounts v1.5.0-p3 featureCounts – DESeq2R package (1.20.0) Bioconductor – Other CD31 microbeads Miltenyi Biotech Cat #130-097-418 CD45 microbeads Miltenyi Biotech Cat #130-052-301
Recombinant:Article Title: Angiogenesis in the mature mouse cortex is governed in a regional- and Notch1-dependent manner.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rat anti-CD31 BD Biosciences Cat #553370 sheep anti-CD93 R&D Systems Cat #AF1696 donkey anti-rat (Cy5) Invitrogen Cat #A10523 donkey anti-sheep (Alexa 488) Thermo Fisher Cat #A-11015 Bacterial and virus strains AAV-BR1-iCre Dr. J.Körbelin’s laboratory48 N/A AAV-BR1-eGFP Dr. J.Körbelin’s laboratory48 N/A Chemicals, peptides, and recombinant proteins dexamethasone Vetoquinol DIN: 00617210 lidocaine Hikma Canada Limited DIN: 02422026 FITC-dextran Sigma Aldrich Cat #46945 Texas Red dextran Thermo Fisher Cat #D1830 euthanyl Bimedia-MTC Animal Health Inc. DIN: 00141704 DNase treatment Qiagen Cat #79254 HBSS Thermo Fisher Cat #14175095 Auto-MACS Rinsing Solution Miltenyi Biotec Cat #130-091-222 BSA Miltenyi Biotec Cat #130-091-376 Critical commercial assays RNeasy Mini Kit Qiagen Cat #73104 High-Capacity cDNA synthesis kit Applied Biosystems Cat #4368814 SYBR Green Master Mix Applied Biosystems Cat #4309155 Adult Brain Dissociation Kit Miltenyi Biotec Cat #130-107-677 Myelin Removal Kit Miltenyi Biotec Cat #130-042-401 Deposited data Primer-Blast National Library of Medicine Primer designing tool (nih.gov) Primer Bank Harvard University PrimerBank (harvard.edu) Genome Browser University of California Santa Cruz UCSC Genome Browser Gateway Bulk endothelial RNA seq dataset This paper SRA data: PRJNA1179510 Experimental models: Organisms/strains mouse: C57BL/6J Jackson Laboratories RRID:IMSR_JAX:000664 mouse: Vegfr2/Flk1 Dr. Jane Rossant N/A mouse: Notch1flox Jackson Laboratories RRID:IMSR_JAX:007181 mouse: Ai9 Jackson Laboratories RRID:IMSR_JAX:007909 Oligonucleotides Primers for RT-qPCR are listed in Table S1 – – Software and algorithms Fiji software (ImageJ 1.53q) National Institute of Health Fiji Downloads (imagej.net) BrainVision SciMedia BV Workbench | Data Acquisition/Analysis Software for Neuro/Cardiac Imaging (scimedia.com) Fluoview FV10-ASW software Olympus Corp. – Python 3.9.12 Python Software Foundation Python Release Python 3.9.12 | Python.org Seaborn KDE package Seaborn seaborn.kdeplot — seaborn 0.13.2 documentation (pydata.org) (Continued on next page) Cell Reports 43, 115029, December 24, 2024 13 .. REAGENT or RESOURCE SOURCE IDENTIFIER Jupyter notebook Project Jupyter https://jupyter.org/ Prism (v7 & 8) GraphPad Software RRID:SCR_002798 featureCounts v1.5.0-p3 featureCounts – DESeq2R package (1.20.0) Bioconductor – Other CD31 microbeads Miltenyi Biotech Cat #130-097-418 CD45 microbeads Miltenyi Biotech Cat #130-052-301
Article Title: An automated do-it-yourself system for dynamic stem cell and organoid culture in standard multi-well plates
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit monoclonal anti-FOXA2 Abcam Cat# ab108422; RRID: AB_11157157 Goat polyclonal anti-SOX1 R&D Systems Cat# AF3369; RRID: AB_2239879 Mouse monoclonal anti-Cardiac Troponin T (cTnT) Thermo Fisher Scientific Cat# MA5-12960; RRID: AB_11000742 Chemicals, peptides, and recombinant proteins StemMACS CHIR99021 in Solution Miltenyi Biotec Cat# 130-106-539 StemMACS PD0325901 in Solution Miltenyi Biotec Cat# 130-106-541 CHIR99021 (3D gastruloid stimulation) Merck/Millipore Cat# 361559 Recombinant Human/Murine/Rat Activin A PeproTech Cat# 120-14-10 Recombinant Human bFGF Thermo Fisher Scientific Cat# 13256029 Alexa Fluor 647-Dextran, 10,000 MW Thermo Fisher Scientific Cat# D22914 Fluoresceinisothiocyanat (FITC)-Dextran, 10,000 MW Sigma Cat# FD10S CellTrace Violet Cell Proliferation Kit Thermo Fisher Scientific Cat# C34557 Experimental models: Cell lines Rex1-GFP Mouse ESCs Laboratory of Austin Smith E14Tg2a; RRID: CVCL_9108 Sox1-GFP::Brachyury-mCherry (SBr) Mouse ESCs Laboratory of David Suter CGR8, strain 129; RRID: CVCL_3987 SBr WT Mouse ESCs; Parental strain corresponding to Sox1-GFP::Brachyury-mCherry (SBr) Laboratory of David Suter CGR8, strain 129; RRID: CVCL_3987 Software and algorithms AutoCAD Autodesk https://www.autodesk.com Fiji/ImageJ Schindelin et al., 2012 RRID: SCR_002285; https://imagej.net/software/fiji/ FlowJo BD RRID: SCR_008520; https://www.flowjo.com LabVIEW v14.0 National Instruments RRID: SCR_014325; https://www.ni.com/en-us/shop/ labview.html NIS-Elements Nikon RRID: SCR_014329; https://www.nikonmetrology. com/en-us/industrial-microscopes/nis-software -nis-elements-microscope-imaging-software LabVIEW scripts for microfluidic device operation This paper, deposited on Zenodo https://doi.org/10.5281/zenodo.6579452 Fiji script to calculate gastruloid elongation indices Guiet et al., 2021 https://doi.org/10.5281/zenodo.4544369 Custom processing pipeline for quantifying fluorescent intensities (reporter gene expression levels) along gastruloid posterior-to-anterior poles This paper, deposited on Zenodo https://doi.org/10.5281/zenodo.5717752 Other Design files (AutoCAD) for microfluidic devices This paper, deposited on Zenodo https://doi.org/10.5281/zenodo.6579452 ..
cDNA Synthesis:Article Title: Angiogenesis in the mature mouse cortex is governed in a regional- and Notch1-dependent manner.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rat anti-CD31 BD Biosciences Cat #553370 sheep anti-CD93 R&D Systems Cat #AF1696 donkey anti-rat (Cy5) Invitrogen Cat #A10523 donkey anti-sheep (Alexa 488) Thermo Fisher Cat #A-11015 Bacterial and virus strains AAV-BR1-iCre Dr. J.Körbelin’s laboratory48 N/A AAV-BR1-eGFP Dr. J.Körbelin’s laboratory48 N/A Chemicals, peptides, and recombinant proteins dexamethasone Vetoquinol DIN: 00617210 lidocaine Hikma Canada Limited DIN: 02422026 FITC-dextran Sigma Aldrich Cat #46945 Texas Red dextran Thermo Fisher Cat #D1830 euthanyl Bimedia-MTC Animal Health Inc. DIN: 00141704 DNase treatment Qiagen Cat #79254 HBSS Thermo Fisher Cat #14175095 Auto-MACS Rinsing Solution Miltenyi Biotec Cat #130-091-222 BSA Miltenyi Biotec Cat #130-091-376 Critical commercial assays RNeasy Mini Kit Qiagen Cat #73104 High-Capacity cDNA synthesis kit Applied Biosystems Cat #4368814 SYBR Green Master Mix Applied Biosystems Cat #4309155 Adult Brain Dissociation Kit Miltenyi Biotec Cat #130-107-677 Myelin Removal Kit Miltenyi Biotec Cat #130-042-401 Deposited data Primer-Blast National Library of Medicine Primer designing tool (nih.gov) Primer Bank Harvard University PrimerBank (harvard.edu) Genome Browser University of California Santa Cruz UCSC Genome Browser Gateway Bulk endothelial RNA seq dataset This paper SRA data: PRJNA1179510 Experimental models: Organisms/strains mouse: C57BL/6J Jackson Laboratories RRID:IMSR_JAX:000664 mouse: Vegfr2/Flk1 Dr. Jane Rossant N/A mouse: Notch1flox Jackson Laboratories RRID:IMSR_JAX:007181 mouse: Ai9 Jackson Laboratories RRID:IMSR_JAX:007909 Oligonucleotides Primers for RT-qPCR are listed in Table S1 – – Software and algorithms Fiji software (ImageJ 1.53q) National Institute of Health Fiji Downloads (imagej.net) BrainVision SciMedia BV Workbench | Data Acquisition/Analysis Software for Neuro/Cardiac Imaging (scimedia.com) Fluoview FV10-ASW software Olympus Corp. – Python 3.9.12 Python Software Foundation Python Release Python 3.9.12 | Python.org Seaborn KDE package Seaborn seaborn.kdeplot — seaborn 0.13.2 documentation (pydata.org) (Continued on next page) Cell Reports 43, 115029, December 24, 2024 13 .. REAGENT or RESOURCE SOURCE IDENTIFIER Jupyter notebook Project Jupyter https://jupyter.org/ Prism (v7 & 8) GraphPad Software RRID:SCR_002798 featureCounts v1.5.0-p3 featureCounts – DESeq2R package (1.20.0) Bioconductor – Other CD31 microbeads Miltenyi Biotech Cat #130-097-418 CD45 microbeads Miltenyi Biotech Cat #130-052-301
SYBR Green Assay:Article Title: Angiogenesis in the mature mouse cortex is governed in a regional- and Notch1-dependent manner.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rat anti-CD31 BD Biosciences Cat #553370 sheep anti-CD93 R&D Systems Cat #AF1696 donkey anti-rat (Cy5) Invitrogen Cat #A10523 donkey anti-sheep (Alexa 488) Thermo Fisher Cat #A-11015 Bacterial and virus strains AAV-BR1-iCre Dr. J.Körbelin’s laboratory48 N/A AAV-BR1-eGFP Dr. J.Körbelin’s laboratory48 N/A Chemicals, peptides, and recombinant proteins dexamethasone Vetoquinol DIN: 00617210 lidocaine Hikma Canada Limited DIN: 02422026 FITC-dextran Sigma Aldrich Cat #46945 Texas Red dextran Thermo Fisher Cat #D1830 euthanyl Bimedia-MTC Animal Health Inc. DIN: 00141704 DNase treatment Qiagen Cat #79254 HBSS Thermo Fisher Cat #14175095 Auto-MACS Rinsing Solution Miltenyi Biotec Cat #130-091-222 BSA Miltenyi Biotec Cat #130-091-376 Critical commercial assays RNeasy Mini Kit Qiagen Cat #73104 High-Capacity cDNA synthesis kit Applied Biosystems Cat #4368814 SYBR Green Master Mix Applied Biosystems Cat #4309155 Adult Brain Dissociation Kit Miltenyi Biotec Cat #130-107-677 Myelin Removal Kit Miltenyi Biotec Cat #130-042-401 Deposited data Primer-Blast National Library of Medicine Primer designing tool (nih.gov) Primer Bank Harvard University PrimerBank (harvard.edu) Genome Browser University of California Santa Cruz UCSC Genome Browser Gateway Bulk endothelial RNA seq dataset This paper SRA data: PRJNA1179510 Experimental models: Organisms/strains mouse: C57BL/6J Jackson Laboratories RRID:IMSR_JAX:000664 mouse: Vegfr2/Flk1 Dr. Jane Rossant N/A mouse: Notch1flox Jackson Laboratories RRID:IMSR_JAX:007181 mouse: Ai9 Jackson Laboratories RRID:IMSR_JAX:007909 Oligonucleotides Primers for RT-qPCR are listed in Table S1 – – Software and algorithms Fiji software (ImageJ 1.53q) National Institute of Health Fiji Downloads (imagej.net) BrainVision SciMedia BV Workbench | Data Acquisition/Analysis Software for Neuro/Cardiac Imaging (scimedia.com) Fluoview FV10-ASW software Olympus Corp. – Python 3.9.12 Python Software Foundation Python Release Python 3.9.12 | Python.org Seaborn KDE package Seaborn seaborn.kdeplot — seaborn 0.13.2 documentation (pydata.org) (Continued on next page) Cell Reports 43, 115029, December 24, 2024 13 .. REAGENT or RESOURCE SOURCE IDENTIFIER Jupyter notebook Project Jupyter https://jupyter.org/ Prism (v7 & 8) GraphPad Software RRID:SCR_002798 featureCounts v1.5.0-p3 featureCounts – DESeq2R package (1.20.0) Bioconductor – Other CD31 microbeads Miltenyi Biotech Cat #130-097-418 CD45 microbeads Miltenyi Biotech Cat #130-052-301
RNA Sequencing:Article Title: Angiogenesis in the mature mouse cortex is governed in a regional- and Notch1-dependent manner.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rat anti-CD31 BD Biosciences Cat #553370 sheep anti-CD93 R&D Systems Cat #AF1696 donkey anti-rat (Cy5) Invitrogen Cat #A10523 donkey anti-sheep (Alexa 488) Thermo Fisher Cat #A-11015 Bacterial and virus strains AAV-BR1-iCre Dr. J.Körbelin’s laboratory48 N/A AAV-BR1-eGFP Dr. J.Körbelin’s laboratory48 N/A Chemicals, peptides, and recombinant proteins dexamethasone Vetoquinol DIN: 00617210 lidocaine Hikma Canada Limited DIN: 02422026 FITC-dextran Sigma Aldrich Cat #46945 Texas Red dextran Thermo Fisher Cat #D1830 euthanyl Bimedia-MTC Animal Health Inc. DIN: 00141704 DNase treatment Qiagen Cat #79254 HBSS Thermo Fisher Cat #14175095 Auto-MACS Rinsing Solution Miltenyi Biotec Cat #130-091-222 BSA Miltenyi Biotec Cat #130-091-376 Critical commercial assays RNeasy Mini Kit Qiagen Cat #73104 High-Capacity cDNA synthesis kit Applied Biosystems Cat #4368814 SYBR Green Master Mix Applied Biosystems Cat #4309155 Adult Brain Dissociation Kit Miltenyi Biotec Cat #130-107-677 Myelin Removal Kit Miltenyi Biotec Cat #130-042-401 Deposited data Primer-Blast National Library of Medicine Primer designing tool (nih.gov) Primer Bank Harvard University PrimerBank (harvard.edu) Genome Browser University of California Santa Cruz UCSC Genome Browser Gateway Bulk endothelial RNA seq dataset This paper SRA data: PRJNA1179510 Experimental models: Organisms/strains mouse: C57BL/6J Jackson Laboratories RRID:IMSR_JAX:000664 mouse: Vegfr2/Flk1 Dr. Jane Rossant N/A mouse: Notch1flox Jackson Laboratories RRID:IMSR_JAX:007181 mouse: Ai9 Jackson Laboratories RRID:IMSR_JAX:007909 Oligonucleotides Primers for RT-qPCR are listed in Table S1 – – Software and algorithms Fiji software (ImageJ 1.53q) National Institute of Health Fiji Downloads (imagej.net) BrainVision SciMedia BV Workbench | Data Acquisition/Analysis Software for Neuro/Cardiac Imaging (scimedia.com) Fluoview FV10-ASW software Olympus Corp. – Python 3.9.12 Python Software Foundation Python Release Python 3.9.12 | Python.org Seaborn KDE package Seaborn seaborn.kdeplot — seaborn 0.13.2 documentation (pydata.org) (Continued on next page) Cell Reports 43, 115029, December 24, 2024 13 .. REAGENT or RESOURCE SOURCE IDENTIFIER Jupyter notebook Project Jupyter https://jupyter.org/ Prism (v7 & 8) GraphPad Software RRID:SCR_002798 featureCounts v1.5.0-p3 featureCounts – DESeq2R package (1.20.0) Bioconductor – Other CD31 microbeads Miltenyi Biotech Cat #130-097-418 CD45 microbeads Miltenyi Biotech Cat #130-052-301
Quantitative RT-PCR:Article Title: Angiogenesis in the mature mouse cortex is governed in a regional- and Notch1-dependent manner.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rat anti-CD31 BD Biosciences Cat #553370 sheep anti-CD93 R&D Systems Cat #AF1696 donkey anti-rat (Cy5) Invitrogen Cat #A10523 donkey anti-sheep (Alexa 488) Thermo Fisher Cat #A-11015 Bacterial and virus strains AAV-BR1-iCre Dr. J.Körbelin’s laboratory48 N/A AAV-BR1-eGFP Dr. J.Körbelin’s laboratory48 N/A Chemicals, peptides, and recombinant proteins dexamethasone Vetoquinol DIN: 00617210 lidocaine Hikma Canada Limited DIN: 02422026 FITC-dextran Sigma Aldrich Cat #46945 Texas Red dextran Thermo Fisher Cat #D1830 euthanyl Bimedia-MTC Animal Health Inc. DIN: 00141704 DNase treatment Qiagen Cat #79254 HBSS Thermo Fisher Cat #14175095 Auto-MACS Rinsing Solution Miltenyi Biotec Cat #130-091-222 BSA Miltenyi Biotec Cat #130-091-376 Critical commercial assays RNeasy Mini Kit Qiagen Cat #73104 High-Capacity cDNA synthesis kit Applied Biosystems Cat #4368814 SYBR Green Master Mix Applied Biosystems Cat #4309155 Adult Brain Dissociation Kit Miltenyi Biotec Cat #130-107-677 Myelin Removal Kit Miltenyi Biotec Cat #130-042-401 Deposited data Primer-Blast National Library of Medicine Primer designing tool (nih.gov) Primer Bank Harvard University PrimerBank (harvard.edu) Genome Browser University of California Santa Cruz UCSC Genome Browser Gateway Bulk endothelial RNA seq dataset This paper SRA data: PRJNA1179510 Experimental models: Organisms/strains mouse: C57BL/6J Jackson Laboratories RRID:IMSR_JAX:000664 mouse: Vegfr2/Flk1 Dr. Jane Rossant N/A mouse: Notch1flox Jackson Laboratories RRID:IMSR_JAX:007181 mouse: Ai9 Jackson Laboratories RRID:IMSR_JAX:007909 Oligonucleotides Primers for RT-qPCR are listed in Table S1 – – Software and algorithms Fiji software (ImageJ 1.53q) National Institute of Health Fiji Downloads (imagej.net) BrainVision SciMedia BV Workbench | Data Acquisition/Analysis Software for Neuro/Cardiac Imaging (scimedia.com) Fluoview FV10-ASW software Olympus Corp. – Python 3.9.12 Python Software Foundation Python Release Python 3.9.12 | Python.org Seaborn KDE package Seaborn seaborn.kdeplot — seaborn 0.13.2 documentation (pydata.org) (Continued on next page) Cell Reports 43, 115029, December 24, 2024 13 .. REAGENT or RESOURCE SOURCE IDENTIFIER Jupyter notebook Project Jupyter https://jupyter.org/ Prism (v7 & 8) GraphPad Software RRID:SCR_002798 featureCounts v1.5.0-p3 featureCounts – DESeq2R package (1.20.0) Bioconductor – Other CD31 microbeads Miltenyi Biotech Cat #130-097-418 CD45 microbeads Miltenyi Biotech Cat #130-052-301
Software:Article Title: Angiogenesis in the mature mouse cortex is governed in a regional- and Notch1-dependent manner.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rat anti-CD31 BD Biosciences Cat #553370 sheep anti-CD93 R&D Systems Cat #AF1696 donkey anti-rat (Cy5) Invitrogen Cat #A10523 donkey anti-sheep (Alexa 488) Thermo Fisher Cat #A-11015 Bacterial and virus strains AAV-BR1-iCre Dr. J.Körbelin’s laboratory48 N/A AAV-BR1-eGFP Dr. J.Körbelin’s laboratory48 N/A Chemicals, peptides, and recombinant proteins dexamethasone Vetoquinol DIN: 00617210 lidocaine Hikma Canada Limited DIN: 02422026 FITC-dextran Sigma Aldrich Cat #46945 Texas Red dextran Thermo Fisher Cat #D1830 euthanyl Bimedia-MTC Animal Health Inc. DIN: 00141704 DNase treatment Qiagen Cat #79254 HBSS Thermo Fisher Cat #14175095 Auto-MACS Rinsing Solution Miltenyi Biotec Cat #130-091-222 BSA Miltenyi Biotec Cat #130-091-376 Critical commercial assays RNeasy Mini Kit Qiagen Cat #73104 High-Capacity cDNA synthesis kit Applied Biosystems Cat #4368814 SYBR Green Master Mix Applied Biosystems Cat #4309155 Adult Brain Dissociation Kit Miltenyi Biotec Cat #130-107-677 Myelin Removal Kit Miltenyi Biotec Cat #130-042-401 Deposited data Primer-Blast National Library of Medicine Primer designing tool (nih.gov) Primer Bank Harvard University PrimerBank (harvard.edu) Genome Browser University of California Santa Cruz UCSC Genome Browser Gateway Bulk endothelial RNA seq dataset This paper SRA data: PRJNA1179510 Experimental models: Organisms/strains mouse: C57BL/6J Jackson Laboratories RRID:IMSR_JAX:000664 mouse: Vegfr2/Flk1 Dr. Jane Rossant N/A mouse: Notch1flox Jackson Laboratories RRID:IMSR_JAX:007181 mouse: Ai9 Jackson Laboratories RRID:IMSR_JAX:007909 Oligonucleotides Primers for RT-qPCR are listed in Table S1 – – Software and algorithms Fiji software (ImageJ 1.53q) National Institute of Health Fiji Downloads (imagej.net) BrainVision SciMedia BV Workbench | Data Acquisition/Analysis Software for Neuro/Cardiac Imaging (scimedia.com) Fluoview FV10-ASW software Olympus Corp. – Python 3.9.12 Python Software Foundation Python Release Python 3.9.12 | Python.org Seaborn KDE package Seaborn seaborn.kdeplot — seaborn 0.13.2 documentation (pydata.org) (Continued on next page) Cell Reports 43, 115029, December 24, 2024 13 .. REAGENT or RESOURCE SOURCE IDENTIFIER Jupyter notebook Project Jupyter https://jupyter.org/ Prism (v7 & 8) GraphPad Software RRID:SCR_002798 featureCounts v1.5.0-p3 featureCounts – DESeq2R package (1.20.0) Bioconductor – Other CD31 microbeads Miltenyi Biotech Cat #130-097-418 CD45 microbeads Miltenyi Biotech Cat #130-052-301
Article Title: An automated do-it-yourself system for dynamic stem cell and organoid culture in standard multi-well plates
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit monoclonal anti-FOXA2 Abcam Cat# ab108422; RRID: AB_11157157 Goat polyclonal anti-SOX1 R&D Systems Cat# AF3369; RRID: AB_2239879 Mouse monoclonal anti-Cardiac Troponin T (cTnT) Thermo Fisher Scientific Cat# MA5-12960; RRID: AB_11000742 Chemicals, peptides, and recombinant proteins StemMACS CHIR99021 in Solution Miltenyi Biotec Cat# 130-106-539 StemMACS PD0325901 in Solution Miltenyi Biotec Cat# 130-106-541 CHIR99021 (3D gastruloid stimulation) Merck/Millipore Cat# 361559 Recombinant Human/Murine/Rat Activin A PeproTech Cat# 120-14-10 Recombinant Human bFGF Thermo Fisher Scientific Cat# 13256029 Alexa Fluor 647-Dextran, 10,000 MW Thermo Fisher Scientific Cat# D22914 Fluoresceinisothiocyanat (FITC)-Dextran, 10,000 MW Sigma Cat# FD10S CellTrace Violet Cell Proliferation Kit Thermo Fisher Scientific Cat# C34557 Experimental models: Cell lines Rex1-GFP Mouse ESCs Laboratory of Austin Smith E14Tg2a; RRID: CVCL_9108 Sox1-GFP::Brachyury-mCherry (SBr) Mouse ESCs Laboratory of David Suter CGR8, strain 129; RRID: CVCL_3987 SBr WT Mouse ESCs; Parental strain corresponding to Sox1-GFP::Brachyury-mCherry (SBr) Laboratory of David Suter CGR8, strain 129; RRID: CVCL_3987 Software and algorithms AutoCAD Autodesk https://www.autodesk.com Fiji/ImageJ Schindelin et al., 2012 RRID: SCR_002285; https://imagej.net/software/fiji/ FlowJo BD RRID: SCR_008520; https://www.flowjo.com LabVIEW v14.0 National Instruments RRID: SCR_014325; https://www.ni.com/en-us/shop/ labview.html NIS-Elements Nikon RRID: SCR_014329; https://www.nikonmetrology. com/en-us/industrial-microscopes/nis-software -nis-elements-microscope-imaging-software LabVIEW scripts for microfluidic device operation This paper, deposited on Zenodo https://doi.org/10.5281/zenodo.6579452 Fiji script to calculate gastruloid elongation indices Guiet et al., 2021 https://doi.org/10.5281/zenodo.4544369 Custom processing pipeline for quantifying fluorescent intensities (reporter gene expression levels) along gastruloid posterior-to-anterior poles This paper, deposited on Zenodo https://doi.org/10.5281/zenodo.5717752 Other Design files (AutoCAD) for microfluidic devices This paper, deposited on Zenodo https://doi.org/10.5281/zenodo.6579452 ..
Imaging:Article Title: Angiogenesis in the mature mouse cortex is governed in a regional- and Notch1-dependent manner.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rat anti-CD31 BD Biosciences Cat #553370 sheep anti-CD93 R&D Systems Cat #AF1696 donkey anti-rat (Cy5) Invitrogen Cat #A10523 donkey anti-sheep (Alexa 488) Thermo Fisher Cat #A-11015 Bacterial and virus strains AAV-BR1-iCre Dr. J.Körbelin’s laboratory48 N/A AAV-BR1-eGFP Dr. J.Körbelin’s laboratory48 N/A Chemicals, peptides, and recombinant proteins dexamethasone Vetoquinol DIN: 00617210 lidocaine Hikma Canada Limited DIN: 02422026 FITC-dextran Sigma Aldrich Cat #46945 Texas Red dextran Thermo Fisher Cat #D1830 euthanyl Bimedia-MTC Animal Health Inc. DIN: 00141704 DNase treatment Qiagen Cat #79254 HBSS Thermo Fisher Cat #14175095 Auto-MACS Rinsing Solution Miltenyi Biotec Cat #130-091-222 BSA Miltenyi Biotec Cat #130-091-376 Critical commercial assays RNeasy Mini Kit Qiagen Cat #73104 High-Capacity cDNA synthesis kit Applied Biosystems Cat #4368814 SYBR Green Master Mix Applied Biosystems Cat #4309155 Adult Brain Dissociation Kit Miltenyi Biotec Cat #130-107-677 Myelin Removal Kit Miltenyi Biotec Cat #130-042-401 Deposited data Primer-Blast National Library of Medicine Primer designing tool (nih.gov) Primer Bank Harvard University PrimerBank (harvard.edu) Genome Browser University of California Santa Cruz UCSC Genome Browser Gateway Bulk endothelial RNA seq dataset This paper SRA data: PRJNA1179510 Experimental models: Organisms/strains mouse: C57BL/6J Jackson Laboratories RRID:IMSR_JAX:000664 mouse: Vegfr2/Flk1 Dr. Jane Rossant N/A mouse: Notch1flox Jackson Laboratories RRID:IMSR_JAX:007181 mouse: Ai9 Jackson Laboratories RRID:IMSR_JAX:007909 Oligonucleotides Primers for RT-qPCR are listed in Table S1 – – Software and algorithms Fiji software (ImageJ 1.53q) National Institute of Health Fiji Downloads (imagej.net) BrainVision SciMedia BV Workbench | Data Acquisition/Analysis Software for Neuro/Cardiac Imaging (scimedia.com) Fluoview FV10-ASW software Olympus Corp. – Python 3.9.12 Python Software Foundation Python Release Python 3.9.12 | Python.org Seaborn KDE package Seaborn seaborn.kdeplot — seaborn 0.13.2 documentation (pydata.org) (Continued on next page) Cell Reports 43, 115029, December 24, 2024 13 .. REAGENT or RESOURCE SOURCE IDENTIFIER Jupyter notebook Project Jupyter https://jupyter.org/ Prism (v7 & 8) GraphPad Software RRID:SCR_002798 featureCounts v1.5.0-p3 featureCounts – DESeq2R package (1.20.0) Bioconductor – Other CD31 microbeads Miltenyi Biotech Cat #130-097-418 CD45 microbeads Miltenyi Biotech Cat #130-052-301
Gene Expression:Article Title: An automated do-it-yourself system for dynamic stem cell and organoid culture in standard multi-well plates
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit monoclonal anti-FOXA2 Abcam Cat# ab108422; RRID: AB_11157157 Goat polyclonal anti-SOX1 R&D Systems Cat# AF3369; RRID: AB_2239879 Mouse monoclonal anti-Cardiac Troponin T (cTnT) Thermo Fisher Scientific Cat# MA5-12960; RRID: AB_11000742 Chemicals, peptides, and recombinant proteins StemMACS CHIR99021 in Solution Miltenyi Biotec Cat# 130-106-539 StemMACS PD0325901 in Solution Miltenyi Biotec Cat# 130-106-541 CHIR99021 (3D gastruloid stimulation) Merck/Millipore Cat# 361559 Recombinant Human/Murine/Rat Activin A PeproTech Cat# 120-14-10 Recombinant Human bFGF Thermo Fisher Scientific Cat# 13256029 Alexa Fluor 647-Dextran, 10,000 MW Thermo Fisher Scientific Cat# D22914 Fluoresceinisothiocyanat (FITC)-Dextran, 10,000 MW Sigma Cat# FD10S CellTrace Violet Cell Proliferation Kit Thermo Fisher Scientific Cat# C34557 Experimental models: Cell lines Rex1-GFP Mouse ESCs Laboratory of Austin Smith E14Tg2a; RRID: CVCL_9108 Sox1-GFP::Brachyury-mCherry (SBr) Mouse ESCs Laboratory of David Suter CGR8, strain 129; RRID: CVCL_3987 SBr WT Mouse ESCs; Parental strain corresponding to Sox1-GFP::Brachyury-mCherry (SBr) Laboratory of David Suter CGR8, strain 129; RRID: CVCL_3987 Software and algorithms AutoCAD Autodesk https://www.autodesk.com Fiji/ImageJ Schindelin et al., 2012 RRID: SCR_002285; https://imagej.net/software/fiji/ FlowJo BD RRID: SCR_008520; https://www.flowjo.com LabVIEW v14.0 National Instruments RRID: SCR_014325; https://www.ni.com/en-us/shop/ labview.html NIS-Elements Nikon RRID: SCR_014329; https://www.nikonmetrology. com/en-us/industrial-microscopes/nis-software -nis-elements-microscope-imaging-software LabVIEW scripts for microfluidic device operation This paper, deposited on Zenodo https://doi.org/10.5281/zenodo.6579452 Fiji script to calculate gastruloid elongation indices Guiet et al., 2021 https://doi.org/10.5281/zenodo.4544369 Custom processing pipeline for quantifying fluorescent intensities (reporter gene expression levels) along gastruloid posterior-to-anterior poles This paper, deposited on Zenodo https://doi.org/10.5281/zenodo.5717752 Other Design files (AutoCAD) for microfluidic devices This paper, deposited on Zenodo https://doi.org/10.5281/zenodo.6579452 ..
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