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. Author manuscript; available in PMC: 2023 Oct 23.
Published in final edited form as: Cell Rep. 2023 Jan 30;42(2):112049. doi: 10.1016/j.celrep.2023.112049

KEY RESOURCES TABLE

REAGENT or RESOURCE Antibodies SOURCE IDENTIFIER
Antibodies
mouse anti-fentanyl monoclonal antibody M. Pravetoni, University of Washington N/A
mouse anti-fentanyl-FITC monoclonal antibody this paper N/A
mouse anti-VSG3 monoclonal antibody Pingeretal., 201714 N/A
goat anti-mouse IgG-HRP Jackson Immuno Research Cat#115-035-062; RRID: AB_2338504
streptavidin-BV785 BioLegend Cat#405249
rat anti-mouse CD19-BV412 BioLegend Cat#115537; RRID: AB_10895761
rat anti-mouse IgG1-BV650 BioLegend Cat#406629; RRID: AB_2716013
rat anti-mouse CD138-BV510 BioLegend Cat#142521; RRID: AB_2562727
rat anti-mouse GL-7-FITC BD Pharmingen Cat#553666; RRID: AB_394981
rat anti-mouse CD38-PE-Cy7 BioLegend Cat#102718; RRID AB_2275531
goat anti-mouse IgM-biotin Jackson ImmunoResearch Cat#115-065-075, RRID AB_2338566
rat anti-mouse IgD-APC-Cy7 BioLegend Cat#405716; RRID AB_10662544
streptavidin-HRP ThermoFisher Scientific Cat#N100
Bacterial and virus strains
E. coli DH5a Thermofisher Cat#18265017
E. coli BL21 (DE3) Thermofisher Cat#C600003
Chemicals, peptides, and recombinant proteins
fentanyl-LPSTGG this paper N/A
FITC Abcam Cat#ab102884
FITC-LPSTGG this paper N/A
fen-G4 peptide this paper N/A
fentanyl-citrate Sigma-Aldrich Cat#990-73-8
Fentanyl-citrate West-Ward N/A
fentanyl solution Sigma-Aldrich Cat#F-013
fentanyl-hapten-biotin this paper N/A
fentanyl LGC LGCAMP0528.00-02
fentanyl-d5 LGC LGCAMP0528.80-02
fentanyl-PE Marco Pravetoni, University of Washington N/A
decoy-PE-AF647 Marco Pravetoni, University of Washington N/A
EDC crosslinker ThermoFisher Scientific Cat#22980
ABTS tablets Roche Cat#11112422001
Srt-VSG3 protein this paper N/A
Recombinant RNase Inhibitor Takara Bio Europe S.A.S Cat#2313A
Penta-His-biotin conjugate Qiagen Cat#34440
Sortase A from S. pyogenes this paper N/A
Trizma® Hydrochlorid -hydrochlorid Sigma-Aldrich Cat#T3253
Sodium chloride Carl-Roth Cat# 3957.1
Imidazole Carl-Roth Cat#X998.4
2-Mercaptoethanol Sigma-Aldrich Cat#M6250
1,4-Dithiothreitol (DTT) Carl-Roth Cat#6908.1
LB-broth (Miller) Sigma-Aldrich Cat#L3522-250G
HEPES Carl-Roth Cat#9105
Dulbecco’s PBS Sigma-Aldrich Cat#D8537
Ammonium sulfate Carl-Roth Cat#3746
N-(2-Acetamido)-iminodiacetic acid Sigma-Aldrich Cat#00307
Polyethelene glycol 400 Merck Cat#8.07485.1000
Polyethelene glycol 6000 VWR Cat#26603-293
Glycerol Carl-Roth Cat#3783
Ethanol Sigma-Aldrich Cat#32205-M
Sodium acetate Carl-Roth Cat#6773
Triethanolamine Sigma-Aldrich Cat#90279
Magnesium sulfate heptahydrate Merck Cat#1.05886.0500
Sodium citrate tribasic dihydrate Sigma-Aldrich Cat#71402
Ethelene glycol MP Cat#151089
Hexylene glycol (MPD) Sigma-Aldrich Cat#112100
HMI-9 Medium PAN Biotech SO-15701
FreeStyle 293 Expression Medium Gibco Cat#12338-018
Carbonate-bicarbonate buffer capsules Sigma-Aldrich Cat#C3041
20x PBS Tween 20 Thermo Scientific Cat#PI28352
Gelatin from porcine skin Sigma-Aldrich Cat#G2500
Octet Streptavidin biosensors Sartorius Cat#18-5019
Tramadol hydrochloride Fagron 20L09-U10-009586
Naloxone hydrochloride dihydrate Sigma-Aldrich N7758
Acetonitrile (LC-MS Grade) Carl Roth Cat#AE70.2
Phosphoric acid Carl Roth Cat#6366.1
Methanol (ROTISOLV®) Carl Roth Cat#AE71.1
Formic acid Carl Roth Cat#1EHK.1
Ammonium hydroxide Carl Roth Cat#6774.1
Ammonium formate Carl Roth Cat#5093.1
Critical commercial assays
Quantum™ FITC-5 MESF kit Bangs Laboratories CAT#555
LIVE/DEAD™ Fixable Blue Dead Cell Stain Kit Invitrogen Cat#L23105
Maxima H Minus Reverse Transcriptase, 10000U ThermoScientific Cat#EP0752
Kapa High Fidelity Hot Start Roche Cat#7958935001
Nextera XT DNA Library Preparation Kit (96SMP) illumina GmbH Cat#FC-131-1096
QuikChange Lightning site-directed mutagenesis kit Agilent technologies Cat#210513
Pierce™ Protein G Agarose ThermoFisher Scientific Cat#20397
Gibco™ 293fectin™ Transfection Reagent ThermoFisher Scientific Cat#12347750
Ni-NTA agarose Qiagen Cat#30230
SigmaFAST OPD Sigma-Aldrich Cat#P9187-5SET
Superdex 200 Increase 10/300 GL column Cytiva Cat#28-9909-44
Q-Sepharose Fast-Flow Cytiva Cat#17-0510-01
NEBuilder Master Mix New England Biolabs Cat#M5520AA
Phusion HiFi DNA Polymerase New England Biolabs Cat#M0530L
FreeStyle™ MAX Reagent Gibco Cat#16447100
GeneJET Plasmid Miniprep Kit Thermo Scientific Cat#K0502
Monarch® DNA Gel Extraction Kit New England Biolabs Cat#T1020S
Q5® High-Fidelity 2x Master Mix New England Biolabs Cat#M0492S
AgeI-HF® New England Biolabs Cat#R3552S
SalI-HF® New England Biolabs Cat#R3138S
BsiWI-HF® New England Biolabs Cat#R3553S
EcoRI-HF® New England Biolabs Cat#R3101S
Deposited data
Crystal structures Protein DataBank PDB codes: 7QT0, 7QT2, 7QT3, 7QT4
RNA-seq data GEO Upon request
Experimental models: Cell lines
FreeStyle 293F ThermoFisher Scientific Cat#R79007
Experimental models: Organisms/Strains
C57BL/6JRj Javier-labs Cat#C57BL/6JRj
Trypanosoma brucei brucei Lister 427 2T1 Srt-VSG3-S317A GPI-PLC WT Pingeretal., 201714 N/A
Trypanosoma brucei brucei Lister 427 Srt-VSG3-S317A GPI-PLC −/− this paper N/A
Oligonucleotides
dNTP Mix (10 mM each)-1 mL ThermoFisher Scientific Cat#R0192
Oligonucleotides See Table S2 N/A
Recombinant DNA
IGγ1-, IGκ- or IGλ-expression vectors Tiller et al., 200862 N/A
Fab heavy and light chain expression vectors Mirjana Lilic, The Rockefeller University N/A
Sortase A from Streptococcus pyogenes with N-terminal His6-Tag in pET28a expression vector this paper N/A
Software and algorithms
FlowJo v10.0.8 Tree Star https://www.flowjo.com/solutions/flowjo/downloads
GraphPad Prism v6.07 GraphPad http://www.graphpad.com
R v4.0.3 and v4.1 The R project for statistical computing http://www.R-project.org/
FACSDiVa v8.0.1 Becton Dickinson Cat#659528
Adobe Illustrator CS6 v16.0.3 Adobe http://www.adobe.com/de/products/illustrator.html
Adobe Photoshop 2021 v22.0.0 Adobe https://www.adobe.com/de/products/photoshop
Microsoft PowerPoint v16 Microsoft https://www.microsoft.com/de-de/microsoft-365/powerpoint
Microsoft Excel v16 Microsoft https://www.microsoft.com/de-de/microsoft-365/excel
CCP4MG v2.10.11 McNicholas et al., 201163; de Beeretal., 201 464; https://pymol.org/2/ https://www.ccp4.ac.uk/MG/
Biorender Biorender https://biorender.com/
XDS Kabschetal., 201065 http://xds.mpimf-heidelberg.mpg.de
Phaser McCoy et al., 200766 https://www.phenix-online.org
Phenix Adams et al., 201067 https://www.phenix-online.org
Coot Emsleyetal., 201068 https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
PDB-redo Joosten et al., 201469 https://pdb-redo.eu/
PyMol v2.4.2 N/A https://pymol.sourceforge.net
TrimGalore v0.6.4_dev Krueger et al., 201570 http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
MultiQC v0.4 Ewelsetal., 201671 https://multiqc.info/
FastQC v0.11.9 N/A https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Samtools v1.9 Danecek et al., 202172 http://www.htslib.org/
STAR v2.6.0a Dobinetal., 201373 https://github.com/alexdobin/STAR
Bioconductor v3.12 Bioconductor Software Packages https://bioconductor.org/packages/3.12/bioc/
Bioconductor v3.14 Bioconductor Software Packages https://bioconductor.org/packages/3.14/bioc/
GenomicFeatures v1.42.3 Lawrence et al., 201374 https://bioconductor.org/packages/3.12/bioc/html/GenomicFeatures.html
Ensembldb v2.14.1 Raineretal., 201975 https://bioconductor.org/packages/3.12/bioc/html/ensembldb.html
GenomicAlignments v1.26.0 Lawrence et al., 201374 https://bioconductor.org/packages/3.12/bioc/html/GenomicAlignments.html
AnnotationDbi v1.52.0 Pagès et al., 202076 https://bioconductor.org/packages/3.12/bioc/html/AnnotationDbi.html
SingleCellExperiment v1.16.0 Amezquita et al., 202077 https://bioconductor.org/packages/3.14/bioc/html/SingleCellExperiment.html
scater v1.22 McCarthy et al., 201778 https://bioconductor.org/packages/3.14/bioc/html/scater.html
scran v1.22.1 Lunetal., 201679 https://bioconductor.org/packages/3.14/bioc/html/scran.html
org.Mm.eg.db v3.12.0 Carlson etal.,201980 https://bioconductor.statistik.tu-dortmund.de/packages/3.12/data/annotation/html/org.Mm.eg.db.html
rLiger v1.0.0 Welch etal., 201941 https://www.rdocumentation.org/packages/rliger/versions/1.0.0
MAST v1.16.0 Finaketal., 201581 https://bioconductor.org/packages/3.12/bioc/html/MAST.html
Seurat v4.0 Haoetal., 202182 https://satijalab.org/seurat/
BASIC v1.5.0 Canzar et al., 201783 https://people.cs.uchicago.edu/~aakhan/BASIC/
Blast v2.11.0 Alquicira-Hernandez et al., 202184 https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastNews
Igblast v1.16.0 Ye etal., 201385 https://ncbi.github.io/igblast/
Change-O v1.0.0 Gupta etal.,201586 https://changeo.readthedocs.io/en/stable/
Shazam v1.1.0 Gupta etal.,201586 https://shazam.readthedocs.io/en/stable/#shazam
ggplot2 v3.3.5 Wickham, 200987 https://github.com/tidyverse/ggplot2/releases/tag/v3.3.5
gridExtra v2.3 B. Auguie https://cran.r-project.org/web/packages/gridExtra/index.html
ggrepel v0.9.1 K. Slowikowski https://cran.r-project.org/web/packages/ggrepel/index.html
Circlize vO.4.13 Gu etal., 201488 https://mran.revolutionanalytics.com/snapshot/2021-11-01/web/packages/circlize/index.html
Octet DataAnalysis v12.0.2.3 Sartorius N/A
LABORAS v2 Metris https://www.metris.nl/en/products/laboras/laboras2/
Analyst v1.6 Sciex https://de-store.sciex.com/de/EUR/software
MassHunter Agilent https://www.agilent.com/en/product/software-informatics/mass-spectrometry-software