Polymerase Chain Reaction:
cDNA Library Assay:
other:
Virus:Article Title: Sequencing of N 6 -methyl-deoxyadenosine at single-base resolution across the mammalian genome.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-N6-Methyladenosine (m6A) antibody Millipore Cat# ABE572; RRID:AB_2892213 Anti-N6-Methyladenosine (m6A) antibody Abcam Cat# ab151230; RR1D:AB_2753144 Anti-H3K9me3 antibody Cell Signaling Technology Cat# 13969; RRID:AB_2798355 Anti-H3K27me3 antibody Cell Signaling Technology Cat# 9733; RRID:AB_2616029 Bacterial and virus strains E. coli BL21 (DE3) Thermo Scientific EC0114 Biological samples E. coli K-12 gDNA ATCC 10798D-5 Human brain gDNA Zyagen HG-201 Human liver gDNA Zyagen HG-314 Human heart gDNA Zyagen HG-801 Human testis gDNA Zyagen HG-401 Mouse Genomic DNA (control) Sigma 69239 Human Genomic DNA (control) Sigma 69237 Chemicals, peptides, and recombinant proteins 2-Thio-dTTP Trilink N-2035 Biotin-dCTP Lumiprobe 2715 Recombinant human FTO protein This study This study Ammonium iron(II) sulfate hexahydrate Sigma 7783-85-9 L-Ascorbic acid Sigma 50-81-7 a-Ketoglutaric acid Sigma 328-50-7 Silver nitrate solution Sigma 7761-88-8 Deposited data E. coli K-12 SMRT sequencing data Gene Expression Omnibus (GEO) GSE69872 GSM1711630 Experimental models: Cell lines HepG2 ATCC HB-8065 NIH/3T3 ATCC CRL-1658 B104-1-1 ATCC CRL-1887 NIH/3T3 (ECACC) Sigma 93061524-1VL Experimental models: Organisms/strains C57BL/6J mice The Jackson Laboratory IMSR_JAX:000664 Oligonucleotides Model DNAs, adaptors, and primers used in this study This study Table S10 Software and algorithms Trim Galore! https://github.com/FelixKrueger/ TrimGalore/tree/0.6.10 https://www.bioinformatics.babraham.ac. uk/projects/trim_galore/ Bowtie2 https://www.nature.com/articles/ nmeth.1923 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml Samtools https://academic.oup.com/bioinformatics/ article/25/16/2078/204688?login=true http://www.htslib.org/ VarScan https://genome.cshlp.org/content/ 22/3/568 http://dkoboldt.github.io/varscan/ (Continued on next page) e1 Molecular Cell 84, 1–15.e1–e6, February 1, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bedtools https://academic.oup.com/bioinformatics/ article/26/6/841/244688 https://bedtools.readthedocs.io/en/latest/ Homer https://www.sciencedirect.com/science/ article/pii/S1097276510003667?via% 3Dihub http://homer.ucsd.edu/homer/ STAR 2.7.10a https://academic.oup.com/bioinformatics/ article/29/1/15/272537 https://github.com/alexdobin/STAR MACS2 2.2.7.1 https://genomebiology.biomedcentral. com/articles/10.1186/gb-2008-9-9-r137 https://pypi.org/project/MACS2/ DeepTools v3.5.0 https://academic.oup.com/nar/article/44/ W1/W160/2499308 https://deeptools.readthedocs.io/en/ develop/ IGV (version 2.6.3) Broad Institute https://software.broadinstitute.org/ software/igv/download Prism (version 8.4.0) www.graphpad.com N/A Deposited data Deposited Data This study GSE213876 Other Detailed protocol of DR-6mA-seq This study Methods S1
Article Title: The structure of lipid nanodisc-reconstituted TRPV3 reveals the gating mechanism.
Article Snippet: 1Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.. 2Division of Cell Signaling, National Institute for Physiological Sciences, National Institute of Natural Sciences, Okazaki, Japan.. 3Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan.
Article Title: Cryo-EM structure of the volume-regulated anion channel LRRC8D isoform identifies features important for substrate permeation
Article Snippet: Protein expression, purification, and sample preparation were performed as described previously , except that Sf9 insect cells from Spodoptera frugiperda (ATCC, CRL-1711) were used as the protein expression host. .. The human LRRC8D wild-type protein (NCBI Reference sequence number: NP_060573.2) was cloned from human brain cDNA (ZYAGEN) into the pFastBac1 vector (Thermo Fisher Scientific), with a C-terminal GFP-His8 tag and a tobacco etch virus (TEV) cleavage site, and was expressed in Sf9 insect cells. .. Cells were collected by centrifugation (5000 × g , 10 min, 4 °C) and disrupted by sonication in buffer (50 mM Tris, pH 8.0, 150 mM NaCl) supplemented with 5.2 μg mL −1 aprotinin, 2 μg mL −1 leupeptin, and 1.4 μg mL −1 pepstatin A (all from Calbiochem).
Article Title: Structural insights into inhibitory mechanism of human excitatory amino acid transporter EAAT2
Article Snippet: .. The sequence encoding the full-length human EAAT2 isoform 1 (SLC1A2; Uniprot ID P43004) was amplified from a human brain complementary DNA library (Zyagen) and inserted into the pEG BacMam vector , with the C-terminally fused tobacco etch virus (TEV) protease cleavage site, enhanced green fluorescent protein (eGFP) and His 8 -tag. .. Baculoviruses were generated in Spodoptera frugiperda Sf9 cells, using the Bac-to-Bac system (Invitrogen).
Control:Article Title: Sequencing of N 6 -methyl-deoxyadenosine at single-base resolution across the mammalian genome.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-N6-Methyladenosine (m6A) antibody Millipore Cat# ABE572; RRID:AB_2892213 Anti-N6-Methyladenosine (m6A) antibody Abcam Cat# ab151230; RR1D:AB_2753144 Anti-H3K9me3 antibody Cell Signaling Technology Cat# 13969; RRID:AB_2798355 Anti-H3K27me3 antibody Cell Signaling Technology Cat# 9733; RRID:AB_2616029 Bacterial and virus strains E. coli BL21 (DE3) Thermo Scientific EC0114 Biological samples E. coli K-12 gDNA ATCC 10798D-5 Human brain gDNA Zyagen HG-201 Human liver gDNA Zyagen HG-314 Human heart gDNA Zyagen HG-801 Human testis gDNA Zyagen HG-401 Mouse Genomic DNA (control) Sigma 69239 Human Genomic DNA (control) Sigma 69237 Chemicals, peptides, and recombinant proteins 2-Thio-dTTP Trilink N-2035 Biotin-dCTP Lumiprobe 2715 Recombinant human FTO protein This study This study Ammonium iron(II) sulfate hexahydrate Sigma 7783-85-9 L-Ascorbic acid Sigma 50-81-7 a-Ketoglutaric acid Sigma 328-50-7 Silver nitrate solution Sigma 7761-88-8 Deposited data E. coli K-12 SMRT sequencing data Gene Expression Omnibus (GEO) GSE69872 GSM1711630 Experimental models: Cell lines HepG2 ATCC HB-8065 NIH/3T3 ATCC CRL-1658 B104-1-1 ATCC CRL-1887 NIH/3T3 (ECACC) Sigma 93061524-1VL Experimental models: Organisms/strains C57BL/6J mice The Jackson Laboratory IMSR_JAX:000664 Oligonucleotides Model DNAs, adaptors, and primers used in this study This study Table S10 Software and algorithms Trim Galore! https://github.com/FelixKrueger/ TrimGalore/tree/0.6.10 https://www.bioinformatics.babraham.ac. uk/projects/trim_galore/ Bowtie2 https://www.nature.com/articles/ nmeth.1923 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml Samtools https://academic.oup.com/bioinformatics/ article/25/16/2078/204688?login=true http://www.htslib.org/ VarScan https://genome.cshlp.org/content/ 22/3/568 http://dkoboldt.github.io/varscan/ (Continued on next page) e1 Molecular Cell 84, 1–15.e1–e6, February 1, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bedtools https://academic.oup.com/bioinformatics/ article/26/6/841/244688 https://bedtools.readthedocs.io/en/latest/ Homer https://www.sciencedirect.com/science/ article/pii/S1097276510003667?via% 3Dihub http://homer.ucsd.edu/homer/ STAR 2.7.10a https://academic.oup.com/bioinformatics/ article/29/1/15/272537 https://github.com/alexdobin/STAR MACS2 2.2.7.1 https://genomebiology.biomedcentral. com/articles/10.1186/gb-2008-9-9-r137 https://pypi.org/project/MACS2/ DeepTools v3.5.0 https://academic.oup.com/nar/article/44/ W1/W160/2499308 https://deeptools.readthedocs.io/en/ develop/ IGV (version 2.6.3) Broad Institute https://software.broadinstitute.org/ software/igv/download Prism (version 8.4.0) www.graphpad.com N/A Deposited data Deposited Data This study GSE213876 Other Detailed protocol of DR-6mA-seq This study Methods S1
Recombinant:Article Title: Sequencing of N 6 -methyl-deoxyadenosine at single-base resolution across the mammalian genome.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-N6-Methyladenosine (m6A) antibody Millipore Cat# ABE572; RRID:AB_2892213 Anti-N6-Methyladenosine (m6A) antibody Abcam Cat# ab151230; RR1D:AB_2753144 Anti-H3K9me3 antibody Cell Signaling Technology Cat# 13969; RRID:AB_2798355 Anti-H3K27me3 antibody Cell Signaling Technology Cat# 9733; RRID:AB_2616029 Bacterial and virus strains E. coli BL21 (DE3) Thermo Scientific EC0114 Biological samples E. coli K-12 gDNA ATCC 10798D-5 Human brain gDNA Zyagen HG-201 Human liver gDNA Zyagen HG-314 Human heart gDNA Zyagen HG-801 Human testis gDNA Zyagen HG-401 Mouse Genomic DNA (control) Sigma 69239 Human Genomic DNA (control) Sigma 69237 Chemicals, peptides, and recombinant proteins 2-Thio-dTTP Trilink N-2035 Biotin-dCTP Lumiprobe 2715 Recombinant human FTO protein This study This study Ammonium iron(II) sulfate hexahydrate Sigma 7783-85-9 L-Ascorbic acid Sigma 50-81-7 a-Ketoglutaric acid Sigma 328-50-7 Silver nitrate solution Sigma 7761-88-8 Deposited data E. coli K-12 SMRT sequencing data Gene Expression Omnibus (GEO) GSE69872 GSM1711630 Experimental models: Cell lines HepG2 ATCC HB-8065 NIH/3T3 ATCC CRL-1658 B104-1-1 ATCC CRL-1887 NIH/3T3 (ECACC) Sigma 93061524-1VL Experimental models: Organisms/strains C57BL/6J mice The Jackson Laboratory IMSR_JAX:000664 Oligonucleotides Model DNAs, adaptors, and primers used in this study This study Table S10 Software and algorithms Trim Galore! https://github.com/FelixKrueger/ TrimGalore/tree/0.6.10 https://www.bioinformatics.babraham.ac. uk/projects/trim_galore/ Bowtie2 https://www.nature.com/articles/ nmeth.1923 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml Samtools https://academic.oup.com/bioinformatics/ article/25/16/2078/204688?login=true http://www.htslib.org/ VarScan https://genome.cshlp.org/content/ 22/3/568 http://dkoboldt.github.io/varscan/ (Continued on next page) e1 Molecular Cell 84, 1–15.e1–e6, February 1, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bedtools https://academic.oup.com/bioinformatics/ article/26/6/841/244688 https://bedtools.readthedocs.io/en/latest/ Homer https://www.sciencedirect.com/science/ article/pii/S1097276510003667?via% 3Dihub http://homer.ucsd.edu/homer/ STAR 2.7.10a https://academic.oup.com/bioinformatics/ article/29/1/15/272537 https://github.com/alexdobin/STAR MACS2 2.2.7.1 https://genomebiology.biomedcentral. com/articles/10.1186/gb-2008-9-9-r137 https://pypi.org/project/MACS2/ DeepTools v3.5.0 https://academic.oup.com/nar/article/44/ W1/W160/2499308 https://deeptools.readthedocs.io/en/ develop/ IGV (version 2.6.3) Broad Institute https://software.broadinstitute.org/ software/igv/download Prism (version 8.4.0) www.graphpad.com N/A Deposited data Deposited Data This study GSE213876 Other Detailed protocol of DR-6mA-seq This study Methods S1
Sequencing:Article Title: Sequencing of N 6 -methyl-deoxyadenosine at single-base resolution across the mammalian genome.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-N6-Methyladenosine (m6A) antibody Millipore Cat# ABE572; RRID:AB_2892213 Anti-N6-Methyladenosine (m6A) antibody Abcam Cat# ab151230; RR1D:AB_2753144 Anti-H3K9me3 antibody Cell Signaling Technology Cat# 13969; RRID:AB_2798355 Anti-H3K27me3 antibody Cell Signaling Technology Cat# 9733; RRID:AB_2616029 Bacterial and virus strains E. coli BL21 (DE3) Thermo Scientific EC0114 Biological samples E. coli K-12 gDNA ATCC 10798D-5 Human brain gDNA Zyagen HG-201 Human liver gDNA Zyagen HG-314 Human heart gDNA Zyagen HG-801 Human testis gDNA Zyagen HG-401 Mouse Genomic DNA (control) Sigma 69239 Human Genomic DNA (control) Sigma 69237 Chemicals, peptides, and recombinant proteins 2-Thio-dTTP Trilink N-2035 Biotin-dCTP Lumiprobe 2715 Recombinant human FTO protein This study This study Ammonium iron(II) sulfate hexahydrate Sigma 7783-85-9 L-Ascorbic acid Sigma 50-81-7 a-Ketoglutaric acid Sigma 328-50-7 Silver nitrate solution Sigma 7761-88-8 Deposited data E. coli K-12 SMRT sequencing data Gene Expression Omnibus (GEO) GSE69872 GSM1711630 Experimental models: Cell lines HepG2 ATCC HB-8065 NIH/3T3 ATCC CRL-1658 B104-1-1 ATCC CRL-1887 NIH/3T3 (ECACC) Sigma 93061524-1VL Experimental models: Organisms/strains C57BL/6J mice The Jackson Laboratory IMSR_JAX:000664 Oligonucleotides Model DNAs, adaptors, and primers used in this study This study Table S10 Software and algorithms Trim Galore! https://github.com/FelixKrueger/ TrimGalore/tree/0.6.10 https://www.bioinformatics.babraham.ac. uk/projects/trim_galore/ Bowtie2 https://www.nature.com/articles/ nmeth.1923 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml Samtools https://academic.oup.com/bioinformatics/ article/25/16/2078/204688?login=true http://www.htslib.org/ VarScan https://genome.cshlp.org/content/ 22/3/568 http://dkoboldt.github.io/varscan/ (Continued on next page) e1 Molecular Cell 84, 1–15.e1–e6, February 1, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bedtools https://academic.oup.com/bioinformatics/ article/26/6/841/244688 https://bedtools.readthedocs.io/en/latest/ Homer https://www.sciencedirect.com/science/ article/pii/S1097276510003667?via% 3Dihub http://homer.ucsd.edu/homer/ STAR 2.7.10a https://academic.oup.com/bioinformatics/ article/29/1/15/272537 https://github.com/alexdobin/STAR MACS2 2.2.7.1 https://genomebiology.biomedcentral. com/articles/10.1186/gb-2008-9-9-r137 https://pypi.org/project/MACS2/ DeepTools v3.5.0 https://academic.oup.com/nar/article/44/ W1/W160/2499308 https://deeptools.readthedocs.io/en/ develop/ IGV (version 2.6.3) Broad Institute https://software.broadinstitute.org/ software/igv/download Prism (version 8.4.0) www.graphpad.com N/A Deposited data Deposited Data This study GSE213876 Other Detailed protocol of DR-6mA-seq This study Methods S1
Article Title: Cryo-EM structure of the volume-regulated anion channel LRRC8D isoform identifies features important for substrate permeation
Article Snippet: Protein expression, purification, and sample preparation were performed as described previously , except that Sf9 insect cells from Spodoptera frugiperda (ATCC, CRL-1711) were used as the protein expression host. .. The human LRRC8D wild-type protein (NCBI Reference sequence number: NP_060573.2) was cloned from human brain cDNA (ZYAGEN) into the pFastBac1 vector (Thermo Fisher Scientific), with a C-terminal GFP-His8 tag and a tobacco etch virus (TEV) cleavage site, and was expressed in Sf9 insect cells. .. Cells were collected by centrifugation (5000 × g , 10 min, 4 °C) and disrupted by sonication in buffer (50 mM Tris, pH 8.0, 150 mM NaCl) supplemented with 5.2 μg mL −1 aprotinin, 2 μg mL −1 leupeptin, and 1.4 μg mL −1 pepstatin A (all from Calbiochem).
Article Title: Structural insights into inhibitory mechanism of human excitatory amino acid transporter EAAT2
Article Snippet: .. The sequence encoding the full-length human EAAT2 isoform 1 (SLC1A2; Uniprot ID P43004) was amplified from a human brain complementary DNA library (Zyagen) and inserted into the pEG BacMam vector , with the C-terminally fused tobacco etch virus (TEV) protease cleavage site, enhanced green fluorescent protein (eGFP) and His 8 -tag. .. Baculoviruses were generated in Spodoptera frugiperda Sf9 cells, using the Bac-to-Bac system (Invitrogen).
Gene Expression:Article Title: Sequencing of N 6 -methyl-deoxyadenosine at single-base resolution across the mammalian genome.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-N6-Methyladenosine (m6A) antibody Millipore Cat# ABE572; RRID:AB_2892213 Anti-N6-Methyladenosine (m6A) antibody Abcam Cat# ab151230; RR1D:AB_2753144 Anti-H3K9me3 antibody Cell Signaling Technology Cat# 13969; RRID:AB_2798355 Anti-H3K27me3 antibody Cell Signaling Technology Cat# 9733; RRID:AB_2616029 Bacterial and virus strains E. coli BL21 (DE3) Thermo Scientific EC0114 Biological samples E. coli K-12 gDNA ATCC 10798D-5 Human brain gDNA Zyagen HG-201 Human liver gDNA Zyagen HG-314 Human heart gDNA Zyagen HG-801 Human testis gDNA Zyagen HG-401 Mouse Genomic DNA (control) Sigma 69239 Human Genomic DNA (control) Sigma 69237 Chemicals, peptides, and recombinant proteins 2-Thio-dTTP Trilink N-2035 Biotin-dCTP Lumiprobe 2715 Recombinant human FTO protein This study This study Ammonium iron(II) sulfate hexahydrate Sigma 7783-85-9 L-Ascorbic acid Sigma 50-81-7 a-Ketoglutaric acid Sigma 328-50-7 Silver nitrate solution Sigma 7761-88-8 Deposited data E. coli K-12 SMRT sequencing data Gene Expression Omnibus (GEO) GSE69872 GSM1711630 Experimental models: Cell lines HepG2 ATCC HB-8065 NIH/3T3 ATCC CRL-1658 B104-1-1 ATCC CRL-1887 NIH/3T3 (ECACC) Sigma 93061524-1VL Experimental models: Organisms/strains C57BL/6J mice The Jackson Laboratory IMSR_JAX:000664 Oligonucleotides Model DNAs, adaptors, and primers used in this study This study Table S10 Software and algorithms Trim Galore! https://github.com/FelixKrueger/ TrimGalore/tree/0.6.10 https://www.bioinformatics.babraham.ac. uk/projects/trim_galore/ Bowtie2 https://www.nature.com/articles/ nmeth.1923 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml Samtools https://academic.oup.com/bioinformatics/ article/25/16/2078/204688?login=true http://www.htslib.org/ VarScan https://genome.cshlp.org/content/ 22/3/568 http://dkoboldt.github.io/varscan/ (Continued on next page) e1 Molecular Cell 84, 1–15.e1–e6, February 1, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bedtools https://academic.oup.com/bioinformatics/ article/26/6/841/244688 https://bedtools.readthedocs.io/en/latest/ Homer https://www.sciencedirect.com/science/ article/pii/S1097276510003667?via% 3Dihub http://homer.ucsd.edu/homer/ STAR 2.7.10a https://academic.oup.com/bioinformatics/ article/29/1/15/272537 https://github.com/alexdobin/STAR MACS2 2.2.7.1 https://genomebiology.biomedcentral. com/articles/10.1186/gb-2008-9-9-r137 https://pypi.org/project/MACS2/ DeepTools v3.5.0 https://academic.oup.com/nar/article/44/ W1/W160/2499308 https://deeptools.readthedocs.io/en/ develop/ IGV (version 2.6.3) Broad Institute https://software.broadinstitute.org/ software/igv/download Prism (version 8.4.0) www.graphpad.com N/A Deposited data Deposited Data This study GSE213876 Other Detailed protocol of DR-6mA-seq This study Methods S1
Software:Article Title: Sequencing of N 6 -methyl-deoxyadenosine at single-base resolution across the mammalian genome.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-N6-Methyladenosine (m6A) antibody Millipore Cat# ABE572; RRID:AB_2892213 Anti-N6-Methyladenosine (m6A) antibody Abcam Cat# ab151230; RR1D:AB_2753144 Anti-H3K9me3 antibody Cell Signaling Technology Cat# 13969; RRID:AB_2798355 Anti-H3K27me3 antibody Cell Signaling Technology Cat# 9733; RRID:AB_2616029 Bacterial and virus strains E. coli BL21 (DE3) Thermo Scientific EC0114 Biological samples E. coli K-12 gDNA ATCC 10798D-5 Human brain gDNA Zyagen HG-201 Human liver gDNA Zyagen HG-314 Human heart gDNA Zyagen HG-801 Human testis gDNA Zyagen HG-401 Mouse Genomic DNA (control) Sigma 69239 Human Genomic DNA (control) Sigma 69237 Chemicals, peptides, and recombinant proteins 2-Thio-dTTP Trilink N-2035 Biotin-dCTP Lumiprobe 2715 Recombinant human FTO protein This study This study Ammonium iron(II) sulfate hexahydrate Sigma 7783-85-9 L-Ascorbic acid Sigma 50-81-7 a-Ketoglutaric acid Sigma 328-50-7 Silver nitrate solution Sigma 7761-88-8 Deposited data E. coli K-12 SMRT sequencing data Gene Expression Omnibus (GEO) GSE69872 GSM1711630 Experimental models: Cell lines HepG2 ATCC HB-8065 NIH/3T3 ATCC CRL-1658 B104-1-1 ATCC CRL-1887 NIH/3T3 (ECACC) Sigma 93061524-1VL Experimental models: Organisms/strains C57BL/6J mice The Jackson Laboratory IMSR_JAX:000664 Oligonucleotides Model DNAs, adaptors, and primers used in this study This study Table S10 Software and algorithms Trim Galore! https://github.com/FelixKrueger/ TrimGalore/tree/0.6.10 https://www.bioinformatics.babraham.ac. uk/projects/trim_galore/ Bowtie2 https://www.nature.com/articles/ nmeth.1923 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml Samtools https://academic.oup.com/bioinformatics/ article/25/16/2078/204688?login=true http://www.htslib.org/ VarScan https://genome.cshlp.org/content/ 22/3/568 http://dkoboldt.github.io/varscan/ (Continued on next page) e1 Molecular Cell 84, 1–15.e1–e6, February 1, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bedtools https://academic.oup.com/bioinformatics/ article/26/6/841/244688 https://bedtools.readthedocs.io/en/latest/ Homer https://www.sciencedirect.com/science/ article/pii/S1097276510003667?via% 3Dihub http://homer.ucsd.edu/homer/ STAR 2.7.10a https://academic.oup.com/bioinformatics/ article/29/1/15/272537 https://github.com/alexdobin/STAR MACS2 2.2.7.1 https://genomebiology.biomedcentral. com/articles/10.1186/gb-2008-9-9-r137 https://pypi.org/project/MACS2/ DeepTools v3.5.0 https://academic.oup.com/nar/article/44/ W1/W160/2499308 https://deeptools.readthedocs.io/en/ develop/ IGV (version 2.6.3) Broad Institute https://software.broadinstitute.org/ software/igv/download Prism (version 8.4.0) www.graphpad.com N/A Deposited data Deposited Data This study GSE213876 Other Detailed protocol of DR-6mA-seq This study Methods S1
Clone Assay:Article Title: The structure of lipid nanodisc-reconstituted TRPV3 reveals the gating mechanism.
Article Snippet: 1Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.. 2Division of Cell Signaling, National Institute for Physiological Sciences, National Institute of Natural Sciences, Okazaki, Japan.. 3Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan.
Article Title: Cryo-EM structure of the volume-regulated anion channel LRRC8D isoform identifies features important for substrate permeation
Article Snippet: Protein expression, purification, and sample preparation were performed as described previously , except that Sf9 insect cells from Spodoptera frugiperda (ATCC, CRL-1711) were used as the protein expression host. .. The human LRRC8D wild-type protein (NCBI Reference sequence number: NP_060573.2) was cloned from human brain cDNA (ZYAGEN) into the pFastBac1 vector (Thermo Fisher Scientific), with a C-terminal GFP-His8 tag and a tobacco etch virus (TEV) cleavage site, and was expressed in Sf9 insect cells. .. Cells were collected by centrifugation (5000 × g , 10 min, 4 °C) and disrupted by sonication in buffer (50 mM Tris, pH 8.0, 150 mM NaCl) supplemented with 5.2 μg mL −1 aprotinin, 2 μg mL −1 leupeptin, and 1.4 μg mL −1 pepstatin A (all from Calbiochem).
Plasmid Preparation:Article Title: The structure of lipid nanodisc-reconstituted TRPV3 reveals the gating mechanism.
Article Snippet: 1Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.. 2Division of Cell Signaling, National Institute for Physiological Sciences, National Institute of Natural Sciences, Okazaki, Japan.. 3Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan.
Article Title: Cryo-EM structure of the volume-regulated anion channel LRRC8D isoform identifies features important for substrate permeation
Article Snippet: Protein expression, purification, and sample preparation were performed as described previously , except that Sf9 insect cells from Spodoptera frugiperda (ATCC, CRL-1711) were used as the protein expression host. .. The human LRRC8D wild-type protein (NCBI Reference sequence number: NP_060573.2) was cloned from human brain cDNA (ZYAGEN) into the pFastBac1 vector (Thermo Fisher Scientific), with a C-terminal GFP-His8 tag and a tobacco etch virus (TEV) cleavage site, and was expressed in Sf9 insect cells. .. Cells were collected by centrifugation (5000 × g , 10 min, 4 °C) and disrupted by sonication in buffer (50 mM Tris, pH 8.0, 150 mM NaCl) supplemented with 5.2 μg mL −1 aprotinin, 2 μg mL −1 leupeptin, and 1.4 μg mL −1 pepstatin A (all from Calbiochem).
Article Title: Structural insights into inhibitory mechanism of human excitatory amino acid transporter EAAT2
Article Snippet: .. The sequence encoding the full-length human EAAT2 isoform 1 (SLC1A2; Uniprot ID P43004) was amplified from a human brain complementary DNA library (Zyagen) and inserted into the pEG BacMam vector , with the C-terminally fused tobacco etch virus (TEV) protease cleavage site, enhanced green fluorescent protein (eGFP) and His 8 -tag. .. Baculoviruses were generated in Spodoptera frugiperda Sf9 cells, using the Bac-to-Bac system (Invitrogen).
Amplification:
Article Title: Structural insights into inhibitory mechanism of human excitatory amino acid transporter EAAT2
Article Snippet: .. The sequence encoding the full-length human EAAT2 isoform 1 (SLC1A2; Uniprot ID P43004) was amplified from a human brain complementary DNA library (Zyagen) and inserted into the pEG BacMam vector , with the C-terminally fused tobacco etch virus (TEV) protease cleavage site, enhanced green fluorescent protein (eGFP) and His 8 -tag. .. Baculoviruses were generated in Spodoptera frugiperda Sf9 cells, using the Bac-to-Bac system (Invitrogen).
Real-time Polymerase Chain Reaction:
Serial Dilution:
|
