Merge branch 'key-resources' into 'master'

add key resources as markdown table

See merge request ceplas/publications/Wanke-2023!1

_publication/key-resources-table.md

+REAGENT or RESOURCE | SOURCE | IDENTIFIER
+--------------------|--------|-----------
+Bacterial and virus strains
+Escherichia coli MachI | University of Cologne, Germany (Prof. Dr. Ute Hoecker) | N/A
+Agrobacterium tumefaciens GV3101::pMP90RK | this paper | N/A
+Agrobacterium tumefaciens GV3101::pBIN61-p19 | this paper | N/A
+Chemicals, peptides, and recombinant proteins
+Horseradish peroxidase | Sigma-Aldrich | P6782; CAS: 9003-99-0
+L-012 | Wako Chemicals | 120-04891; CAS: 143556-24-5
+Rifampicin | Roth | 4163.2; CAS: 13292-46-1
+Kanamycin | Duchefa | K0126.0010; CAS: 25389-94-0
+Carbenicillin | Roth | 6344.1; CAS: 4800-94-6
+Gentamicin | Roth | 0233.2; CAS: 1405-41-0
+Sodium hypochlorite | Roth | 9062.4; CAS: 7681-52-9
+T4 polynucleotide kinase | New England BioLabs | CAT#M0201S
+T4 DNA ligase | New England BioLabs | CAT#M0202M
+DpnI | New England BioLabs | CAT#R0176L
+T4 DNA ligase buffer | New England BioLabs | CAT#B0202S
+N-naphthol | Sigma Aldrich | N1000-10G; CAS: 90-15-3
+D-glucose | Roth | 6887.2; CAS: 77938-63-7
+Laminaribiose β-1-3-(Glc)2 | Megazyme | O-LAM2; CAS: 34980-39-7
+Laminaritriose β-1-3-(Glc)3 | Megazyme | O-LAM3; CAS: 3256-04-0
+Laminaripentaose β-1-3-(Glc)5 | Megazyme | O-LAM5; CAS: 23743-55-7
+Gentiobiose β-1-6-(Glc)2 | Megazyme | O-GENT; CAS: 554-91-6
+endo-1,3-β-D-glucanase (barley BGLUII) | Megazyme | E-LAMHV; CAS: 9025-37-0
+Chitohexaose | Megazyme | O-CHI6; CAS: 38854-46-5
+Cellohexaose | Megazyme | O-CHE; CAS: 2478-35-5
+Xyloglucan oligomer (XXXG) | Megazyme | O-X3G4; CAS: 121591-98-8
+Laminarin from Eisenia bicyclis | Biosynth | YL02421; CAS: 9008-22-4
+Laminarin from Laminaria digitata | Sigma Aldrich | L9634-1G; CAS: 9008-22-4
+Elf18 | The Sainsbury Laboratory, United Kingdom (Prof. Dr. Cyril Zipfel) | N/A
+EZ-Link Hydrazide-Biotin | Thermo Scientific | CAT#21339
+Sodium cyanoborohydride | Sigma Aldrich | 42077-10G; CAS: 25895-60-7
+Aniline blue | Sigma Aldrich | 415049-25G; CAS: 666787-07-8
+Concanavalin A (ConA) - Alexa Fluor 633 | Invitrogen, Thermo Fisher Scientific | CAT#C21402
+Wheat Germ Agglutinin (WGA) - Alexa Fluor 488 | Invitrogen, Thermo Fisher Scientific | CAT#W11261
+Avidin | Sigma Aldrich | A9275-5MG; CAS: 1405-69-2
+Acetosyringone | Roth | 6003.2; CAS: 2478-38-8
+NeutrAvidin agarose resin | Thermo Fisher Scientific | CAT#29200
+Blue ink | Pelikan | 301010
+Gelrite | Duchefa | G1101; CAS: 71010-52-1
+Strep-Tactin Macroprep | IBA Lifesciences GmbH | 2-1505-010
+Critical commercial assays
+NucleoSpin Gel and PCR Clean-up Kit | Macherey-Nagel | 740609.50
+NucleoSpin Plasmid Kit | Macherey-Nagel | 740588.50
+Deposited data
+Proteomic data | ProteomeXchange Consortium via PRIDE partner repository (Perez-Riverol et al.73) | PXD046129
+Experimental models: Organisms/strains
+Serendipita indica: DSM11827 | German Collection of Microorganisms and Cell Cultures (DSMZ) | NCBI Taxonomy ID: 1109443
+Serendipita vermifera: MAFF305830 | NARO Research Center of Genetic Resources, Japan | NCBI Taxonomy ID: 933852
+Bipolaris sorokiniana: ND90Pr | Max Planck Institute for Terrestrial Microbiology, Marburg, Germany (Shadab Nizam) | NCBI Taxonomy ID: 665912
+Blumeria hordei: K1 | Hinze et al.74 | NCBI Taxonomy ID: 1283759
+Rhizophagus irregularis: DAOM197198 | Symplanta | 00101SP; https://www.symplanta.com/productcatalog.html
+Barley: control: Hordeum vulgare (cv. Golden Promise Fast) | Gol et al.42 | N/A
+Barley: gbp1 gbp2 #1: Hordeum vulgare (cv. Golden Promise Fast) gbp1-1 gbp2-1 | this paper | N/A
+Barley: gbp1 gbp2 #2: Hordeum vulgare (cv. Golden Promise Fast) gbp1-2 gbp2-2/gbp2-3 | this paper | N/A
+Nicotiana benthamiana | The Sainsbury Laboratory, United Kingdom (Prof. Dr. Cyril Zipfel) | N/A
+Oligonucleotides
+Primers for cloning see Table S1 | this paper | N/A
+Primers for site-directed mutagenesis see Table S1 | this paper | N/A
+Primers for CRISPR/Cas9 gRNA see Table S1 | this paper | N/A
+Primers for S. indica colonization assay (qPCR) see Table S1 | Chandrasekar et al.33 | N/A
+Primers for S. vermifera colonization assay (qPCR) see Table S1 | Mahdi et al.75 | N/A
+Primers for B. sorokiniana colonization assay (qPCR) see Table S1 | Mahdi et al.75 | N/A
+Primers for H. vulgare colonization assay (qPCR) see Table S1 | Deshmukh et al.76 | Accession no. M60175
+Primers for barley PR10 expression (qPCR) see Table S1 | Schäfer et al.77 | N/A
+Recombinant DNA
+pXCScpmv-HAStrep | Witte et al.78; Myrach et al.79 | N/A
+pXCScpmv-GBP1-HAStrep | This paper | N/A
+pXCScpmv-GBP1_E500A-HAStrep | This paper | N/A
+pMGE625 | Martin Luther University Halle-Wittenburg, Germany (Prof. Dr. Johannes Stuttmann) | N/A
+pMGE626 | Martin Luther University Halle-Wittenburg, Germany (Prof. Dr. Johannes Stuttmann) | N/A
+pMGE628 | Martin Luther University Halle-Wittenburg, Germany (Prof. Dr. Johannes Stuttmann) | N/A
+pMGE629 | Martin Luther University Halle-Wittenburg, Germany (Prof. Dr. Johannes Stuttmann) | N/A
+pMGE599 | Martin Luther University Halle-Wittenburg, Germany (Prof. Dr. Johannes Stuttmann) | N/A
+pMP202 | Martin Luther University Halle-Wittenburg, Germany (Prof. Dr. Johannes Stuttmann) | N/A
+Software and algorithms
+Flexanalysis software (v. 4.0) | Bruker Daltonics | https://www.bruker.com/en.html
+CRISPOR web tool (v. 4.97) | Concordet and Haeussler80 | http://crispor.tefor.net/
+ImageJ (v. 1.53) | Schneider et al.81 | https://imagej.nih.gov/ij/
+SparkControl (v. 2.1) | Tecan | https://lifesciences.tecan.com/multimode-plate-reader?p=tab--3
+Scaffold (v. 4) | Proteome Software | https://www.proteomesoftware.com/products/scaffold-5
+MSConvert package | ProteoWizard | https://proteowizard.sourceforge.io/download.html
+Mascot server (v. 2.3) | Matrix Science | https://www.matrixscience.com/server.html
+Other
+TECAN SPARK 10 M multiwell plate reader | Tecan | N/A
+PD MidiTrap G-10 column | Cytiva | 28918011
+TCS SP8 confocal microscope | Leica | https://www.leica-microsystems.com/
+AxioStar light microscope | Carl Zeiss | N/A
+Silica gel 60 F254 aluminum TLC plate | Merck Millipore | 105554
+MALDI-TOF mass spectrometer (rapifleX instrument) | Bruker | https://www.bruker.com/en/products-and-solutions/mass-spectrometry/maldi-tof/rapiflex.html
+Reverse phase trap column (Acclaim PepMap, C18 5 μm, 100 μm x 2 cm) | Thermo Scientific | N/A
+Analytical column (Acclaim PepMap 100, C18 3 μm, 75 μm x 50 cm) | Thermo Scientific | CAT#164570
+Orbitrap Fusion Tribrid mass spectrometer | Thermo Scientific | https://www.thermofisher.com/de/de/home/industrial/mass-spectrometry/liquid-chromatography-mass-spectrometry-lc-ms/lc-ms-systems/orbitrap-lc-ms/orbitrap-tribrid-mass-spectrometers.html#fusion-tribrid
+Nanoflow-UHPLC system (UltiMate3000 Dionex) | Thermo Scientific | N/A
+PD-10 desalting column | Sigma Aldrich | GE17-0851-01