Saline:Article Title: Chimeric TNT-3 antibody/murine interferon-gamma fusion protein for the immunotherapy of solid malignancies.
Article Snippet: Interferon-g (IFN-g) has been used in the experimental treatment of cancer with limited success.. Despite direct cytotoxic effects on tumor cells and the ability to stimulate the antitumor activities of a variety of effector cells, IFN-g has not been found to produce impressive therapeutic responses partly because of inadequate sustained intratumoral concentrations and systemic toxicity.. To overcome these obstacles, we have developed an antibody/murine IFN-g fusion protein (chTNT-3/muIFN-g), which utilizes the tumor necrosis therapy antibody, chTNT-3, to target murine IFN-g to necrotic regions of solid tumors implanted in immunocompetent BALB/c mice.
other:Article Title: Protocol for the isolation and purification of human follicular dendritic cells for functional assays.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Brilliant Violet 421 anti-human CD31 Antibody Biolegend Cat# 303124; RRID: AB_2563810 FITC anti-human CD35 Antibody Biolegend Cat# 333404, RRID: AB_2085022 PE/Cyanine7 anti-human Podoplanin Antibody Biolegend Cat# 337014, RRID: AB_2563368 PerCP/Cyanine5.5 anti-human CD55 Antibody Biolegend Cat# 311316, RRID: AB_2565480 APC anti-human CD55 Antibody Biolegend Cat# 311311, RRID: AB_2075857 Helix NP NIR Biolegend Cat# 425301 Purified anti-human CD35 Sony Cat# 2267010 MojoSort Streptavidin Nanobeads Biolegend Cat# 480016 UltraComp eBeads Compensation Beads Invitrogen Cat# 01-2222-41 Biological samples Human tonsils (from infants, 2–16 years old) Diakonessenhuis Utrecht N/A Chemicals, peptides, and recombinant proteins HBSS, no calcium, no magnesium, no phenol red Gibco Cat# 14175095 IMDM Gibco Cat# 12440053 FBS Gibco Cat# 16000044 (Continued on next page) 2 STAR Protocols 4, 102404, September 15, 2023 Continued REAGENT or RESOURCE SOURCE IDENTIFIER DNase I Roche Cat# 10104159001 Collagenase, Type IV, powder Gibco Cat# 17104019 HEPES (1 M) Gibco Cat# 15630080 Penicillin-Streptomycin (10,000 U/mL) Gibco Cat# 15140122 MEM Non-Essential Amino Acids Solution (1003) Gibco Cat# 11140035 Sodium pyruvate (100 mM) Gibco Cat# 11360070 Gentamycin Sigma-Aldrich Cat# G1397 Percoll Cytiva Cat# 17-0891-01 Phosphate buffered saline Sigma Cat# 806552-500ML Poly-D-Lysine Gibco Cat# A3890401 Collagen, Type I solution from rat tail Sigma-Aldrich Cat# C3867-1VL Laminin Roche Cat# 11243217001 EZ-Link Sulfo-NHS-LC-Biotinylation Kit Thermo Scientific Cat# 21435 Software and algorithms FlowJo Software BD Biosciences N/A Other 96-well plate for microscopy and culture Cellvis Cat# P96-1.5P RVS sieve 18 cm Blokker Cat# 0722559 RVS mini sieve 7,5 cm Blokker Cat# 0722551 Pipette Filler, S1, Thermo Scientific (Pipetboy) Thermo Scientific Cat# 89204-754 CELLSTAR Centrifuge Tubes Greiner Bio-One Cat# 227261 Disposable serological pipettes 10 mL Greiner Bio-One Cat# 607180 Disposable serological pipettes 25 mL Greiner Bio-One Cat# 760180 Scissors Fine Science Tools Cat# 14060-11 Petri dish Falcon Cat# 351029 MojoSort Magnet Biolegend Cat# 480019 Round-bottom polystyrene tubes Corning Cat# 734-0442 Sony MA900 Multi-Application Cell Sorter Sony N/A Cell strainer 70 mm VWR Cat# 76327-100 Pasteur pipettes Kartell Cat# KART334 ll OPEN ACCESSProtocol
Recombinant:Article Title: Quantify permeability using on-a-chip models in high-throughput applications.
Article Snippet: Traditionally, to quantify permeability of a biological barrier, the initial slope is used, based on the assumption of sink condition (concentration of the donor is constant, and the receiver increases less than 10%).. With on-a-chip barrier models, this assumption fails in cell-free or leaky conditions, which requires the use of the exact solution.. To encounter a time delay from performing the assay and acquiring the data, we present a protocol with the exact equation modified to incorporate a time offset.
Article Title: Single-molecule footprinting identifies context-dependent regulation of enhancers by DNA methylation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, Peptides, and Recombinant Proteins Dulbecco’s Modified Eagle Medium, high glucose Gibco Cat#41965039 FBS Embryomax Millipore Cat#ES-009-B L-glutamine Gibco Cat#A2916801 Leukemia inhibitory factor (LIF) prepared in house N/A MEM Non-Essential Amino Acids Solution (1003) Gibco Cat11140050 2-Mercaptoethanol Merck Cat#M6250 Sodium pyruvate Gibco Cat#11360070 Trypsin-EDTA (0.25%) Gibco Cat#25200056 GpC Methyltransferase (M.CviPI) New England Biolabs Cat#M0227 S-adenosylmethionine (SAM) NEB Cat#86867-01-8 Biotin-11-UTP PerkinElmer Cat#NEL544001EA Biotin-11-CTP PerkinElmer Cat#NEL542001EA GTP Roche Cat#11277057001 ATP Roche Cat#11277057001 Streptavidin M280 beads Invitrogen Cat#112.06D GlycoBlue Invitrogen Cat#AM9515 SUPERase,In RNase Inhibitor Invitrogen Cat#AM2694 T4 RNA ligase I NEB Cat#M0204 RNA50 pyrophosphohydrolase (RppH) NEB Cat#M0356S ThermoPol Reaction Buffer NEB Cat#B9004S T4 polynucleotide kinase (PNK) NEB Cat#M0201 Superscript IV reverse transcriptase Invitrogen Cat#18090010 Phusion polymerase NEB Cat#M0530 Critical Commercial Assays EZ DNA Methylation-Gold Kit Zymo Research Cat#D5005 SureSelectXT Mouse Methyl-Seq Capture Library Agilent Cat#931052 SureSelectXT Methyl-Seq Reagent Kit Agilent Cat#G9651A NEBNext Ultra II DNA Library Prep Kit for Illumina NEB Cat#E7645L NEBNext Multiplex Oligos for Illumina NEB Cat#E7335L Quick-RNA Miniprep Kit Zymo Research Cat#R1054 Deposited Data ChIP Myc mESC WT Chronis et al.,58 Das et al.,59 and Mor et al.60 GEO: GSM1059010; GSM2417145; GSM2739921 ChIP CTCF mESC WT Stadler et al.10 GEO: GSM747534; GSM747535; GSM747536 ChIP H3K4me1 mESC WT Stadler et al.10 GEO: GSM747542 ChIP H3K4me3 mESC WT Shen et al.61 GEO: GSM723017 ChIP H3K27Ac mESC WT Shen et al.61 GEO: GSM851278 (Continued on next page) Molecular Cell 83, 787–802.e1–e9, March 2, 2023 e1 ..
Software:Article Title: Quantify permeability using on-a-chip models in high-throughput applications.
Article Snippet: Traditionally, to quantify permeability of a biological barrier, the initial slope is used, based on the assumption of sink condition (concentration of the donor is constant, and the receiver increases less than 10%).. With on-a-chip barrier models, this assumption fails in cell-free or leaky conditions, which requires the use of the exact solution.. To encounter a time delay from performing the assay and acquiring the data, we present a protocol with the exact equation modified to incorporate a time offset.
Microscopy:Article Title: Quantify permeability using on-a-chip models in high-throughput applications.
Article Snippet: Traditionally, to quantify permeability of a biological barrier, the initial slope is used, based on the assumption of sink condition (concentration of the donor is constant, and the receiver increases less than 10%).. With on-a-chip barrier models, this assumption fails in cell-free or leaky conditions, which requires the use of the exact solution.. To encounter a time delay from performing the assay and acquiring the data, we present a protocol with the exact equation modified to incorporate a time offset.
Modification:Article Title: Single-molecule footprinting identifies context-dependent regulation of enhancers by DNA methylation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, Peptides, and Recombinant Proteins Dulbecco’s Modified Eagle Medium, high glucose Gibco Cat#41965039 FBS Embryomax Millipore Cat#ES-009-B L-glutamine Gibco Cat#A2916801 Leukemia inhibitory factor (LIF) prepared in house N/A MEM Non-Essential Amino Acids Solution (1003) Gibco Cat11140050 2-Mercaptoethanol Merck Cat#M6250 Sodium pyruvate Gibco Cat#11360070 Trypsin-EDTA (0.25%) Gibco Cat#25200056 GpC Methyltransferase (M.CviPI) New England Biolabs Cat#M0227 S-adenosylmethionine (SAM) NEB Cat#86867-01-8 Biotin-11-UTP PerkinElmer Cat#NEL544001EA Biotin-11-CTP PerkinElmer Cat#NEL542001EA GTP Roche Cat#11277057001 ATP Roche Cat#11277057001 Streptavidin M280 beads Invitrogen Cat#112.06D GlycoBlue Invitrogen Cat#AM9515 SUPERase,In RNase Inhibitor Invitrogen Cat#AM2694 T4 RNA ligase I NEB Cat#M0204 RNA50 pyrophosphohydrolase (RppH) NEB Cat#M0356S ThermoPol Reaction Buffer NEB Cat#B9004S T4 polynucleotide kinase (PNK) NEB Cat#M0201 Superscript IV reverse transcriptase Invitrogen Cat#18090010 Phusion polymerase NEB Cat#M0530 Critical Commercial Assays EZ DNA Methylation-Gold Kit Zymo Research Cat#D5005 SureSelectXT Mouse Methyl-Seq Capture Library Agilent Cat#931052 SureSelectXT Methyl-Seq Reagent Kit Agilent Cat#G9651A NEBNext Ultra II DNA Library Prep Kit for Illumina NEB Cat#E7645L NEBNext Multiplex Oligos for Illumina NEB Cat#E7335L Quick-RNA Miniprep Kit Zymo Research Cat#R1054 Deposited Data ChIP Myc mESC WT Chronis et al.,58 Das et al.,59 and Mor et al.60 GEO: GSM1059010; GSM2417145; GSM2739921 ChIP CTCF mESC WT Stadler et al.10 GEO: GSM747534; GSM747535; GSM747536 ChIP H3K4me1 mESC WT Stadler et al.10 GEO: GSM747542 ChIP H3K4me3 mESC WT Shen et al.61 GEO: GSM723017 ChIP H3K27Ac mESC WT Shen et al.61 GEO: GSM851278 (Continued on next page) Molecular Cell 83, 787–802.e1–e9, March 2, 2023 e1 ..
Reverse Transcription:Article Title: Single-molecule footprinting identifies context-dependent regulation of enhancers by DNA methylation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, Peptides, and Recombinant Proteins Dulbecco’s Modified Eagle Medium, high glucose Gibco Cat#41965039 FBS Embryomax Millipore Cat#ES-009-B L-glutamine Gibco Cat#A2916801 Leukemia inhibitory factor (LIF) prepared in house N/A MEM Non-Essential Amino Acids Solution (1003) Gibco Cat11140050 2-Mercaptoethanol Merck Cat#M6250 Sodium pyruvate Gibco Cat#11360070 Trypsin-EDTA (0.25%) Gibco Cat#25200056 GpC Methyltransferase (M.CviPI) New England Biolabs Cat#M0227 S-adenosylmethionine (SAM) NEB Cat#86867-01-8 Biotin-11-UTP PerkinElmer Cat#NEL544001EA Biotin-11-CTP PerkinElmer Cat#NEL542001EA GTP Roche Cat#11277057001 ATP Roche Cat#11277057001 Streptavidin M280 beads Invitrogen Cat#112.06D GlycoBlue Invitrogen Cat#AM9515 SUPERase,In RNase Inhibitor Invitrogen Cat#AM2694 T4 RNA ligase I NEB Cat#M0204 RNA50 pyrophosphohydrolase (RppH) NEB Cat#M0356S ThermoPol Reaction Buffer NEB Cat#B9004S T4 polynucleotide kinase (PNK) NEB Cat#M0201 Superscript IV reverse transcriptase Invitrogen Cat#18090010 Phusion polymerase NEB Cat#M0530 Critical Commercial Assays EZ DNA Methylation-Gold Kit Zymo Research Cat#D5005 SureSelectXT Mouse Methyl-Seq Capture Library Agilent Cat#931052 SureSelectXT Methyl-Seq Reagent Kit Agilent Cat#G9651A NEBNext Ultra II DNA Library Prep Kit for Illumina NEB Cat#E7645L NEBNext Multiplex Oligos for Illumina NEB Cat#E7335L Quick-RNA Miniprep Kit Zymo Research Cat#R1054 Deposited Data ChIP Myc mESC WT Chronis et al.,58 Das et al.,59 and Mor et al.60 GEO: GSM1059010; GSM2417145; GSM2739921 ChIP CTCF mESC WT Stadler et al.10 GEO: GSM747534; GSM747535; GSM747536 ChIP H3K4me1 mESC WT Stadler et al.10 GEO: GSM747542 ChIP H3K4me3 mESC WT Shen et al.61 GEO: GSM723017 ChIP H3K27Ac mESC WT Shen et al.61 GEO: GSM851278 (Continued on next page) Molecular Cell 83, 787–802.e1–e9, March 2, 2023 e1 ..
Methylation:Article Title: Single-molecule footprinting identifies context-dependent regulation of enhancers by DNA methylation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, Peptides, and Recombinant Proteins Dulbecco’s Modified Eagle Medium, high glucose Gibco Cat#41965039 FBS Embryomax Millipore Cat#ES-009-B L-glutamine Gibco Cat#A2916801 Leukemia inhibitory factor (LIF) prepared in house N/A MEM Non-Essential Amino Acids Solution (1003) Gibco Cat11140050 2-Mercaptoethanol Merck Cat#M6250 Sodium pyruvate Gibco Cat#11360070 Trypsin-EDTA (0.25%) Gibco Cat#25200056 GpC Methyltransferase (M.CviPI) New England Biolabs Cat#M0227 S-adenosylmethionine (SAM) NEB Cat#86867-01-8 Biotin-11-UTP PerkinElmer Cat#NEL544001EA Biotin-11-CTP PerkinElmer Cat#NEL542001EA GTP Roche Cat#11277057001 ATP Roche Cat#11277057001 Streptavidin M280 beads Invitrogen Cat#112.06D GlycoBlue Invitrogen Cat#AM9515 SUPERase,In RNase Inhibitor Invitrogen Cat#AM2694 T4 RNA ligase I NEB Cat#M0204 RNA50 pyrophosphohydrolase (RppH) NEB Cat#M0356S ThermoPol Reaction Buffer NEB Cat#B9004S T4 polynucleotide kinase (PNK) NEB Cat#M0201 Superscript IV reverse transcriptase Invitrogen Cat#18090010 Phusion polymerase NEB Cat#M0530 Critical Commercial Assays EZ DNA Methylation-Gold Kit Zymo Research Cat#D5005 SureSelectXT Mouse Methyl-Seq Capture Library Agilent Cat#931052 SureSelectXT Methyl-Seq Reagent Kit Agilent Cat#G9651A NEBNext Ultra II DNA Library Prep Kit for Illumina NEB Cat#E7645L NEBNext Multiplex Oligos for Illumina NEB Cat#E7335L Quick-RNA Miniprep Kit Zymo Research Cat#R1054 Deposited Data ChIP Myc mESC WT Chronis et al.,58 Das et al.,59 and Mor et al.60 GEO: GSM1059010; GSM2417145; GSM2739921 ChIP CTCF mESC WT Stadler et al.10 GEO: GSM747534; GSM747535; GSM747536 ChIP H3K4me1 mESC WT Stadler et al.10 GEO: GSM747542 ChIP H3K4me3 mESC WT Shen et al.61 GEO: GSM723017 ChIP H3K27Ac mESC WT Shen et al.61 GEO: GSM851278 (Continued on next page) Molecular Cell 83, 787–802.e1–e9, March 2, 2023 e1 ..
Multiplex Assay:Article Title: Single-molecule footprinting identifies context-dependent regulation of enhancers by DNA methylation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, Peptides, and Recombinant Proteins Dulbecco’s Modified Eagle Medium, high glucose Gibco Cat#41965039 FBS Embryomax Millipore Cat#ES-009-B L-glutamine Gibco Cat#A2916801 Leukemia inhibitory factor (LIF) prepared in house N/A MEM Non-Essential Amino Acids Solution (1003) Gibco Cat11140050 2-Mercaptoethanol Merck Cat#M6250 Sodium pyruvate Gibco Cat#11360070 Trypsin-EDTA (0.25%) Gibco Cat#25200056 GpC Methyltransferase (M.CviPI) New England Biolabs Cat#M0227 S-adenosylmethionine (SAM) NEB Cat#86867-01-8 Biotin-11-UTP PerkinElmer Cat#NEL544001EA Biotin-11-CTP PerkinElmer Cat#NEL542001EA GTP Roche Cat#11277057001 ATP Roche Cat#11277057001 Streptavidin M280 beads Invitrogen Cat#112.06D GlycoBlue Invitrogen Cat#AM9515 SUPERase,In RNase Inhibitor Invitrogen Cat#AM2694 T4 RNA ligase I NEB Cat#M0204 RNA50 pyrophosphohydrolase (RppH) NEB Cat#M0356S ThermoPol Reaction Buffer NEB Cat#B9004S T4 polynucleotide kinase (PNK) NEB Cat#M0201 Superscript IV reverse transcriptase Invitrogen Cat#18090010 Phusion polymerase NEB Cat#M0530 Critical Commercial Assays EZ DNA Methylation-Gold Kit Zymo Research Cat#D5005 SureSelectXT Mouse Methyl-Seq Capture Library Agilent Cat#931052 SureSelectXT Methyl-Seq Reagent Kit Agilent Cat#G9651A NEBNext Ultra II DNA Library Prep Kit for Illumina NEB Cat#E7645L NEBNext Multiplex Oligos for Illumina NEB Cat#E7335L Quick-RNA Miniprep Kit Zymo Research Cat#R1054 Deposited Data ChIP Myc mESC WT Chronis et al.,58 Das et al.,59 and Mor et al.60 GEO: GSM1059010; GSM2417145; GSM2739921 ChIP CTCF mESC WT Stadler et al.10 GEO: GSM747534; GSM747535; GSM747536 ChIP H3K4me1 mESC WT Stadler et al.10 GEO: GSM747542 ChIP H3K4me3 mESC WT Shen et al.61 GEO: GSM723017 ChIP H3K27Ac mESC WT Shen et al.61 GEO: GSM851278 (Continued on next page) Molecular Cell 83, 787–802.e1–e9, March 2, 2023 e1 ..
Chromatin Immunoprecipitation:Article Title: Single-molecule footprinting identifies context-dependent regulation of enhancers by DNA methylation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, Peptides, and Recombinant Proteins Dulbecco’s Modified Eagle Medium, high glucose Gibco Cat#41965039 FBS Embryomax Millipore Cat#ES-009-B L-glutamine Gibco Cat#A2916801 Leukemia inhibitory factor (LIF) prepared in house N/A MEM Non-Essential Amino Acids Solution (1003) Gibco Cat11140050 2-Mercaptoethanol Merck Cat#M6250 Sodium pyruvate Gibco Cat#11360070 Trypsin-EDTA (0.25%) Gibco Cat#25200056 GpC Methyltransferase (M.CviPI) New England Biolabs Cat#M0227 S-adenosylmethionine (SAM) NEB Cat#86867-01-8 Biotin-11-UTP PerkinElmer Cat#NEL544001EA Biotin-11-CTP PerkinElmer Cat#NEL542001EA GTP Roche Cat#11277057001 ATP Roche Cat#11277057001 Streptavidin M280 beads Invitrogen Cat#112.06D GlycoBlue Invitrogen Cat#AM9515 SUPERase,In RNase Inhibitor Invitrogen Cat#AM2694 T4 RNA ligase I NEB Cat#M0204 RNA50 pyrophosphohydrolase (RppH) NEB Cat#M0356S ThermoPol Reaction Buffer NEB Cat#B9004S T4 polynucleotide kinase (PNK) NEB Cat#M0201 Superscript IV reverse transcriptase Invitrogen Cat#18090010 Phusion polymerase NEB Cat#M0530 Critical Commercial Assays EZ DNA Methylation-Gold Kit Zymo Research Cat#D5005 SureSelectXT Mouse Methyl-Seq Capture Library Agilent Cat#931052 SureSelectXT Methyl-Seq Reagent Kit Agilent Cat#G9651A NEBNext Ultra II DNA Library Prep Kit for Illumina NEB Cat#E7645L NEBNext Multiplex Oligos for Illumina NEB Cat#E7335L Quick-RNA Miniprep Kit Zymo Research Cat#R1054 Deposited Data ChIP Myc mESC WT Chronis et al.,58 Das et al.,59 and Mor et al.60 GEO: GSM1059010; GSM2417145; GSM2739921 ChIP CTCF mESC WT Stadler et al.10 GEO: GSM747534; GSM747535; GSM747536 ChIP H3K4me1 mESC WT Stadler et al.10 GEO: GSM747542 ChIP H3K4me3 mESC WT Shen et al.61 GEO: GSM723017 ChIP H3K27Ac mESC WT Shen et al.61 GEO: GSM851278 (Continued on next page) Molecular Cell 83, 787–802.e1–e9, March 2, 2023 e1 ..
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