Amplification:Article Title: Revisiting the coding potential of the E. coli genome through Hfq co-immunoprecipitation
Article Snippet: The constructs used for epitope introduction were generated as follows. .. First, the region directly d own s tream of hfq (DS-hfq ) was amplified in a polymerase chain reaction (PCR) from MG1655 strain genomic DNA using primers SalI-DS-Hfq-F and HindIII-DS-Hfq-R, purified and subjected to restriction digest by enzymes SalI and HindIII. pUC19 was used for subcloning; sticky ends were generated through restriction by SalI and HindIII and were subsequently dephosphorylated by CIP (New England Biolabs) and ligated with DS-hfq fragment. .. Next, kanamycin resistance cassette was amplified from FRT-PGK-gb2-neo-FRT template DNA (Gene Bridges) using primers BamHI-BmtI-Kan-F and SalI-Kan-R, followed by a BamHI and SalI restriction digest, and ligated to pre-digested and dephosphorylated pUC19-DS-hfq plasmid.
Article Title: Radial Glial Fibers Promote Neuronal Migration and Functional Recovery after Neonatal Brain Injury.
Article Snippet: .. ContinuedREAGENT or RESOURCE SOURCE IDENTIFIER AffiniPure Fab Fragment Donkey anti-Mouse IgG (H+L) Jackson ImmunoResearch Cat#715-007-003; RRID: AB_2307338 Rat monoclonal anti-HA High Affinity Roche Cat#11867423001; RRID: AB_10094468 Mouse monoclonal anti-actin Millipore Cat#MAB1501; RRID: AB_2223041 Anti-Human IgG (Fc specific)-FITC antibody produced in goat Sigma-Aldrich Cat#F9512; RRID: AB_259808 Anti-Human IgG (Fc specific) antibody produced in goat Sigma-Aldrich Cat#I2136; RRID: AB_260147 Bacterial and Virus Strains Ad-CMV-iCre Vector BioLabs Cat#1045 Ad-CMV-DN-N-cadherin-IRES-Cre This paper N/A Ad-CMV-tdTomato-miR-N-cadherin This paper N/A Ad-CMV-tdTomato-miR-lacZ This paper N/A Chemicals, Peptides, and Recombinant Proteins BamHI New England Biolabs Cat#R0136S SalI New England Biolabs CatR0138S BspMI New England Biolabs Cat#R0502S Fast green Sigma-Aldrich Cat#F7252 Normal donkey serum Millipore Cat#S30-100ML Immobilon-P membrane PVDF Millipore Cat# IPVH00010 beMatrix Gelatin LS-H Nitta Gelatin Cat#633-25751 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide Wako Cat#348-03631 Neurobasal medium GIBCO Cat#21103049 N-cadherin-Fc (IgG-Fc fused with the extracellular domain of mouse N-cadherin) Toshihiro Akaike; Yue et al., 2010 N/A IgG-Fc Toshihiro Akaike; Yue et al., 2010 N/A HBSS (Hank’s Balanced Salt Solution) GIBCO Cat#14170-112 trypsin-EDTA Invitrogen Cat#25300-054 Leibovitz’s L-15 GIBCO Cat#11415-064 DNase I Roche Cat#10104159001 RPMI-1640 Wako Cat#189-02145 Matrigel BD Biosciences Cat#354234 Supernatant B-27 Plus Invitrogen Cat#130-093-566 L-glutamine GIBCO Cat#25030-081 Penicillin-Streptomycin GIBCO Cat#15140-122 Raichu-1298X Michiyuki Matsuda; Yoshizaki et al., 2003 N/A Gateway LR Clonase II Enzyme Mix Invitrogen Cat#11791-020 Critical Commercial Assays Mouse Neural Stem Cell Nucleofector Kit Lonza Cat#VPG-1004 PureLink HiPure Plasmid Maxiprep Kit Invitrogen Cat#K2100-06 ViraPower Adenoviral Gateway Expression Kit Invitrogen Cat#K4930-00 Vectastain Elite ABC-peroxidase kit Vector Laboratories Cat#PK-6100; RRID: AB_2336819 TSA Cyanine 3 System antibody amplification kit PerkinElmer Cat#NEL704A001KT; RRID: AB_2572409 Amersham ECL Prime Western Blotting Detection Reagent GE Healthcare Cat#RPN2232 Deposited Data Catwalk raw data This paper; Mendeley Data https://doi.org/10.17632/t4r38rrf3d.1 (Continued on next page) Cell Stem Cell 22, 128–137.e1–e9, January 4, 2018 e2. .. ContinuedREAGENT or RESOURCE SOURCE IDENTIFIER Experimental Models: Organisms/Strains Mouse: ICR Japan SLC N/A Mouse: C57BL6/J Japan SLC N/A Mouse: R26-tdTomato The Jackson Laboratory Stock#007914; RRID: IMSR_JAX:007914 Mouse: Neurog2-d4Venus Takaki Miyata; Kawaue et al., 2014 N/A Mouse: NSE-DTA Shigeyoshi Itohara; Kobayakawa et al., 2007; Imayoshi et al., 2008 N/A Mouse: Dcx-EGFP Mutant Mouse Research Resource Center (MMRRC) Cat#000244-MU; RRID: MMRRC_000244-MU Oligonucleotides See Table S2 for oligonucleotide sequences This study N/A Recombinant DNA pLV-CMV-tdTomato-IRES-Cre Magdalena Götz; Robel et al., 2011 N/A pCAG-MCS2-DN-N-cadherin Richard L. Huganir; Nuriya and Huganir, 2006 N/A pCAG-MCS2-HA-N-cadherin Richard L. Huganir; Nuriya and Huganir, 2006 N/A pEGFPC1-FAK Kozo Kaibuchi; Itoh et al., 2010 N/A pCMV6-L1-CAM Origene Technologies Cat#MC203533 pENTR4-H1 RIKEN Cat#RDB04395 BLOCK-iT Pol II miR RNAi Expression Vector Kit with EmGFP Invitrogen Cat#K493600 ptdTomato-N1 Clontech Laboratories Cat#632532 pCAGGS-EmGFP Kazunobu Sawamoto; Ota et al., 2014 N/A pCAGGS-tdTomato-miR-N-cadherin This paper N/A pCAGGS-DsRed-miR-FAK This paper N/A pCAGGS-DsRed-miR-L1-CAM This paper N/A pCAGGS-tdTomato-miR-lacZ This paper N/A pAd/CMV/V5-DEST Gateway Vector Kit Invitrogen Cat#V493-20 Software and Algorithms ImageJ National Institutes of Health https://imagej.nih.gov/ij/ Neurolucida MBF Bioscience http://www.mbfbioscience.com/neurolucida Stereo Investigator MBF Bioscience http://www.mbfbioscience.com/ stereo-investigator MetaMorph Molecular Devices https://www.moleculardevices.com/systems/ metamorph-research-imaging/metamorphmicroscopy-automation-and-image-analysissoftware ZEN Carl Zeiss https://www.zeiss.com/microscopy/int/products/ microscope-software/zen.html Other Silicon matrices (50-mm wide) Martin Bastmeyer (Karlsruhe Institute of Technology) http://znbio.zoo.kit.edu Wiretrol I (5 ml) Drummond Scientific Company Cat#5-000-1005 e3 Cell Stem Cell 22, 128–137.e1–e9, January 4, 2018.
Article Title: Ddc2ATRIP promotes Mec1ATR activation at RPA-ssDNA tracts
Article Snippet: .. Purification of MBP-Ddc2 and MBP-Ddc2-S4 protein The coding sequences for DDC2 and ddc2-S4 were amplified by PCR using YCpT-myc-DDC2 [ ] and YCp-myc-DDC2-S4 [ ] with the primer pair KS3620 and KSX001, and cloned into the BamHI and SalI sites of pMAL-c2X (New England Biolabs) to generate the plasmid pMAL-Ddc2 and pMAL-Ddc2-S4, respectively. .. Proteins were expressed in E . coli Rosetta (Novagen) after the incubation with 1 mM IPTG at 30°C for 4 hr.
Polymerase Chain Reaction:Article Title: Revisiting the coding potential of the E. coli genome through Hfq co-immunoprecipitation
Article Snippet: The constructs used for epitope introduction were generated as follows. .. First, the region directly d own s tream of hfq (DS-hfq ) was amplified in a polymerase chain reaction (PCR) from MG1655 strain genomic DNA using primers SalI-DS-Hfq-F and HindIII-DS-Hfq-R, purified and subjected to restriction digest by enzymes SalI and HindIII. pUC19 was used for subcloning; sticky ends were generated through restriction by SalI and HindIII and were subsequently dephosphorylated by CIP (New England Biolabs) and ligated with DS-hfq fragment. .. Next, kanamycin resistance cassette was amplified from FRT-PGK-gb2-neo-FRT template DNA (Gene Bridges) using primers BamHI-BmtI-Kan-F and SalI-Kan-R, followed by a BamHI and SalI restriction digest, and ligated to pre-digested and dephosphorylated pUC19-DS-hfq plasmid.
Article Title: Human Antiviral Protein IFIX Suppresses Viral Gene Expression during Herpes Simplex Virus 1 (HSV-1) Infection and Is Counteracted by Virus-induced Proteasomal Degradation *
Article Snippet: Primary human fibroblasts stably expressing GFP, mGFP, IFIX-GFP, or IFIX-mGFP were generated for this study by retrovirus transduction. .. IFIX was cloned from pEGFP , PCR-amplified, and subcloned into pLXSN-EGFP or pLXSN-mGFP using restriction enzymes SalI and AgeI (New England Biolabs). .. To generate retrovirus, Phoenix cells were transfected using Lipofectamine 2000 (Invitrogen) with the pLXSN constructs, and supernatant was collected at 48 and 72 h post-transfection, filtered (0.45-μm membrane, Millipore), and concentrated using Retro-X concentrator (Clontech) as per the manufacturer's instructions.
Article Title: Ddc2ATRIP promotes Mec1ATR activation at RPA-ssDNA tracts
Article Snippet: .. Purification of MBP-Ddc2 and MBP-Ddc2-S4 protein The coding sequences for DDC2 and ddc2-S4 were amplified by PCR using YCpT-myc-DDC2 [ ] and YCp-myc-DDC2-S4 [ ] with the primer pair KS3620 and KSX001, and cloned into the BamHI and SalI sites of pMAL-c2X (New England Biolabs) to generate the plasmid pMAL-Ddc2 and pMAL-Ddc2-S4, respectively. .. Proteins were expressed in E . coli Rosetta (Novagen) after the incubation with 1 mM IPTG at 30°C for 4 hr.
Purification:Article Title: Revisiting the coding potential of the E. coli genome through Hfq co-immunoprecipitation
Article Snippet: The constructs used for epitope introduction were generated as follows. .. First, the region directly d own s tream of hfq (DS-hfq ) was amplified in a polymerase chain reaction (PCR) from MG1655 strain genomic DNA using primers SalI-DS-Hfq-F and HindIII-DS-Hfq-R, purified and subjected to restriction digest by enzymes SalI and HindIII. pUC19 was used for subcloning; sticky ends were generated through restriction by SalI and HindIII and were subsequently dephosphorylated by CIP (New England Biolabs) and ligated with DS-hfq fragment. .. Next, kanamycin resistance cassette was amplified from FRT-PGK-gb2-neo-FRT template DNA (Gene Bridges) using primers BamHI-BmtI-Kan-F and SalI-Kan-R, followed by a BamHI and SalI restriction digest, and ligated to pre-digested and dephosphorylated pUC19-DS-hfq plasmid.
Article Title: Ddc2ATRIP promotes Mec1ATR activation at RPA-ssDNA tracts
Article Snippet: .. Purification of MBP-Ddc2 and MBP-Ddc2-S4 protein The coding sequences for DDC2 and ddc2-S4 were amplified by PCR using YCpT-myc-DDC2 [ ] and YCp-myc-DDC2-S4 [ ] with the primer pair KS3620 and KSX001, and cloned into the BamHI and SalI sites of pMAL-c2X (New England Biolabs) to generate the plasmid pMAL-Ddc2 and pMAL-Ddc2-S4, respectively. .. Proteins were expressed in E . coli Rosetta (Novagen) after the incubation with 1 mM IPTG at 30°C for 4 hr.
Subcloning:Article Title: Revisiting the coding potential of the E. coli genome through Hfq co-immunoprecipitation
Article Snippet: The constructs used for epitope introduction were generated as follows. .. First, the region directly d own s tream of hfq (DS-hfq ) was amplified in a polymerase chain reaction (PCR) from MG1655 strain genomic DNA using primers SalI-DS-Hfq-F and HindIII-DS-Hfq-R, purified and subjected to restriction digest by enzymes SalI and HindIII. pUC19 was used for subcloning; sticky ends were generated through restriction by SalI and HindIII and were subsequently dephosphorylated by CIP (New England Biolabs) and ligated with DS-hfq fragment. .. Next, kanamycin resistance cassette was amplified from FRT-PGK-gb2-neo-FRT template DNA (Gene Bridges) using primers BamHI-BmtI-Kan-F and SalI-Kan-R, followed by a BamHI and SalI restriction digest, and ligated to pre-digested and dephosphorylated pUC19-DS-hfq plasmid.
Generated:Article Title: Revisiting the coding potential of the E. coli genome through Hfq co-immunoprecipitation
Article Snippet: The constructs used for epitope introduction were generated as follows. .. First, the region directly d own s tream of hfq (DS-hfq ) was amplified in a polymerase chain reaction (PCR) from MG1655 strain genomic DNA using primers SalI-DS-Hfq-F and HindIII-DS-Hfq-R, purified and subjected to restriction digest by enzymes SalI and HindIII. pUC19 was used for subcloning; sticky ends were generated through restriction by SalI and HindIII and were subsequently dephosphorylated by CIP (New England Biolabs) and ligated with DS-hfq fragment. .. Next, kanamycin resistance cassette was amplified from FRT-PGK-gb2-neo-FRT template DNA (Gene Bridges) using primers BamHI-BmtI-Kan-F and SalI-Kan-R, followed by a BamHI and SalI restriction digest, and ligated to pre-digested and dephosphorylated pUC19-DS-hfq plasmid.
Produced:Article Title: Radial Glial Fibers Promote Neuronal Migration and Functional Recovery after Neonatal Brain Injury.
Article Snippet: .. ContinuedREAGENT or RESOURCE SOURCE IDENTIFIER AffiniPure Fab Fragment Donkey anti-Mouse IgG (H+L) Jackson ImmunoResearch Cat#715-007-003; RRID: AB_2307338 Rat monoclonal anti-HA High Affinity Roche Cat#11867423001; RRID: AB_10094468 Mouse monoclonal anti-actin Millipore Cat#MAB1501; RRID: AB_2223041 Anti-Human IgG (Fc specific)-FITC antibody produced in goat Sigma-Aldrich Cat#F9512; RRID: AB_259808 Anti-Human IgG (Fc specific) antibody produced in goat Sigma-Aldrich Cat#I2136; RRID: AB_260147 Bacterial and Virus Strains Ad-CMV-iCre Vector BioLabs Cat#1045 Ad-CMV-DN-N-cadherin-IRES-Cre This paper N/A Ad-CMV-tdTomato-miR-N-cadherin This paper N/A Ad-CMV-tdTomato-miR-lacZ This paper N/A Chemicals, Peptides, and Recombinant Proteins BamHI New England Biolabs Cat#R0136S SalI New England Biolabs CatR0138S BspMI New England Biolabs Cat#R0502S Fast green Sigma-Aldrich Cat#F7252 Normal donkey serum Millipore Cat#S30-100ML Immobilon-P membrane PVDF Millipore Cat# IPVH00010 beMatrix Gelatin LS-H Nitta Gelatin Cat#633-25751 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide Wako Cat#348-03631 Neurobasal medium GIBCO Cat#21103049 N-cadherin-Fc (IgG-Fc fused with the extracellular domain of mouse N-cadherin) Toshihiro Akaike; Yue et al., 2010 N/A IgG-Fc Toshihiro Akaike; Yue et al., 2010 N/A HBSS (Hank’s Balanced Salt Solution) GIBCO Cat#14170-112 trypsin-EDTA Invitrogen Cat#25300-054 Leibovitz’s L-15 GIBCO Cat#11415-064 DNase I Roche Cat#10104159001 RPMI-1640 Wako Cat#189-02145 Matrigel BD Biosciences Cat#354234 Supernatant B-27 Plus Invitrogen Cat#130-093-566 L-glutamine GIBCO Cat#25030-081 Penicillin-Streptomycin GIBCO Cat#15140-122 Raichu-1298X Michiyuki Matsuda; Yoshizaki et al., 2003 N/A Gateway LR Clonase II Enzyme Mix Invitrogen Cat#11791-020 Critical Commercial Assays Mouse Neural Stem Cell Nucleofector Kit Lonza Cat#VPG-1004 PureLink HiPure Plasmid Maxiprep Kit Invitrogen Cat#K2100-06 ViraPower Adenoviral Gateway Expression Kit Invitrogen Cat#K4930-00 Vectastain Elite ABC-peroxidase kit Vector Laboratories Cat#PK-6100; RRID: AB_2336819 TSA Cyanine 3 System antibody amplification kit PerkinElmer Cat#NEL704A001KT; RRID: AB_2572409 Amersham ECL Prime Western Blotting Detection Reagent GE Healthcare Cat#RPN2232 Deposited Data Catwalk raw data This paper; Mendeley Data https://doi.org/10.17632/t4r38rrf3d.1 (Continued on next page) Cell Stem Cell 22, 128–137.e1–e9, January 4, 2018 e2. .. ContinuedREAGENT or RESOURCE SOURCE IDENTIFIER Experimental Models: Organisms/Strains Mouse: ICR Japan SLC N/A Mouse: C57BL6/J Japan SLC N/A Mouse: R26-tdTomato The Jackson Laboratory Stock#007914; RRID: IMSR_JAX:007914 Mouse: Neurog2-d4Venus Takaki Miyata; Kawaue et al., 2014 N/A Mouse: NSE-DTA Shigeyoshi Itohara; Kobayakawa et al., 2007; Imayoshi et al., 2008 N/A Mouse: Dcx-EGFP Mutant Mouse Research Resource Center (MMRRC) Cat#000244-MU; RRID: MMRRC_000244-MU Oligonucleotides See Table S2 for oligonucleotide sequences This study N/A Recombinant DNA pLV-CMV-tdTomato-IRES-Cre Magdalena Götz; Robel et al., 2011 N/A pCAG-MCS2-DN-N-cadherin Richard L. Huganir; Nuriya and Huganir, 2006 N/A pCAG-MCS2-HA-N-cadherin Richard L. Huganir; Nuriya and Huganir, 2006 N/A pEGFPC1-FAK Kozo Kaibuchi; Itoh et al., 2010 N/A pCMV6-L1-CAM Origene Technologies Cat#MC203533 pENTR4-H1 RIKEN Cat#RDB04395 BLOCK-iT Pol II miR RNAi Expression Vector Kit with EmGFP Invitrogen Cat#K493600 ptdTomato-N1 Clontech Laboratories Cat#632532 pCAGGS-EmGFP Kazunobu Sawamoto; Ota et al., 2014 N/A pCAGGS-tdTomato-miR-N-cadherin This paper N/A pCAGGS-DsRed-miR-FAK This paper N/A pCAGGS-DsRed-miR-L1-CAM This paper N/A pCAGGS-tdTomato-miR-lacZ This paper N/A pAd/CMV/V5-DEST Gateway Vector Kit Invitrogen Cat#V493-20 Software and Algorithms ImageJ National Institutes of Health https://imagej.nih.gov/ij/ Neurolucida MBF Bioscience http://www.mbfbioscience.com/neurolucida Stereo Investigator MBF Bioscience http://www.mbfbioscience.com/ stereo-investigator MetaMorph Molecular Devices https://www.moleculardevices.com/systems/ metamorph-research-imaging/metamorphmicroscopy-automation-and-image-analysissoftware ZEN Carl Zeiss https://www.zeiss.com/microscopy/int/products/ microscope-software/zen.html Other Silicon matrices (50-mm wide) Martin Bastmeyer (Karlsruhe Institute of Technology) http://znbio.zoo.kit.edu Wiretrol I (5 ml) Drummond Scientific Company Cat#5-000-1005 e3 Cell Stem Cell 22, 128–137.e1–e9, January 4, 2018.
Recombinant:Article Title: Radial Glial Fibers Promote Neuronal Migration and Functional Recovery after Neonatal Brain Injury.
Article Snippet: .. ContinuedREAGENT or RESOURCE SOURCE IDENTIFIER AffiniPure Fab Fragment Donkey anti-Mouse IgG (H+L) Jackson ImmunoResearch Cat#715-007-003; RRID: AB_2307338 Rat monoclonal anti-HA High Affinity Roche Cat#11867423001; RRID: AB_10094468 Mouse monoclonal anti-actin Millipore Cat#MAB1501; RRID: AB_2223041 Anti-Human IgG (Fc specific)-FITC antibody produced in goat Sigma-Aldrich Cat#F9512; RRID: AB_259808 Anti-Human IgG (Fc specific) antibody produced in goat Sigma-Aldrich Cat#I2136; RRID: AB_260147 Bacterial and Virus Strains Ad-CMV-iCre Vector BioLabs Cat#1045 Ad-CMV-DN-N-cadherin-IRES-Cre This paper N/A Ad-CMV-tdTomato-miR-N-cadherin This paper N/A Ad-CMV-tdTomato-miR-lacZ This paper N/A Chemicals, Peptides, and Recombinant Proteins BamHI New England Biolabs Cat#R0136S SalI New England Biolabs CatR0138S BspMI New England Biolabs Cat#R0502S Fast green Sigma-Aldrich Cat#F7252 Normal donkey serum Millipore Cat#S30-100ML Immobilon-P membrane PVDF Millipore Cat# IPVH00010 beMatrix Gelatin LS-H Nitta Gelatin Cat#633-25751 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide Wako Cat#348-03631 Neurobasal medium GIBCO Cat#21103049 N-cadherin-Fc (IgG-Fc fused with the extracellular domain of mouse N-cadherin) Toshihiro Akaike; Yue et al., 2010 N/A IgG-Fc Toshihiro Akaike; Yue et al., 2010 N/A HBSS (Hank’s Balanced Salt Solution) GIBCO Cat#14170-112 trypsin-EDTA Invitrogen Cat#25300-054 Leibovitz’s L-15 GIBCO Cat#11415-064 DNase I Roche Cat#10104159001 RPMI-1640 Wako Cat#189-02145 Matrigel BD Biosciences Cat#354234 Supernatant B-27 Plus Invitrogen Cat#130-093-566 L-glutamine GIBCO Cat#25030-081 Penicillin-Streptomycin GIBCO Cat#15140-122 Raichu-1298X Michiyuki Matsuda; Yoshizaki et al., 2003 N/A Gateway LR Clonase II Enzyme Mix Invitrogen Cat#11791-020 Critical Commercial Assays Mouse Neural Stem Cell Nucleofector Kit Lonza Cat#VPG-1004 PureLink HiPure Plasmid Maxiprep Kit Invitrogen Cat#K2100-06 ViraPower Adenoviral Gateway Expression Kit Invitrogen Cat#K4930-00 Vectastain Elite ABC-peroxidase kit Vector Laboratories Cat#PK-6100; RRID: AB_2336819 TSA Cyanine 3 System antibody amplification kit PerkinElmer Cat#NEL704A001KT; RRID: AB_2572409 Amersham ECL Prime Western Blotting Detection Reagent GE Healthcare Cat#RPN2232 Deposited Data Catwalk raw data This paper; Mendeley Data https://doi.org/10.17632/t4r38rrf3d.1 (Continued on next page) Cell Stem Cell 22, 128–137.e1–e9, January 4, 2018 e2. .. ContinuedREAGENT or RESOURCE SOURCE IDENTIFIER Experimental Models: Organisms/Strains Mouse: ICR Japan SLC N/A Mouse: C57BL6/J Japan SLC N/A Mouse: R26-tdTomato The Jackson Laboratory Stock#007914; RRID: IMSR_JAX:007914 Mouse: Neurog2-d4Venus Takaki Miyata; Kawaue et al., 2014 N/A Mouse: NSE-DTA Shigeyoshi Itohara; Kobayakawa et al., 2007; Imayoshi et al., 2008 N/A Mouse: Dcx-EGFP Mutant Mouse Research Resource Center (MMRRC) Cat#000244-MU; RRID: MMRRC_000244-MU Oligonucleotides See Table S2 for oligonucleotide sequences This study N/A Recombinant DNA pLV-CMV-tdTomato-IRES-Cre Magdalena Götz; Robel et al., 2011 N/A pCAG-MCS2-DN-N-cadherin Richard L. Huganir; Nuriya and Huganir, 2006 N/A pCAG-MCS2-HA-N-cadherin Richard L. Huganir; Nuriya and Huganir, 2006 N/A pEGFPC1-FAK Kozo Kaibuchi; Itoh et al., 2010 N/A pCMV6-L1-CAM Origene Technologies Cat#MC203533 pENTR4-H1 RIKEN Cat#RDB04395 BLOCK-iT Pol II miR RNAi Expression Vector Kit with EmGFP Invitrogen Cat#K493600 ptdTomato-N1 Clontech Laboratories Cat#632532 pCAGGS-EmGFP Kazunobu Sawamoto; Ota et al., 2014 N/A pCAGGS-tdTomato-miR-N-cadherin This paper N/A pCAGGS-DsRed-miR-FAK This paper N/A pCAGGS-DsRed-miR-L1-CAM This paper N/A pCAGGS-tdTomato-miR-lacZ This paper N/A pAd/CMV/V5-DEST Gateway Vector Kit Invitrogen Cat#V493-20 Software and Algorithms ImageJ National Institutes of Health https://imagej.nih.gov/ij/ Neurolucida MBF Bioscience http://www.mbfbioscience.com/neurolucida Stereo Investigator MBF Bioscience http://www.mbfbioscience.com/ stereo-investigator MetaMorph Molecular Devices https://www.moleculardevices.com/systems/ metamorph-research-imaging/metamorphmicroscopy-automation-and-image-analysissoftware ZEN Carl Zeiss https://www.zeiss.com/microscopy/int/products/ microscope-software/zen.html Other Silicon matrices (50-mm wide) Martin Bastmeyer (Karlsruhe Institute of Technology) http://znbio.zoo.kit.edu Wiretrol I (5 ml) Drummond Scientific Company Cat#5-000-1005 e3 Cell Stem Cell 22, 128–137.e1–e9, January 4, 2018.
Plasmid Preparation:Article Title: Radial Glial Fibers Promote Neuronal Migration and Functional Recovery after Neonatal Brain Injury.
Article Snippet: .. ContinuedREAGENT or RESOURCE SOURCE IDENTIFIER AffiniPure Fab Fragment Donkey anti-Mouse IgG (H+L) Jackson ImmunoResearch Cat#715-007-003; RRID: AB_2307338 Rat monoclonal anti-HA High Affinity Roche Cat#11867423001; RRID: AB_10094468 Mouse monoclonal anti-actin Millipore Cat#MAB1501; RRID: AB_2223041 Anti-Human IgG (Fc specific)-FITC antibody produced in goat Sigma-Aldrich Cat#F9512; RRID: AB_259808 Anti-Human IgG (Fc specific) antibody produced in goat Sigma-Aldrich Cat#I2136; RRID: AB_260147 Bacterial and Virus Strains Ad-CMV-iCre Vector BioLabs Cat#1045 Ad-CMV-DN-N-cadherin-IRES-Cre This paper N/A Ad-CMV-tdTomato-miR-N-cadherin This paper N/A Ad-CMV-tdTomato-miR-lacZ This paper N/A Chemicals, Peptides, and Recombinant Proteins BamHI New England Biolabs Cat#R0136S SalI New England Biolabs CatR0138S BspMI New England Biolabs Cat#R0502S Fast green Sigma-Aldrich Cat#F7252 Normal donkey serum Millipore Cat#S30-100ML Immobilon-P membrane PVDF Millipore Cat# IPVH00010 beMatrix Gelatin LS-H Nitta Gelatin Cat#633-25751 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide Wako Cat#348-03631 Neurobasal medium GIBCO Cat#21103049 N-cadherin-Fc (IgG-Fc fused with the extracellular domain of mouse N-cadherin) Toshihiro Akaike; Yue et al., 2010 N/A IgG-Fc Toshihiro Akaike; Yue et al., 2010 N/A HBSS (Hank’s Balanced Salt Solution) GIBCO Cat#14170-112 trypsin-EDTA Invitrogen Cat#25300-054 Leibovitz’s L-15 GIBCO Cat#11415-064 DNase I Roche Cat#10104159001 RPMI-1640 Wako Cat#189-02145 Matrigel BD Biosciences Cat#354234 Supernatant B-27 Plus Invitrogen Cat#130-093-566 L-glutamine GIBCO Cat#25030-081 Penicillin-Streptomycin GIBCO Cat#15140-122 Raichu-1298X Michiyuki Matsuda; Yoshizaki et al., 2003 N/A Gateway LR Clonase II Enzyme Mix Invitrogen Cat#11791-020 Critical Commercial Assays Mouse Neural Stem Cell Nucleofector Kit Lonza Cat#VPG-1004 PureLink HiPure Plasmid Maxiprep Kit Invitrogen Cat#K2100-06 ViraPower Adenoviral Gateway Expression Kit Invitrogen Cat#K4930-00 Vectastain Elite ABC-peroxidase kit Vector Laboratories Cat#PK-6100; RRID: AB_2336819 TSA Cyanine 3 System antibody amplification kit PerkinElmer Cat#NEL704A001KT; RRID: AB_2572409 Amersham ECL Prime Western Blotting Detection Reagent GE Healthcare Cat#RPN2232 Deposited Data Catwalk raw data This paper; Mendeley Data https://doi.org/10.17632/t4r38rrf3d.1 (Continued on next page) Cell Stem Cell 22, 128–137.e1–e9, January 4, 2018 e2. .. ContinuedREAGENT or RESOURCE SOURCE IDENTIFIER Experimental Models: Organisms/Strains Mouse: ICR Japan SLC N/A Mouse: C57BL6/J Japan SLC N/A Mouse: R26-tdTomato The Jackson Laboratory Stock#007914; RRID: IMSR_JAX:007914 Mouse: Neurog2-d4Venus Takaki Miyata; Kawaue et al., 2014 N/A Mouse: NSE-DTA Shigeyoshi Itohara; Kobayakawa et al., 2007; Imayoshi et al., 2008 N/A Mouse: Dcx-EGFP Mutant Mouse Research Resource Center (MMRRC) Cat#000244-MU; RRID: MMRRC_000244-MU Oligonucleotides See Table S2 for oligonucleotide sequences This study N/A Recombinant DNA pLV-CMV-tdTomato-IRES-Cre Magdalena Götz; Robel et al., 2011 N/A pCAG-MCS2-DN-N-cadherin Richard L. Huganir; Nuriya and Huganir, 2006 N/A pCAG-MCS2-HA-N-cadherin Richard L. Huganir; Nuriya and Huganir, 2006 N/A pEGFPC1-FAK Kozo Kaibuchi; Itoh et al., 2010 N/A pCMV6-L1-CAM Origene Technologies Cat#MC203533 pENTR4-H1 RIKEN Cat#RDB04395 BLOCK-iT Pol II miR RNAi Expression Vector Kit with EmGFP Invitrogen Cat#K493600 ptdTomato-N1 Clontech Laboratories Cat#632532 pCAGGS-EmGFP Kazunobu Sawamoto; Ota et al., 2014 N/A pCAGGS-tdTomato-miR-N-cadherin This paper N/A pCAGGS-DsRed-miR-FAK This paper N/A pCAGGS-DsRed-miR-L1-CAM This paper N/A pCAGGS-tdTomato-miR-lacZ This paper N/A pAd/CMV/V5-DEST Gateway Vector Kit Invitrogen Cat#V493-20 Software and Algorithms ImageJ National Institutes of Health https://imagej.nih.gov/ij/ Neurolucida MBF Bioscience http://www.mbfbioscience.com/neurolucida Stereo Investigator MBF Bioscience http://www.mbfbioscience.com/ stereo-investigator MetaMorph Molecular Devices https://www.moleculardevices.com/systems/ metamorph-research-imaging/metamorphmicroscopy-automation-and-image-analysissoftware ZEN Carl Zeiss https://www.zeiss.com/microscopy/int/products/ microscope-software/zen.html Other Silicon matrices (50-mm wide) Martin Bastmeyer (Karlsruhe Institute of Technology) http://znbio.zoo.kit.edu Wiretrol I (5 ml) Drummond Scientific Company Cat#5-000-1005 e3 Cell Stem Cell 22, 128–137.e1–e9, January 4, 2018.
Article Title: c-Abl Tyrosine Kinase Regulates Serum-induced Nuclear Export of Diacylglycerol Kinase ? by Phosphorylation at Tyr-218 *
Article Snippet: The PCR products were first subcloned into a pUC118 vector (TAKARA, Shiga, Japan). .. After digestion with EcoRI and SalI, the cDNA encoding each fragment was subcloned into the EcoRI and SalI sites in the pMAL-C2 vector (New England BioLabs, Ipswich, MA). ..
Article Title: Ddc2ATRIP promotes Mec1ATR activation at RPA-ssDNA tracts
Article Snippet: .. Purification of MBP-Ddc2 and MBP-Ddc2-S4 protein The coding sequences for DDC2 and ddc2-S4 were amplified by PCR using YCpT-myc-DDC2 [ ] and YCp-myc-DDC2-S4 [ ] with the primer pair KS3620 and KSX001, and cloned into the BamHI and SalI sites of pMAL-c2X (New England Biolabs) to generate the plasmid pMAL-Ddc2 and pMAL-Ddc2-S4, respectively. .. Proteins were expressed in E . coli Rosetta (Novagen) after the incubation with 1 mM IPTG at 30°C for 4 hr.
Expressing:Article Title: Radial Glial Fibers Promote Neuronal Migration and Functional Recovery after Neonatal Brain Injury.
Article Snippet: .. ContinuedREAGENT or RESOURCE SOURCE IDENTIFIER AffiniPure Fab Fragment Donkey anti-Mouse IgG (H+L) Jackson ImmunoResearch Cat#715-007-003; RRID: AB_2307338 Rat monoclonal anti-HA High Affinity Roche Cat#11867423001; RRID: AB_10094468 Mouse monoclonal anti-actin Millipore Cat#MAB1501; RRID: AB_2223041 Anti-Human IgG (Fc specific)-FITC antibody produced in goat Sigma-Aldrich Cat#F9512; RRID: AB_259808 Anti-Human IgG (Fc specific) antibody produced in goat Sigma-Aldrich Cat#I2136; RRID: AB_260147 Bacterial and Virus Strains Ad-CMV-iCre Vector BioLabs Cat#1045 Ad-CMV-DN-N-cadherin-IRES-Cre This paper N/A Ad-CMV-tdTomato-miR-N-cadherin This paper N/A Ad-CMV-tdTomato-miR-lacZ This paper N/A Chemicals, Peptides, and Recombinant Proteins BamHI New England Biolabs Cat#R0136S SalI New England Biolabs CatR0138S BspMI New England Biolabs Cat#R0502S Fast green Sigma-Aldrich Cat#F7252 Normal donkey serum Millipore Cat#S30-100ML Immobilon-P membrane PVDF Millipore Cat# IPVH00010 beMatrix Gelatin LS-H Nitta Gelatin Cat#633-25751 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide Wako Cat#348-03631 Neurobasal medium GIBCO Cat#21103049 N-cadherin-Fc (IgG-Fc fused with the extracellular domain of mouse N-cadherin) Toshihiro Akaike; Yue et al., 2010 N/A IgG-Fc Toshihiro Akaike; Yue et al., 2010 N/A HBSS (Hank’s Balanced Salt Solution) GIBCO Cat#14170-112 trypsin-EDTA Invitrogen Cat#25300-054 Leibovitz’s L-15 GIBCO Cat#11415-064 DNase I Roche Cat#10104159001 RPMI-1640 Wako Cat#189-02145 Matrigel BD Biosciences Cat#354234 Supernatant B-27 Plus Invitrogen Cat#130-093-566 L-glutamine GIBCO Cat#25030-081 Penicillin-Streptomycin GIBCO Cat#15140-122 Raichu-1298X Michiyuki Matsuda; Yoshizaki et al., 2003 N/A Gateway LR Clonase II Enzyme Mix Invitrogen Cat#11791-020 Critical Commercial Assays Mouse Neural Stem Cell Nucleofector Kit Lonza Cat#VPG-1004 PureLink HiPure Plasmid Maxiprep Kit Invitrogen Cat#K2100-06 ViraPower Adenoviral Gateway Expression Kit Invitrogen Cat#K4930-00 Vectastain Elite ABC-peroxidase kit Vector Laboratories Cat#PK-6100; RRID: AB_2336819 TSA Cyanine 3 System antibody amplification kit PerkinElmer Cat#NEL704A001KT; RRID: AB_2572409 Amersham ECL Prime Western Blotting Detection Reagent GE Healthcare Cat#RPN2232 Deposited Data Catwalk raw data This paper; Mendeley Data https://doi.org/10.17632/t4r38rrf3d.1 (Continued on next page) Cell Stem Cell 22, 128–137.e1–e9, January 4, 2018 e2. .. ContinuedREAGENT or RESOURCE SOURCE IDENTIFIER Experimental Models: Organisms/Strains Mouse: ICR Japan SLC N/A Mouse: C57BL6/J Japan SLC N/A Mouse: R26-tdTomato The Jackson Laboratory Stock#007914; RRID: IMSR_JAX:007914 Mouse: Neurog2-d4Venus Takaki Miyata; Kawaue et al., 2014 N/A Mouse: NSE-DTA Shigeyoshi Itohara; Kobayakawa et al., 2007; Imayoshi et al., 2008 N/A Mouse: Dcx-EGFP Mutant Mouse Research Resource Center (MMRRC) Cat#000244-MU; RRID: MMRRC_000244-MU Oligonucleotides See Table S2 for oligonucleotide sequences This study N/A Recombinant DNA pLV-CMV-tdTomato-IRES-Cre Magdalena Götz; Robel et al., 2011 N/A pCAG-MCS2-DN-N-cadherin Richard L. Huganir; Nuriya and Huganir, 2006 N/A pCAG-MCS2-HA-N-cadherin Richard L. Huganir; Nuriya and Huganir, 2006 N/A pEGFPC1-FAK Kozo Kaibuchi; Itoh et al., 2010 N/A pCMV6-L1-CAM Origene Technologies Cat#MC203533 pENTR4-H1 RIKEN Cat#RDB04395 BLOCK-iT Pol II miR RNAi Expression Vector Kit with EmGFP Invitrogen Cat#K493600 ptdTomato-N1 Clontech Laboratories Cat#632532 pCAGGS-EmGFP Kazunobu Sawamoto; Ota et al., 2014 N/A pCAGGS-tdTomato-miR-N-cadherin This paper N/A pCAGGS-DsRed-miR-FAK This paper N/A pCAGGS-DsRed-miR-L1-CAM This paper N/A pCAGGS-tdTomato-miR-lacZ This paper N/A pAd/CMV/V5-DEST Gateway Vector Kit Invitrogen Cat#V493-20 Software and Algorithms ImageJ National Institutes of Health https://imagej.nih.gov/ij/ Neurolucida MBF Bioscience http://www.mbfbioscience.com/neurolucida Stereo Investigator MBF Bioscience http://www.mbfbioscience.com/ stereo-investigator MetaMorph Molecular Devices https://www.moleculardevices.com/systems/ metamorph-research-imaging/metamorphmicroscopy-automation-and-image-analysissoftware ZEN Carl Zeiss https://www.zeiss.com/microscopy/int/products/ microscope-software/zen.html Other Silicon matrices (50-mm wide) Martin Bastmeyer (Karlsruhe Institute of Technology) http://znbio.zoo.kit.edu Wiretrol I (5 ml) Drummond Scientific Company Cat#5-000-1005 e3 Cell Stem Cell 22, 128–137.e1–e9, January 4, 2018.
Western Blot:Article Title: Radial Glial Fibers Promote Neuronal Migration and Functional Recovery after Neonatal Brain Injury.
Article Snippet: .. ContinuedREAGENT or RESOURCE SOURCE IDENTIFIER AffiniPure Fab Fragment Donkey anti-Mouse IgG (H+L) Jackson ImmunoResearch Cat#715-007-003; RRID: AB_2307338 Rat monoclonal anti-HA High Affinity Roche Cat#11867423001; RRID: AB_10094468 Mouse monoclonal anti-actin Millipore Cat#MAB1501; RRID: AB_2223041 Anti-Human IgG (Fc specific)-FITC antibody produced in goat Sigma-Aldrich Cat#F9512; RRID: AB_259808 Anti-Human IgG (Fc specific) antibody produced in goat Sigma-Aldrich Cat#I2136; RRID: AB_260147 Bacterial and Virus Strains Ad-CMV-iCre Vector BioLabs Cat#1045 Ad-CMV-DN-N-cadherin-IRES-Cre This paper N/A Ad-CMV-tdTomato-miR-N-cadherin This paper N/A Ad-CMV-tdTomato-miR-lacZ This paper N/A Chemicals, Peptides, and Recombinant Proteins BamHI New England Biolabs Cat#R0136S SalI New England Biolabs CatR0138S BspMI New England Biolabs Cat#R0502S Fast green Sigma-Aldrich Cat#F7252 Normal donkey serum Millipore Cat#S30-100ML Immobilon-P membrane PVDF Millipore Cat# IPVH00010 beMatrix Gelatin LS-H Nitta Gelatin Cat#633-25751 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide Wako Cat#348-03631 Neurobasal medium GIBCO Cat#21103049 N-cadherin-Fc (IgG-Fc fused with the extracellular domain of mouse N-cadherin) Toshihiro Akaike; Yue et al., 2010 N/A IgG-Fc Toshihiro Akaike; Yue et al., 2010 N/A HBSS (Hank’s Balanced Salt Solution) GIBCO Cat#14170-112 trypsin-EDTA Invitrogen Cat#25300-054 Leibovitz’s L-15 GIBCO Cat#11415-064 DNase I Roche Cat#10104159001 RPMI-1640 Wako Cat#189-02145 Matrigel BD Biosciences Cat#354234 Supernatant B-27 Plus Invitrogen Cat#130-093-566 L-glutamine GIBCO Cat#25030-081 Penicillin-Streptomycin GIBCO Cat#15140-122 Raichu-1298X Michiyuki Matsuda; Yoshizaki et al., 2003 N/A Gateway LR Clonase II Enzyme Mix Invitrogen Cat#11791-020 Critical Commercial Assays Mouse Neural Stem Cell Nucleofector Kit Lonza Cat#VPG-1004 PureLink HiPure Plasmid Maxiprep Kit Invitrogen Cat#K2100-06 ViraPower Adenoviral Gateway Expression Kit Invitrogen Cat#K4930-00 Vectastain Elite ABC-peroxidase kit Vector Laboratories Cat#PK-6100; RRID: AB_2336819 TSA Cyanine 3 System antibody amplification kit PerkinElmer Cat#NEL704A001KT; RRID: AB_2572409 Amersham ECL Prime Western Blotting Detection Reagent GE Healthcare Cat#RPN2232 Deposited Data Catwalk raw data This paper; Mendeley Data https://doi.org/10.17632/t4r38rrf3d.1 (Continued on next page) Cell Stem Cell 22, 128–137.e1–e9, January 4, 2018 e2. .. ContinuedREAGENT or RESOURCE SOURCE IDENTIFIER Experimental Models: Organisms/Strains Mouse: ICR Japan SLC N/A Mouse: C57BL6/J Japan SLC N/A Mouse: R26-tdTomato The Jackson Laboratory Stock#007914; RRID: IMSR_JAX:007914 Mouse: Neurog2-d4Venus Takaki Miyata; Kawaue et al., 2014 N/A Mouse: NSE-DTA Shigeyoshi Itohara; Kobayakawa et al., 2007; Imayoshi et al., 2008 N/A Mouse: Dcx-EGFP Mutant Mouse Research Resource Center (MMRRC) Cat#000244-MU; RRID: MMRRC_000244-MU Oligonucleotides See Table S2 for oligonucleotide sequences This study N/A Recombinant DNA pLV-CMV-tdTomato-IRES-Cre Magdalena Götz; Robel et al., 2011 N/A pCAG-MCS2-DN-N-cadherin Richard L. Huganir; Nuriya and Huganir, 2006 N/A pCAG-MCS2-HA-N-cadherin Richard L. Huganir; Nuriya and Huganir, 2006 N/A pEGFPC1-FAK Kozo Kaibuchi; Itoh et al., 2010 N/A pCMV6-L1-CAM Origene Technologies Cat#MC203533 pENTR4-H1 RIKEN Cat#RDB04395 BLOCK-iT Pol II miR RNAi Expression Vector Kit with EmGFP Invitrogen Cat#K493600 ptdTomato-N1 Clontech Laboratories Cat#632532 pCAGGS-EmGFP Kazunobu Sawamoto; Ota et al., 2014 N/A pCAGGS-tdTomato-miR-N-cadherin This paper N/A pCAGGS-DsRed-miR-FAK This paper N/A pCAGGS-DsRed-miR-L1-CAM This paper N/A pCAGGS-tdTomato-miR-lacZ This paper N/A pAd/CMV/V5-DEST Gateway Vector Kit Invitrogen Cat#V493-20 Software and Algorithms ImageJ National Institutes of Health https://imagej.nih.gov/ij/ Neurolucida MBF Bioscience http://www.mbfbioscience.com/neurolucida Stereo Investigator MBF Bioscience http://www.mbfbioscience.com/ stereo-investigator MetaMorph Molecular Devices https://www.moleculardevices.com/systems/ metamorph-research-imaging/metamorphmicroscopy-automation-and-image-analysissoftware ZEN Carl Zeiss https://www.zeiss.com/microscopy/int/products/ microscope-software/zen.html Other Silicon matrices (50-mm wide) Martin Bastmeyer (Karlsruhe Institute of Technology) http://znbio.zoo.kit.edu Wiretrol I (5 ml) Drummond Scientific Company Cat#5-000-1005 e3 Cell Stem Cell 22, 128–137.e1–e9, January 4, 2018.
Polyacrylamide Gel Electrophoresis:Article Title: Radial Glial Fibers Promote Neuronal Migration and Functional Recovery after Neonatal Brain Injury.
Article Snippet: .. ContinuedREAGENT or RESOURCE SOURCE IDENTIFIER AffiniPure Fab Fragment Donkey anti-Mouse IgG (H+L) Jackson ImmunoResearch Cat#715-007-003; RRID: AB_2307338 Rat monoclonal anti-HA High Affinity Roche Cat#11867423001; RRID: AB_10094468 Mouse monoclonal anti-actin Millipore Cat#MAB1501; RRID: AB_2223041 Anti-Human IgG (Fc specific)-FITC antibody produced in goat Sigma-Aldrich Cat#F9512; RRID: AB_259808 Anti-Human IgG (Fc specific) antibody produced in goat Sigma-Aldrich Cat#I2136; RRID: AB_260147 Bacterial and Virus Strains Ad-CMV-iCre Vector BioLabs Cat#1045 Ad-CMV-DN-N-cadherin-IRES-Cre This paper N/A Ad-CMV-tdTomato-miR-N-cadherin This paper N/A Ad-CMV-tdTomato-miR-lacZ This paper N/A Chemicals, Peptides, and Recombinant Proteins BamHI New England Biolabs Cat#R0136S SalI New England Biolabs CatR0138S BspMI New England Biolabs Cat#R0502S Fast green Sigma-Aldrich Cat#F7252 Normal donkey serum Millipore Cat#S30-100ML Immobilon-P membrane PVDF Millipore Cat# IPVH00010 beMatrix Gelatin LS-H Nitta Gelatin Cat#633-25751 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide Wako Cat#348-03631 Neurobasal medium GIBCO Cat#21103049 N-cadherin-Fc (IgG-Fc fused with the extracellular domain of mouse N-cadherin) Toshihiro Akaike; Yue et al., 2010 N/A IgG-Fc Toshihiro Akaike; Yue et al., 2010 N/A HBSS (Hank’s Balanced Salt Solution) GIBCO Cat#14170-112 trypsin-EDTA Invitrogen Cat#25300-054 Leibovitz’s L-15 GIBCO Cat#11415-064 DNase I Roche Cat#10104159001 RPMI-1640 Wako Cat#189-02145 Matrigel BD Biosciences Cat#354234 Supernatant B-27 Plus Invitrogen Cat#130-093-566 L-glutamine GIBCO Cat#25030-081 Penicillin-Streptomycin GIBCO Cat#15140-122 Raichu-1298X Michiyuki Matsuda; Yoshizaki et al., 2003 N/A Gateway LR Clonase II Enzyme Mix Invitrogen Cat#11791-020 Critical Commercial Assays Mouse Neural Stem Cell Nucleofector Kit Lonza Cat#VPG-1004 PureLink HiPure Plasmid Maxiprep Kit Invitrogen Cat#K2100-06 ViraPower Adenoviral Gateway Expression Kit Invitrogen Cat#K4930-00 Vectastain Elite ABC-peroxidase kit Vector Laboratories Cat#PK-6100; RRID: AB_2336819 TSA Cyanine 3 System antibody amplification kit PerkinElmer Cat#NEL704A001KT; RRID: AB_2572409 Amersham ECL Prime Western Blotting Detection Reagent GE Healthcare Cat#RPN2232 Deposited Data Catwalk raw data This paper; Mendeley Data https://doi.org/10.17632/t4r38rrf3d.1 (Continued on next page) Cell Stem Cell 22, 128–137.e1–e9, January 4, 2018 e2. .. ContinuedREAGENT or RESOURCE SOURCE IDENTIFIER Experimental Models: Organisms/Strains Mouse: ICR Japan SLC N/A Mouse: C57BL6/J Japan SLC N/A Mouse: R26-tdTomato The Jackson Laboratory Stock#007914; RRID: IMSR_JAX:007914 Mouse: Neurog2-d4Venus Takaki Miyata; Kawaue et al., 2014 N/A Mouse: NSE-DTA Shigeyoshi Itohara; Kobayakawa et al., 2007; Imayoshi et al., 2008 N/A Mouse: Dcx-EGFP Mutant Mouse Research Resource Center (MMRRC) Cat#000244-MU; RRID: MMRRC_000244-MU Oligonucleotides See Table S2 for oligonucleotide sequences This study N/A Recombinant DNA pLV-CMV-tdTomato-IRES-Cre Magdalena Götz; Robel et al., 2011 N/A pCAG-MCS2-DN-N-cadherin Richard L. Huganir; Nuriya and Huganir, 2006 N/A pCAG-MCS2-HA-N-cadherin Richard L. Huganir; Nuriya and Huganir, 2006 N/A pEGFPC1-FAK Kozo Kaibuchi; Itoh et al., 2010 N/A pCMV6-L1-CAM Origene Technologies Cat#MC203533 pENTR4-H1 RIKEN Cat#RDB04395 BLOCK-iT Pol II miR RNAi Expression Vector Kit with EmGFP Invitrogen Cat#K493600 ptdTomato-N1 Clontech Laboratories Cat#632532 pCAGGS-EmGFP Kazunobu Sawamoto; Ota et al., 2014 N/A pCAGGS-tdTomato-miR-N-cadherin This paper N/A pCAGGS-DsRed-miR-FAK This paper N/A pCAGGS-DsRed-miR-L1-CAM This paper N/A pCAGGS-tdTomato-miR-lacZ This paper N/A pAd/CMV/V5-DEST Gateway Vector Kit Invitrogen Cat#V493-20 Software and Algorithms ImageJ National Institutes of Health https://imagej.nih.gov/ij/ Neurolucida MBF Bioscience http://www.mbfbioscience.com/neurolucida Stereo Investigator MBF Bioscience http://www.mbfbioscience.com/ stereo-investigator MetaMorph Molecular Devices https://www.moleculardevices.com/systems/ metamorph-research-imaging/metamorphmicroscopy-automation-and-image-analysissoftware ZEN Carl Zeiss https://www.zeiss.com/microscopy/int/products/ microscope-software/zen.html Other Silicon matrices (50-mm wide) Martin Bastmeyer (Karlsruhe Institute of Technology) http://znbio.zoo.kit.edu Wiretrol I (5 ml) Drummond Scientific Company Cat#5-000-1005 e3 Cell Stem Cell 22, 128–137.e1–e9, January 4, 2018.
other:Article Title: Single-molecule analysis of ϕC31 integrase-mediated site-specific recombination by tethered particle motion
Article Snippet: SalI treatment of tethered DNA molecules The DNA molecules were tethered to the glass surface in the reaction chamber containing the SalI digestion buffer (from New England BioLabs).
Clone Assay:Article Title: Human Antiviral Protein IFIX Suppresses Viral Gene Expression during Herpes Simplex Virus 1 (HSV-1) Infection and Is Counteracted by Virus-induced Proteasomal Degradation *
Article Snippet: Primary human fibroblasts stably expressing GFP, mGFP, IFIX-GFP, or IFIX-mGFP were generated for this study by retrovirus transduction. .. IFIX was cloned from pEGFP , PCR-amplified, and subcloned into pLXSN-EGFP or pLXSN-mGFP using restriction enzymes SalI and AgeI (New England Biolabs). .. To generate retrovirus, Phoenix cells were transfected using Lipofectamine 2000 (Invitrogen) with the pLXSN constructs, and supernatant was collected at 48 and 72 h post-transfection, filtered (0.45-μm membrane, Millipore), and concentrated using Retro-X concentrator (Clontech) as per the manufacturer's instructions.
Article Title: Ddc2ATRIP promotes Mec1ATR activation at RPA-ssDNA tracts
Article Snippet: .. Purification of MBP-Ddc2 and MBP-Ddc2-S4 protein The coding sequences for DDC2 and ddc2-S4 were amplified by PCR using YCpT-myc-DDC2 [ ] and YCp-myc-DDC2-S4 [ ] with the primer pair KS3620 and KSX001, and cloned into the BamHI and SalI sites of pMAL-c2X (New England Biolabs) to generate the plasmid pMAL-Ddc2 and pMAL-Ddc2-S4, respectively. .. Proteins were expressed in E . coli Rosetta (Novagen) after the incubation with 1 mM IPTG at 30°C for 4 hr.
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