Plasmid Preparation:Article Title: A conserved differentiation program facilitates inhibitory neuron production in the developing mouse and human cerebellum.
Article Snippet: .. The following transfer vectors were used for this study: Transfer vector Reference Catalogue number Tet-O-FUW-Ascl1 Liu et al (Liu et al., 2018) Addgene cat# 27150 Tet-O-FUW-Foxo1 Liu et al (Liu et al., 2018) Addgene cat# 118588 FUW-tetO-EGFP Panciera et al (Panciera et al., 2016) Addgene cat# 84041 Lenti-SFFV-mNGDamAlone Lim et al (Lim et al., 2023) N/A Lenti-SFFV-mNG-DamAscl1 This paper N/A Lenti-SFFV-mNG-Foxo1Dam This paper N/A pLV-EF1a-IRES-Puro Hayer et al (Hayer et al., 2016) Addgene cat# 85132 Scramble shRNA Sarbassov et al (Sarbassov et al., 2005) Addgene cat# 1864 pLKO.1 Moffat et al (Moffat et al., 2006) Addgene cat# 10878 D ev el o pm en t • A cc ep te d m an us cr ip t Lentiviral infection in vitro Primary NEP neurospheres were dissociated into single cells as described above and incubated with the respective virus at 1-10 multiplicity of infection (MOI) and 4 μg/mL protamine sulfate (Merck, #1101230005) for 12-18 hours. ..
shRNA:Article Title: A conserved differentiation program facilitates inhibitory neuron production in the developing mouse and human cerebellum.
Article Snippet: .. The following transfer vectors were used for this study: Transfer vector Reference Catalogue number Tet-O-FUW-Ascl1 Liu et al (Liu et al., 2018) Addgene cat# 27150 Tet-O-FUW-Foxo1 Liu et al (Liu et al., 2018) Addgene cat# 118588 FUW-tetO-EGFP Panciera et al (Panciera et al., 2016) Addgene cat# 84041 Lenti-SFFV-mNGDamAlone Lim et al (Lim et al., 2023) N/A Lenti-SFFV-mNG-DamAscl1 This paper N/A Lenti-SFFV-mNG-Foxo1Dam This paper N/A pLV-EF1a-IRES-Puro Hayer et al (Hayer et al., 2016) Addgene cat# 85132 Scramble shRNA Sarbassov et al (Sarbassov et al., 2005) Addgene cat# 1864 pLKO.1 Moffat et al (Moffat et al., 2006) Addgene cat# 10878 D ev el o pm en t • A cc ep te d m an us cr ip t Lentiviral infection in vitro Primary NEP neurospheres were dissociated into single cells as described above and incubated with the respective virus at 1-10 multiplicity of infection (MOI) and 4 μg/mL protamine sulfate (Merck, #1101230005) for 12-18 hours. ..
Infection:Article Title: A conserved differentiation program facilitates inhibitory neuron production in the developing mouse and human cerebellum.
Article Snippet: .. The following transfer vectors were used for this study: Transfer vector Reference Catalogue number Tet-O-FUW-Ascl1 Liu et al (Liu et al., 2018) Addgene cat# 27150 Tet-O-FUW-Foxo1 Liu et al (Liu et al., 2018) Addgene cat# 118588 FUW-tetO-EGFP Panciera et al (Panciera et al., 2016) Addgene cat# 84041 Lenti-SFFV-mNGDamAlone Lim et al (Lim et al., 2023) N/A Lenti-SFFV-mNG-DamAscl1 This paper N/A Lenti-SFFV-mNG-Foxo1Dam This paper N/A pLV-EF1a-IRES-Puro Hayer et al (Hayer et al., 2016) Addgene cat# 85132 Scramble shRNA Sarbassov et al (Sarbassov et al., 2005) Addgene cat# 1864 pLKO.1 Moffat et al (Moffat et al., 2006) Addgene cat# 10878 D ev el o pm en t • A cc ep te d m an us cr ip t Lentiviral infection in vitro Primary NEP neurospheres were dissociated into single cells as described above and incubated with the respective virus at 1-10 multiplicity of infection (MOI) and 4 μg/mL protamine sulfate (Merck, #1101230005) for 12-18 hours. ..
In Vitro:Article Title: A conserved differentiation program facilitates inhibitory neuron production in the developing mouse and human cerebellum.
Article Snippet: .. The following transfer vectors were used for this study: Transfer vector Reference Catalogue number Tet-O-FUW-Ascl1 Liu et al (Liu et al., 2018) Addgene cat# 27150 Tet-O-FUW-Foxo1 Liu et al (Liu et al., 2018) Addgene cat# 118588 FUW-tetO-EGFP Panciera et al (Panciera et al., 2016) Addgene cat# 84041 Lenti-SFFV-mNGDamAlone Lim et al (Lim et al., 2023) N/A Lenti-SFFV-mNG-DamAscl1 This paper N/A Lenti-SFFV-mNG-Foxo1Dam This paper N/A pLV-EF1a-IRES-Puro Hayer et al (Hayer et al., 2016) Addgene cat# 85132 Scramble shRNA Sarbassov et al (Sarbassov et al., 2005) Addgene cat# 1864 pLKO.1 Moffat et al (Moffat et al., 2006) Addgene cat# 10878 D ev el o pm en t • A cc ep te d m an us cr ip t Lentiviral infection in vitro Primary NEP neurospheres were dissociated into single cells as described above and incubated with the respective virus at 1-10 multiplicity of infection (MOI) and 4 μg/mL protamine sulfate (Merck, #1101230005) for 12-18 hours. ..
Incubation:Article Title: A conserved differentiation program facilitates inhibitory neuron production in the developing mouse and human cerebellum.
Article Snippet: .. The following transfer vectors were used for this study: Transfer vector Reference Catalogue number Tet-O-FUW-Ascl1 Liu et al (Liu et al., 2018) Addgene cat# 27150 Tet-O-FUW-Foxo1 Liu et al (Liu et al., 2018) Addgene cat# 118588 FUW-tetO-EGFP Panciera et al (Panciera et al., 2016) Addgene cat# 84041 Lenti-SFFV-mNGDamAlone Lim et al (Lim et al., 2023) N/A Lenti-SFFV-mNG-DamAscl1 This paper N/A Lenti-SFFV-mNG-Foxo1Dam This paper N/A pLV-EF1a-IRES-Puro Hayer et al (Hayer et al., 2016) Addgene cat# 85132 Scramble shRNA Sarbassov et al (Sarbassov et al., 2005) Addgene cat# 1864 pLKO.1 Moffat et al (Moffat et al., 2006) Addgene cat# 10878 D ev el o pm en t • A cc ep te d m an us cr ip t Lentiviral infection in vitro Primary NEP neurospheres were dissociated into single cells as described above and incubated with the respective virus at 1-10 multiplicity of infection (MOI) and 4 μg/mL protamine sulfate (Merck, #1101230005) for 12-18 hours. ..
Virus:Article Title: A conserved differentiation program facilitates inhibitory neuron production in the developing mouse and human cerebellum.
Article Snippet: .. The following transfer vectors were used for this study: Transfer vector Reference Catalogue number Tet-O-FUW-Ascl1 Liu et al (Liu et al., 2018) Addgene cat# 27150 Tet-O-FUW-Foxo1 Liu et al (Liu et al., 2018) Addgene cat# 118588 FUW-tetO-EGFP Panciera et al (Panciera et al., 2016) Addgene cat# 84041 Lenti-SFFV-mNGDamAlone Lim et al (Lim et al., 2023) N/A Lenti-SFFV-mNG-DamAscl1 This paper N/A Lenti-SFFV-mNG-Foxo1Dam This paper N/A pLV-EF1a-IRES-Puro Hayer et al (Hayer et al., 2016) Addgene cat# 85132 Scramble shRNA Sarbassov et al (Sarbassov et al., 2005) Addgene cat# 1864 pLKO.1 Moffat et al (Moffat et al., 2006) Addgene cat# 10878 D ev el o pm en t • A cc ep te d m an us cr ip t Lentiviral infection in vitro Primary NEP neurospheres were dissociated into single cells as described above and incubated with the respective virus at 1-10 multiplicity of infection (MOI) and 4 μg/mL protamine sulfate (Merck, #1101230005) for 12-18 hours. ..
Recombinant:Article Title: The Na+/K+ pump dominates control of glycolysis in hippocampal dentate granule cells
Article Snippet: .. resource Designation Source or reference Identifiers Additional information Strain, strain background (Mus musculus, M and F) C57BL/6NCrl Charles River RRID:IMSR_CRL:27 Recombinant DNA reagent AAV.CAG.Peredox.WPRE.SV40 Mongeon et al., 2016 Addgene #73807 Recombinant DNA reagent AAV.hSyn.RCaMP1h.WPRE.SV40 Akerboom et al., 2013 Recombinant DNA reagent AAV. hSyn. mito- RCaMP1h. ..
Article Title: Endogenous tagging using split mNeonGreen in human iPSCs for live imaging studies
Article Snippet: Reagent type (species) or resource Designation Source or reference Identifiers Additional information Strain, strain background (Escherichia coli) DH5α Genome Canada Strain, strain background (Escherichia coli) ER2925 Genome Canada Methylase- deficient strain Cell line (Homo sapiens) 201B7 ATCC ACS- 1023 Cell line (Homo sapiens) smNG2- P This paper Antibody Mouse monoclonal antiNANOG DSHB PCRP- NANOGP1- 2D8 1:25 dilution Antibody Mouse monoclonal anti- OCT3/4 Santa Cruz Biotechnology sc- 5279 1:20 dilution Antibody Mouse monoclonal Alexa488conjugated anti- TRA- 1–60 STEMCELL Technologies 60064AD 1:20 dilution Antibody Rabbit polyclonal Alexa488conjugated anti- mouse Thermo Fisher Scientific A- 11059 1:400 Antibody Mouse monoclonal anti- PAX6 DSHB PAX6 1:45 Antibody Mouse monoclonal anti- NCAM DSHB 5.1H11 1:240 Husser et al. eLife 2023;12:RP92819. .. DOI: https://doi.org/10.7554/eLife.92819 16 of 28 Reagent type (species) or resource Designation Source or reference Identifiers Additional information Antibody Mouse monoclonal PEconjugated anti- FOXA2 BD Biosciences 561589 1:50 Recombinant DNA reagent pNCS- mNeonGreen Allele Biotechnology ABP- FP- MNEONSB Recombinant DNA reagent pAAVS1- P- CAG- GF Oceguera- Yanez et al., 2016 Addgene #80491 Recombinant DNA reagent pAAVS1- P- CAG- mNG21- 10 This paper Addgene #206042 Recombinant DNA reagent pH2B- mNG211 This paper Addgene #206043 Sequence- based reagent sgRNA Sigma- Aldrich Listed in Supplementary file 3 Sequence- based reagent sgRNA Synthego Listed in Supplementary file 3 Sequence- based reagent ssODN BioCorp Listed in Supplementary file 4 Sequence- based reagent Primers Thermo Fisher Scientific Listed in Supplementary file 5 and 6 Sequence- based reagent Hydrolysis probes IDT Sequences listed in the Materials and Methods Peptide, recombinant protein Cas9- eGFP STEMCELL Technologies 76006 Peptide, recombinant protein Cas9 Synthego SpCas9 2NLS Nuclease Commercial assay or kit P3 Nucleofection kit Lonza V4SP- 3096 Commercial assay or kit STEMdiff Trilineage Differentiation Kit STEMCELL Technologies 05230 Commercial assay or kit QuickExtract Biosearch Technologies QE0905T Commercial assay or kit Ligation Sequencing Kit V14 Oxford Nanopore Technologies SQK- LSK114 Commercial assay or kit NEBNext Companion Module New England Biolabs E7180S Commercial assay or kit RNaseP reference assay Thermo Fisher Scientific 4403328 Commercial assay or kit QuantStudio 3D Digital PCR Master Mix V2 Thermo Fisher Scientific A26358 Commercial assay or kit QuantStudio 3D Digital PCR 20 K Chip Kit V2 Thermo Fisher Scientific A26316 Chemical compound, drug CloneR2 STEMCELL Technologies 100–0691 Single- cell recovery reagent Chemical compound, drug NU7441 Tocris Bioscience 3712 NHEJ inhibitor Chemical compound, drug SCR7 Xcess Biosciences M60082 NHEJ inhibitor Chemical compound, drug Hoechst 33342 Thermo Fisher Scientific H1399 Software, algorithm CARE Weigert et al., 2018 https://github.com/CSBDeep/ CSBDeep; Schmidt et al., 2023 Version 0.7.2 Software, algorithm Fiji NIH https://imagej.net/software/fiji/ Version 2.3 Software, algorithm CRISPResso2 Clement et al., 2019 https://github.com/pinellolab/ CRISPResso2; Pinello Lab, 2024 Version 2.2.12 Other 35 mm polymer coverslip dish Cellvis D35- 20- 1.5P Coverslips for live imaging Continued Husser et al. eLife 2023;12:RP92819. ..
Article Title: Cyclotriguaiacyclene-functionalized <i>trans</i>-cinnamic acid with alkyl arms: an efficient supramolecular system for solar cell and liquid crystalline applications
Article Snippet: ll OPEN ACCESS iScience
Bioprocessing:Article Title: The Na+/K+ pump dominates control of glycolysis in hippocampal dentate granule cells
Article Snippet: .. resource Designation Source or reference Identifiers Additional information Strain, strain background (Mus musculus, M and F) C57BL/6NCrl Charles River RRID:IMSR_CRL:27 Recombinant DNA reagent AAV.CAG.Peredox.WPRE.SV40 Mongeon et al., 2016 Addgene #73807 Recombinant DNA reagent AAV.hSyn.RCaMP1h.WPRE.SV40 Akerboom et al., 2013 Recombinant DNA reagent AAV. hSyn. mito- RCaMP1h. ..
Sequencing:Article Title: Endogenous tagging using split mNeonGreen in human iPSCs for live imaging studies
Article Snippet: Reagent type (species) or resource Designation Source or reference Identifiers Additional information Strain, strain background (Escherichia coli) DH5α Genome Canada Strain, strain background (Escherichia coli) ER2925 Genome Canada Methylase- deficient strain Cell line (Homo sapiens) 201B7 ATCC ACS- 1023 Cell line (Homo sapiens) smNG2- P This paper Antibody Mouse monoclonal antiNANOG DSHB PCRP- NANOGP1- 2D8 1:25 dilution Antibody Mouse monoclonal anti- OCT3/4 Santa Cruz Biotechnology sc- 5279 1:20 dilution Antibody Mouse monoclonal Alexa488conjugated anti- TRA- 1–60 STEMCELL Technologies 60064AD 1:20 dilution Antibody Rabbit polyclonal Alexa488conjugated anti- mouse Thermo Fisher Scientific A- 11059 1:400 Antibody Mouse monoclonal anti- PAX6 DSHB PAX6 1:45 Antibody Mouse monoclonal anti- NCAM DSHB 5.1H11 1:240 Husser et al. eLife 2023;12:RP92819. .. DOI: https://doi.org/10.7554/eLife.92819 16 of 28 Reagent type (species) or resource Designation Source or reference Identifiers Additional information Antibody Mouse monoclonal PEconjugated anti- FOXA2 BD Biosciences 561589 1:50 Recombinant DNA reagent pNCS- mNeonGreen Allele Biotechnology ABP- FP- MNEONSB Recombinant DNA reagent pAAVS1- P- CAG- GF Oceguera- Yanez et al., 2016 Addgene #80491 Recombinant DNA reagent pAAVS1- P- CAG- mNG21- 10 This paper Addgene #206042 Recombinant DNA reagent pH2B- mNG211 This paper Addgene #206043 Sequence- based reagent sgRNA Sigma- Aldrich Listed in Supplementary file 3 Sequence- based reagent sgRNA Synthego Listed in Supplementary file 3 Sequence- based reagent ssODN BioCorp Listed in Supplementary file 4 Sequence- based reagent Primers Thermo Fisher Scientific Listed in Supplementary file 5 and 6 Sequence- based reagent Hydrolysis probes IDT Sequences listed in the Materials and Methods Peptide, recombinant protein Cas9- eGFP STEMCELL Technologies 76006 Peptide, recombinant protein Cas9 Synthego SpCas9 2NLS Nuclease Commercial assay or kit P3 Nucleofection kit Lonza V4SP- 3096 Commercial assay or kit STEMdiff Trilineage Differentiation Kit STEMCELL Technologies 05230 Commercial assay or kit QuickExtract Biosearch Technologies QE0905T Commercial assay or kit Ligation Sequencing Kit V14 Oxford Nanopore Technologies SQK- LSK114 Commercial assay or kit NEBNext Companion Module New England Biolabs E7180S Commercial assay or kit RNaseP reference assay Thermo Fisher Scientific 4403328 Commercial assay or kit QuantStudio 3D Digital PCR Master Mix V2 Thermo Fisher Scientific A26358 Commercial assay or kit QuantStudio 3D Digital PCR 20 K Chip Kit V2 Thermo Fisher Scientific A26316 Chemical compound, drug CloneR2 STEMCELL Technologies 100–0691 Single- cell recovery reagent Chemical compound, drug NU7441 Tocris Bioscience 3712 NHEJ inhibitor Chemical compound, drug SCR7 Xcess Biosciences M60082 NHEJ inhibitor Chemical compound, drug Hoechst 33342 Thermo Fisher Scientific H1399 Software, algorithm CARE Weigert et al., 2018 https://github.com/CSBDeep/ CSBDeep; Schmidt et al., 2023 Version 0.7.2 Software, algorithm Fiji NIH https://imagej.net/software/fiji/ Version 2.3 Software, algorithm CRISPResso2 Clement et al., 2019 https://github.com/pinellolab/ CRISPResso2; Pinello Lab, 2024 Version 2.2.12 Other 35 mm polymer coverslip dish Cellvis D35- 20- 1.5P Coverslips for live imaging Continued Husser et al. eLife 2023;12:RP92819. ..
Ligation:Article Title: Endogenous tagging using split mNeonGreen in human iPSCs for live imaging studies
Article Snippet: Reagent type (species) or resource Designation Source or reference Identifiers Additional information Strain, strain background (Escherichia coli) DH5α Genome Canada Strain, strain background (Escherichia coli) ER2925 Genome Canada Methylase- deficient strain Cell line (Homo sapiens) 201B7 ATCC ACS- 1023 Cell line (Homo sapiens) smNG2- P This paper Antibody Mouse monoclonal antiNANOG DSHB PCRP- NANOGP1- 2D8 1:25 dilution Antibody Mouse monoclonal anti- OCT3/4 Santa Cruz Biotechnology sc- 5279 1:20 dilution Antibody Mouse monoclonal Alexa488conjugated anti- TRA- 1–60 STEMCELL Technologies 60064AD 1:20 dilution Antibody Rabbit polyclonal Alexa488conjugated anti- mouse Thermo Fisher Scientific A- 11059 1:400 Antibody Mouse monoclonal anti- PAX6 DSHB PAX6 1:45 Antibody Mouse monoclonal anti- NCAM DSHB 5.1H11 1:240 Husser et al. eLife 2023;12:RP92819. .. DOI: https://doi.org/10.7554/eLife.92819 16 of 28 Reagent type (species) or resource Designation Source or reference Identifiers Additional information Antibody Mouse monoclonal PEconjugated anti- FOXA2 BD Biosciences 561589 1:50 Recombinant DNA reagent pNCS- mNeonGreen Allele Biotechnology ABP- FP- MNEONSB Recombinant DNA reagent pAAVS1- P- CAG- GF Oceguera- Yanez et al., 2016 Addgene #80491 Recombinant DNA reagent pAAVS1- P- CAG- mNG21- 10 This paper Addgene #206042 Recombinant DNA reagent pH2B- mNG211 This paper Addgene #206043 Sequence- based reagent sgRNA Sigma- Aldrich Listed in Supplementary file 3 Sequence- based reagent sgRNA Synthego Listed in Supplementary file 3 Sequence- based reagent ssODN BioCorp Listed in Supplementary file 4 Sequence- based reagent Primers Thermo Fisher Scientific Listed in Supplementary file 5 and 6 Sequence- based reagent Hydrolysis probes IDT Sequences listed in the Materials and Methods Peptide, recombinant protein Cas9- eGFP STEMCELL Technologies 76006 Peptide, recombinant protein Cas9 Synthego SpCas9 2NLS Nuclease Commercial assay or kit P3 Nucleofection kit Lonza V4SP- 3096 Commercial assay or kit STEMdiff Trilineage Differentiation Kit STEMCELL Technologies 05230 Commercial assay or kit QuickExtract Biosearch Technologies QE0905T Commercial assay or kit Ligation Sequencing Kit V14 Oxford Nanopore Technologies SQK- LSK114 Commercial assay or kit NEBNext Companion Module New England Biolabs E7180S Commercial assay or kit RNaseP reference assay Thermo Fisher Scientific 4403328 Commercial assay or kit QuantStudio 3D Digital PCR Master Mix V2 Thermo Fisher Scientific A26358 Commercial assay or kit QuantStudio 3D Digital PCR 20 K Chip Kit V2 Thermo Fisher Scientific A26316 Chemical compound, drug CloneR2 STEMCELL Technologies 100–0691 Single- cell recovery reagent Chemical compound, drug NU7441 Tocris Bioscience 3712 NHEJ inhibitor Chemical compound, drug SCR7 Xcess Biosciences M60082 NHEJ inhibitor Chemical compound, drug Hoechst 33342 Thermo Fisher Scientific H1399 Software, algorithm CARE Weigert et al., 2018 https://github.com/CSBDeep/ CSBDeep; Schmidt et al., 2023 Version 0.7.2 Software, algorithm Fiji NIH https://imagej.net/software/fiji/ Version 2.3 Software, algorithm CRISPResso2 Clement et al., 2019 https://github.com/pinellolab/ CRISPResso2; Pinello Lab, 2024 Version 2.2.12 Other 35 mm polymer coverslip dish Cellvis D35- 20- 1.5P Coverslips for live imaging Continued Husser et al. eLife 2023;12:RP92819. ..
Digital PCR:Article Title: Endogenous tagging using split mNeonGreen in human iPSCs for live imaging studies
Article Snippet: Reagent type (species) or resource Designation Source or reference Identifiers Additional information Strain, strain background (Escherichia coli) DH5α Genome Canada Strain, strain background (Escherichia coli) ER2925 Genome Canada Methylase- deficient strain Cell line (Homo sapiens) 201B7 ATCC ACS- 1023 Cell line (Homo sapiens) smNG2- P This paper Antibody Mouse monoclonal antiNANOG DSHB PCRP- NANOGP1- 2D8 1:25 dilution Antibody Mouse monoclonal anti- OCT3/4 Santa Cruz Biotechnology sc- 5279 1:20 dilution Antibody Mouse monoclonal Alexa488conjugated anti- TRA- 1–60 STEMCELL Technologies 60064AD 1:20 dilution Antibody Rabbit polyclonal Alexa488conjugated anti- mouse Thermo Fisher Scientific A- 11059 1:400 Antibody Mouse monoclonal anti- PAX6 DSHB PAX6 1:45 Antibody Mouse monoclonal anti- NCAM DSHB 5.1H11 1:240 Husser et al. eLife 2023;12:RP92819. .. DOI: https://doi.org/10.7554/eLife.92819 16 of 28 Reagent type (species) or resource Designation Source or reference Identifiers Additional information Antibody Mouse monoclonal PEconjugated anti- FOXA2 BD Biosciences 561589 1:50 Recombinant DNA reagent pNCS- mNeonGreen Allele Biotechnology ABP- FP- MNEONSB Recombinant DNA reagent pAAVS1- P- CAG- GF Oceguera- Yanez et al., 2016 Addgene #80491 Recombinant DNA reagent pAAVS1- P- CAG- mNG21- 10 This paper Addgene #206042 Recombinant DNA reagent pH2B- mNG211 This paper Addgene #206043 Sequence- based reagent sgRNA Sigma- Aldrich Listed in Supplementary file 3 Sequence- based reagent sgRNA Synthego Listed in Supplementary file 3 Sequence- based reagent ssODN BioCorp Listed in Supplementary file 4 Sequence- based reagent Primers Thermo Fisher Scientific Listed in Supplementary file 5 and 6 Sequence- based reagent Hydrolysis probes IDT Sequences listed in the Materials and Methods Peptide, recombinant protein Cas9- eGFP STEMCELL Technologies 76006 Peptide, recombinant protein Cas9 Synthego SpCas9 2NLS Nuclease Commercial assay or kit P3 Nucleofection kit Lonza V4SP- 3096 Commercial assay or kit STEMdiff Trilineage Differentiation Kit STEMCELL Technologies 05230 Commercial assay or kit QuickExtract Biosearch Technologies QE0905T Commercial assay or kit Ligation Sequencing Kit V14 Oxford Nanopore Technologies SQK- LSK114 Commercial assay or kit NEBNext Companion Module New England Biolabs E7180S Commercial assay or kit RNaseP reference assay Thermo Fisher Scientific 4403328 Commercial assay or kit QuantStudio 3D Digital PCR Master Mix V2 Thermo Fisher Scientific A26358 Commercial assay or kit QuantStudio 3D Digital PCR 20 K Chip Kit V2 Thermo Fisher Scientific A26316 Chemical compound, drug CloneR2 STEMCELL Technologies 100–0691 Single- cell recovery reagent Chemical compound, drug NU7441 Tocris Bioscience 3712 NHEJ inhibitor Chemical compound, drug SCR7 Xcess Biosciences M60082 NHEJ inhibitor Chemical compound, drug Hoechst 33342 Thermo Fisher Scientific H1399 Software, algorithm CARE Weigert et al., 2018 https://github.com/CSBDeep/ CSBDeep; Schmidt et al., 2023 Version 0.7.2 Software, algorithm Fiji NIH https://imagej.net/software/fiji/ Version 2.3 Software, algorithm CRISPResso2 Clement et al., 2019 https://github.com/pinellolab/ CRISPResso2; Pinello Lab, 2024 Version 2.2.12 Other 35 mm polymer coverslip dish Cellvis D35- 20- 1.5P Coverslips for live imaging Continued Husser et al. eLife 2023;12:RP92819. ..
Single Cell:Article Title: Endogenous tagging using split mNeonGreen in human iPSCs for live imaging studies
Article Snippet: Reagent type (species) or resource Designation Source or reference Identifiers Additional information Strain, strain background (Escherichia coli) DH5α Genome Canada Strain, strain background (Escherichia coli) ER2925 Genome Canada Methylase- deficient strain Cell line (Homo sapiens) 201B7 ATCC ACS- 1023 Cell line (Homo sapiens) smNG2- P This paper Antibody Mouse monoclonal antiNANOG DSHB PCRP- NANOGP1- 2D8 1:25 dilution Antibody Mouse monoclonal anti- OCT3/4 Santa Cruz Biotechnology sc- 5279 1:20 dilution Antibody Mouse monoclonal Alexa488conjugated anti- TRA- 1–60 STEMCELL Technologies 60064AD 1:20 dilution Antibody Rabbit polyclonal Alexa488conjugated anti- mouse Thermo Fisher Scientific A- 11059 1:400 Antibody Mouse monoclonal anti- PAX6 DSHB PAX6 1:45 Antibody Mouse monoclonal anti- NCAM DSHB 5.1H11 1:240 Husser et al. eLife 2023;12:RP92819. .. DOI: https://doi.org/10.7554/eLife.92819 16 of 28 Reagent type (species) or resource Designation Source or reference Identifiers Additional information Antibody Mouse monoclonal PEconjugated anti- FOXA2 BD Biosciences 561589 1:50 Recombinant DNA reagent pNCS- mNeonGreen Allele Biotechnology ABP- FP- MNEONSB Recombinant DNA reagent pAAVS1- P- CAG- GF Oceguera- Yanez et al., 2016 Addgene #80491 Recombinant DNA reagent pAAVS1- P- CAG- mNG21- 10 This paper Addgene #206042 Recombinant DNA reagent pH2B- mNG211 This paper Addgene #206043 Sequence- based reagent sgRNA Sigma- Aldrich Listed in Supplementary file 3 Sequence- based reagent sgRNA Synthego Listed in Supplementary file 3 Sequence- based reagent ssODN BioCorp Listed in Supplementary file 4 Sequence- based reagent Primers Thermo Fisher Scientific Listed in Supplementary file 5 and 6 Sequence- based reagent Hydrolysis probes IDT Sequences listed in the Materials and Methods Peptide, recombinant protein Cas9- eGFP STEMCELL Technologies 76006 Peptide, recombinant protein Cas9 Synthego SpCas9 2NLS Nuclease Commercial assay or kit P3 Nucleofection kit Lonza V4SP- 3096 Commercial assay or kit STEMdiff Trilineage Differentiation Kit STEMCELL Technologies 05230 Commercial assay or kit QuickExtract Biosearch Technologies QE0905T Commercial assay or kit Ligation Sequencing Kit V14 Oxford Nanopore Technologies SQK- LSK114 Commercial assay or kit NEBNext Companion Module New England Biolabs E7180S Commercial assay or kit RNaseP reference assay Thermo Fisher Scientific 4403328 Commercial assay or kit QuantStudio 3D Digital PCR Master Mix V2 Thermo Fisher Scientific A26358 Commercial assay or kit QuantStudio 3D Digital PCR 20 K Chip Kit V2 Thermo Fisher Scientific A26316 Chemical compound, drug CloneR2 STEMCELL Technologies 100–0691 Single- cell recovery reagent Chemical compound, drug NU7441 Tocris Bioscience 3712 NHEJ inhibitor Chemical compound, drug SCR7 Xcess Biosciences M60082 NHEJ inhibitor Chemical compound, drug Hoechst 33342 Thermo Fisher Scientific H1399 Software, algorithm CARE Weigert et al., 2018 https://github.com/CSBDeep/ CSBDeep; Schmidt et al., 2023 Version 0.7.2 Software, algorithm Fiji NIH https://imagej.net/software/fiji/ Version 2.3 Software, algorithm CRISPResso2 Clement et al., 2019 https://github.com/pinellolab/ CRISPResso2; Pinello Lab, 2024 Version 2.2.12 Other 35 mm polymer coverslip dish Cellvis D35- 20- 1.5P Coverslips for live imaging Continued Husser et al. eLife 2023;12:RP92819. ..
Non-Homologous End Joining:Article Title: Endogenous tagging using split mNeonGreen in human iPSCs for live imaging studies
Article Snippet: Reagent type (species) or resource Designation Source or reference Identifiers Additional information Strain, strain background (Escherichia coli) DH5α Genome Canada Strain, strain background (Escherichia coli) ER2925 Genome Canada Methylase- deficient strain Cell line (Homo sapiens) 201B7 ATCC ACS- 1023 Cell line (Homo sapiens) smNG2- P This paper Antibody Mouse monoclonal antiNANOG DSHB PCRP- NANOGP1- 2D8 1:25 dilution Antibody Mouse monoclonal anti- OCT3/4 Santa Cruz Biotechnology sc- 5279 1:20 dilution Antibody Mouse monoclonal Alexa488conjugated anti- TRA- 1–60 STEMCELL Technologies 60064AD 1:20 dilution Antibody Rabbit polyclonal Alexa488conjugated anti- mouse Thermo Fisher Scientific A- 11059 1:400 Antibody Mouse monoclonal anti- PAX6 DSHB PAX6 1:45 Antibody Mouse monoclonal anti- NCAM DSHB 5.1H11 1:240 Husser et al. eLife 2023;12:RP92819. .. DOI: https://doi.org/10.7554/eLife.92819 16 of 28 Reagent type (species) or resource Designation Source or reference Identifiers Additional information Antibody Mouse monoclonal PEconjugated anti- FOXA2 BD Biosciences 561589 1:50 Recombinant DNA reagent pNCS- mNeonGreen Allele Biotechnology ABP- FP- MNEONSB Recombinant DNA reagent pAAVS1- P- CAG- GF Oceguera- Yanez et al., 2016 Addgene #80491 Recombinant DNA reagent pAAVS1- P- CAG- mNG21- 10 This paper Addgene #206042 Recombinant DNA reagent pH2B- mNG211 This paper Addgene #206043 Sequence- based reagent sgRNA Sigma- Aldrich Listed in Supplementary file 3 Sequence- based reagent sgRNA Synthego Listed in Supplementary file 3 Sequence- based reagent ssODN BioCorp Listed in Supplementary file 4 Sequence- based reagent Primers Thermo Fisher Scientific Listed in Supplementary file 5 and 6 Sequence- based reagent Hydrolysis probes IDT Sequences listed in the Materials and Methods Peptide, recombinant protein Cas9- eGFP STEMCELL Technologies 76006 Peptide, recombinant protein Cas9 Synthego SpCas9 2NLS Nuclease Commercial assay or kit P3 Nucleofection kit Lonza V4SP- 3096 Commercial assay or kit STEMdiff Trilineage Differentiation Kit STEMCELL Technologies 05230 Commercial assay or kit QuickExtract Biosearch Technologies QE0905T Commercial assay or kit Ligation Sequencing Kit V14 Oxford Nanopore Technologies SQK- LSK114 Commercial assay or kit NEBNext Companion Module New England Biolabs E7180S Commercial assay or kit RNaseP reference assay Thermo Fisher Scientific 4403328 Commercial assay or kit QuantStudio 3D Digital PCR Master Mix V2 Thermo Fisher Scientific A26358 Commercial assay or kit QuantStudio 3D Digital PCR 20 K Chip Kit V2 Thermo Fisher Scientific A26316 Chemical compound, drug CloneR2 STEMCELL Technologies 100–0691 Single- cell recovery reagent Chemical compound, drug NU7441 Tocris Bioscience 3712 NHEJ inhibitor Chemical compound, drug SCR7 Xcess Biosciences M60082 NHEJ inhibitor Chemical compound, drug Hoechst 33342 Thermo Fisher Scientific H1399 Software, algorithm CARE Weigert et al., 2018 https://github.com/CSBDeep/ CSBDeep; Schmidt et al., 2023 Version 0.7.2 Software, algorithm Fiji NIH https://imagej.net/software/fiji/ Version 2.3 Software, algorithm CRISPResso2 Clement et al., 2019 https://github.com/pinellolab/ CRISPResso2; Pinello Lab, 2024 Version 2.2.12 Other 35 mm polymer coverslip dish Cellvis D35- 20- 1.5P Coverslips for live imaging Continued Husser et al. eLife 2023;12:RP92819. ..
Software:Article Title: Endogenous tagging using split mNeonGreen in human iPSCs for live imaging studies
Article Snippet: Reagent type (species) or resource Designation Source or reference Identifiers Additional information Strain, strain background (Escherichia coli) DH5α Genome Canada Strain, strain background (Escherichia coli) ER2925 Genome Canada Methylase- deficient strain Cell line (Homo sapiens) 201B7 ATCC ACS- 1023 Cell line (Homo sapiens) smNG2- P This paper Antibody Mouse monoclonal antiNANOG DSHB PCRP- NANOGP1- 2D8 1:25 dilution Antibody Mouse monoclonal anti- OCT3/4 Santa Cruz Biotechnology sc- 5279 1:20 dilution Antibody Mouse monoclonal Alexa488conjugated anti- TRA- 1–60 STEMCELL Technologies 60064AD 1:20 dilution Antibody Rabbit polyclonal Alexa488conjugated anti- mouse Thermo Fisher Scientific A- 11059 1:400 Antibody Mouse monoclonal anti- PAX6 DSHB PAX6 1:45 Antibody Mouse monoclonal anti- NCAM DSHB 5.1H11 1:240 Husser et al. eLife 2023;12:RP92819. .. DOI: https://doi.org/10.7554/eLife.92819 16 of 28 Reagent type (species) or resource Designation Source or reference Identifiers Additional information Antibody Mouse monoclonal PEconjugated anti- FOXA2 BD Biosciences 561589 1:50 Recombinant DNA reagent pNCS- mNeonGreen Allele Biotechnology ABP- FP- MNEONSB Recombinant DNA reagent pAAVS1- P- CAG- GF Oceguera- Yanez et al., 2016 Addgene #80491 Recombinant DNA reagent pAAVS1- P- CAG- mNG21- 10 This paper Addgene #206042 Recombinant DNA reagent pH2B- mNG211 This paper Addgene #206043 Sequence- based reagent sgRNA Sigma- Aldrich Listed in Supplementary file 3 Sequence- based reagent sgRNA Synthego Listed in Supplementary file 3 Sequence- based reagent ssODN BioCorp Listed in Supplementary file 4 Sequence- based reagent Primers Thermo Fisher Scientific Listed in Supplementary file 5 and 6 Sequence- based reagent Hydrolysis probes IDT Sequences listed in the Materials and Methods Peptide, recombinant protein Cas9- eGFP STEMCELL Technologies 76006 Peptide, recombinant protein Cas9 Synthego SpCas9 2NLS Nuclease Commercial assay or kit P3 Nucleofection kit Lonza V4SP- 3096 Commercial assay or kit STEMdiff Trilineage Differentiation Kit STEMCELL Technologies 05230 Commercial assay or kit QuickExtract Biosearch Technologies QE0905T Commercial assay or kit Ligation Sequencing Kit V14 Oxford Nanopore Technologies SQK- LSK114 Commercial assay or kit NEBNext Companion Module New England Biolabs E7180S Commercial assay or kit RNaseP reference assay Thermo Fisher Scientific 4403328 Commercial assay or kit QuantStudio 3D Digital PCR Master Mix V2 Thermo Fisher Scientific A26358 Commercial assay or kit QuantStudio 3D Digital PCR 20 K Chip Kit V2 Thermo Fisher Scientific A26316 Chemical compound, drug CloneR2 STEMCELL Technologies 100–0691 Single- cell recovery reagent Chemical compound, drug NU7441 Tocris Bioscience 3712 NHEJ inhibitor Chemical compound, drug SCR7 Xcess Biosciences M60082 NHEJ inhibitor Chemical compound, drug Hoechst 33342 Thermo Fisher Scientific H1399 Software, algorithm CARE Weigert et al., 2018 https://github.com/CSBDeep/ CSBDeep; Schmidt et al., 2023 Version 0.7.2 Software, algorithm Fiji NIH https://imagej.net/software/fiji/ Version 2.3 Software, algorithm CRISPResso2 Clement et al., 2019 https://github.com/pinellolab/ CRISPResso2; Pinello Lab, 2024 Version 2.2.12 Other 35 mm polymer coverslip dish Cellvis D35- 20- 1.5P Coverslips for live imaging Continued Husser et al. eLife 2023;12:RP92819. ..
Polymer:Article Title: Endogenous tagging using split mNeonGreen in human iPSCs for live imaging studies
Article Snippet: Reagent type (species) or resource Designation Source or reference Identifiers Additional information Strain, strain background (Escherichia coli) DH5α Genome Canada Strain, strain background (Escherichia coli) ER2925 Genome Canada Methylase- deficient strain Cell line (Homo sapiens) 201B7 ATCC ACS- 1023 Cell line (Homo sapiens) smNG2- P This paper Antibody Mouse monoclonal antiNANOG DSHB PCRP- NANOGP1- 2D8 1:25 dilution Antibody Mouse monoclonal anti- OCT3/4 Santa Cruz Biotechnology sc- 5279 1:20 dilution Antibody Mouse monoclonal Alexa488conjugated anti- TRA- 1–60 STEMCELL Technologies 60064AD 1:20 dilution Antibody Rabbit polyclonal Alexa488conjugated anti- mouse Thermo Fisher Scientific A- 11059 1:400 Antibody Mouse monoclonal anti- PAX6 DSHB PAX6 1:45 Antibody Mouse monoclonal anti- NCAM DSHB 5.1H11 1:240 Husser et al. eLife 2023;12:RP92819. .. DOI: https://doi.org/10.7554/eLife.92819 16 of 28 Reagent type (species) or resource Designation Source or reference Identifiers Additional information Antibody Mouse monoclonal PEconjugated anti- FOXA2 BD Biosciences 561589 1:50 Recombinant DNA reagent pNCS- mNeonGreen Allele Biotechnology ABP- FP- MNEONSB Recombinant DNA reagent pAAVS1- P- CAG- GF Oceguera- Yanez et al., 2016 Addgene #80491 Recombinant DNA reagent pAAVS1- P- CAG- mNG21- 10 This paper Addgene #206042 Recombinant DNA reagent pH2B- mNG211 This paper Addgene #206043 Sequence- based reagent sgRNA Sigma- Aldrich Listed in Supplementary file 3 Sequence- based reagent sgRNA Synthego Listed in Supplementary file 3 Sequence- based reagent ssODN BioCorp Listed in Supplementary file 4 Sequence- based reagent Primers Thermo Fisher Scientific Listed in Supplementary file 5 and 6 Sequence- based reagent Hydrolysis probes IDT Sequences listed in the Materials and Methods Peptide, recombinant protein Cas9- eGFP STEMCELL Technologies 76006 Peptide, recombinant protein Cas9 Synthego SpCas9 2NLS Nuclease Commercial assay or kit P3 Nucleofection kit Lonza V4SP- 3096 Commercial assay or kit STEMdiff Trilineage Differentiation Kit STEMCELL Technologies 05230 Commercial assay or kit QuickExtract Biosearch Technologies QE0905T Commercial assay or kit Ligation Sequencing Kit V14 Oxford Nanopore Technologies SQK- LSK114 Commercial assay or kit NEBNext Companion Module New England Biolabs E7180S Commercial assay or kit RNaseP reference assay Thermo Fisher Scientific 4403328 Commercial assay or kit QuantStudio 3D Digital PCR Master Mix V2 Thermo Fisher Scientific A26358 Commercial assay or kit QuantStudio 3D Digital PCR 20 K Chip Kit V2 Thermo Fisher Scientific A26316 Chemical compound, drug CloneR2 STEMCELL Technologies 100–0691 Single- cell recovery reagent Chemical compound, drug NU7441 Tocris Bioscience 3712 NHEJ inhibitor Chemical compound, drug SCR7 Xcess Biosciences M60082 NHEJ inhibitor Chemical compound, drug Hoechst 33342 Thermo Fisher Scientific H1399 Software, algorithm CARE Weigert et al., 2018 https://github.com/CSBDeep/ CSBDeep; Schmidt et al., 2023 Version 0.7.2 Software, algorithm Fiji NIH https://imagej.net/software/fiji/ Version 2.3 Software, algorithm CRISPResso2 Clement et al., 2019 https://github.com/pinellolab/ CRISPResso2; Pinello Lab, 2024 Version 2.2.12 Other 35 mm polymer coverslip dish Cellvis D35- 20- 1.5P Coverslips for live imaging Continued Husser et al. eLife 2023;12:RP92819. ..
Imaging:Article Title: Endogenous tagging using split mNeonGreen in human iPSCs for live imaging studies
Article Snippet: Reagent type (species) or resource Designation Source or reference Identifiers Additional information Strain, strain background (Escherichia coli) DH5α Genome Canada Strain, strain background (Escherichia coli) ER2925 Genome Canada Methylase- deficient strain Cell line (Homo sapiens) 201B7 ATCC ACS- 1023 Cell line (Homo sapiens) smNG2- P This paper Antibody Mouse monoclonal antiNANOG DSHB PCRP- NANOGP1- 2D8 1:25 dilution Antibody Mouse monoclonal anti- OCT3/4 Santa Cruz Biotechnology sc- 5279 1:20 dilution Antibody Mouse monoclonal Alexa488conjugated anti- TRA- 1–60 STEMCELL Technologies 60064AD 1:20 dilution Antibody Rabbit polyclonal Alexa488conjugated anti- mouse Thermo Fisher Scientific A- 11059 1:400 Antibody Mouse monoclonal anti- PAX6 DSHB PAX6 1:45 Antibody Mouse monoclonal anti- NCAM DSHB 5.1H11 1:240 Husser et al. eLife 2023;12:RP92819. .. DOI: https://doi.org/10.7554/eLife.92819 16 of 28 Reagent type (species) or resource Designation Source or reference Identifiers Additional information Antibody Mouse monoclonal PEconjugated anti- FOXA2 BD Biosciences 561589 1:50 Recombinant DNA reagent pNCS- mNeonGreen Allele Biotechnology ABP- FP- MNEONSB Recombinant DNA reagent pAAVS1- P- CAG- GF Oceguera- Yanez et al., 2016 Addgene #80491 Recombinant DNA reagent pAAVS1- P- CAG- mNG21- 10 This paper Addgene #206042 Recombinant DNA reagent pH2B- mNG211 This paper Addgene #206043 Sequence- based reagent sgRNA Sigma- Aldrich Listed in Supplementary file 3 Sequence- based reagent sgRNA Synthego Listed in Supplementary file 3 Sequence- based reagent ssODN BioCorp Listed in Supplementary file 4 Sequence- based reagent Primers Thermo Fisher Scientific Listed in Supplementary file 5 and 6 Sequence- based reagent Hydrolysis probes IDT Sequences listed in the Materials and Methods Peptide, recombinant protein Cas9- eGFP STEMCELL Technologies 76006 Peptide, recombinant protein Cas9 Synthego SpCas9 2NLS Nuclease Commercial assay or kit P3 Nucleofection kit Lonza V4SP- 3096 Commercial assay or kit STEMdiff Trilineage Differentiation Kit STEMCELL Technologies 05230 Commercial assay or kit QuickExtract Biosearch Technologies QE0905T Commercial assay or kit Ligation Sequencing Kit V14 Oxford Nanopore Technologies SQK- LSK114 Commercial assay or kit NEBNext Companion Module New England Biolabs E7180S Commercial assay or kit RNaseP reference assay Thermo Fisher Scientific 4403328 Commercial assay or kit QuantStudio 3D Digital PCR Master Mix V2 Thermo Fisher Scientific A26358 Commercial assay or kit QuantStudio 3D Digital PCR 20 K Chip Kit V2 Thermo Fisher Scientific A26316 Chemical compound, drug CloneR2 STEMCELL Technologies 100–0691 Single- cell recovery reagent Chemical compound, drug NU7441 Tocris Bioscience 3712 NHEJ inhibitor Chemical compound, drug SCR7 Xcess Biosciences M60082 NHEJ inhibitor Chemical compound, drug Hoechst 33342 Thermo Fisher Scientific H1399 Software, algorithm CARE Weigert et al., 2018 https://github.com/CSBDeep/ CSBDeep; Schmidt et al., 2023 Version 0.7.2 Software, algorithm Fiji NIH https://imagej.net/software/fiji/ Version 2.3 Software, algorithm CRISPResso2 Clement et al., 2019 https://github.com/pinellolab/ CRISPResso2; Pinello Lab, 2024 Version 2.2.12 Other 35 mm polymer coverslip dish Cellvis D35- 20- 1.5P Coverslips for live imaging Continued Husser et al. eLife 2023;12:RP92819. ..
other:Article Title: Selective advantage of epigenetically disrupted cancer cells via phenotypic inertia.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER sgRNA sequences in the engineered pLenti-BSD-sgRNA plasmid used for 10x Gemonics scRNAseq with Feature Barcoding Technology for CRISPR screening This paper Table S7 Synthetic crRNAs used to generate KO cells This paper Table S7 Recombinant DNA Plasmid: pCW-Cas9 Monserrat et al., 2021 N/A Plasmid: psPax2 Trono Lab Addgene; Cat#12260; RRID:Addgene_12260 Plasmid: pMD2.G Trono Lab Addgene; Cat#12259; RRID:Addgene_12259 Plasmid: pAdVAntage Vector Promega Cat#E1711 Plasmid: arrayed lentiviral sgRNA library Henser-Brownhill et al., 2017 N/A Plasmid: pTRIP-SFFV-EGFP-NLS Raab et al., 2016 Addgene; Cat#86677; RRID:Addgene_86677 Plasmid: pUAS-mCherry-NLS Zhang et al., 2017 Addgene; Cat#87695; RRID:Addgene_87695 Plasmid: pTRIP-SFFV-mCherry-NLS This paper N/A Plasmid: PiggyBac transposon carrying FRET biosensor Kondo et al., 2021 N/A Plasmid: PB transposase (PBase) Liang et al., 2009 N/A Plasmid: pLenti-BSD-sgRNACapture_seq_1E This paper Table S7 Software and algorithms ImageJ 1.45s NIH RRID:SCR_003070; https://imagej.nih. gov/ij/ QuPath-0.2.2 Bankhead, P. et al., 2017 RRID:SCR_018257; https://qupath. github.io Zeiss Zen software (v2.3) ZEISS N/A Incucyte S3 Live-Cell Analysis System Sartorius RRID:SCR_019874; https://www.sartorius. com/en/products/live-cell-imaging- analysis/live-cell-analysis-instruments Gene Set Enrichment Analysis (GSEA) GSEA (Broad Institute) RRID:SCR_003199; http://www. broadinstitute.org/gsea/ Prism 9 GraphPad Software RRID:SCR_002798; https://www. graphpad.com/ CellRanger (v3.0.2) 10x Genomics RRID:SCR_017344; https://support.
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