other:
Light Microscopy:Article Title: Refined model of common peroneal nerve injury and regeneration: A neurophysiological, morphometric, and functional analysis in the adult rat.
Article Snippet: Muscles were formalin fixed for 24 h, paraffin embedded, cut to 8 μm (Leica Ultracut RM 22359) and NADH stained for 15 min at 37 ◦C (Tris buffer, NBT, NADH). .. Muscle fiber area was recorded using light microscopy (Nikon Eclipse Ts2R) and measurement via a dedicated ImageJ plugin (Image J plugin MyoSAT Version 3.5, Cheetham Lab, Department of Biomedical Science, Ohio University, Athens, Ohio, USA). .. For statistical analysis, all data were collected in Microsoft® Excel® (Microsoft 365 MSO, Version 2505), analyzed and visualized with GraphPad Prism (Version 10.5.0 774).
Software:Article Title: Turn-key mapping of cell receptor force orientation and magnitude using a commercial structured illumination microscope
Article Snippet: .. Accordingly, we have switched from the ImageJ plugin FairSIM to the Nikon Elements 12 software, which offers greater control over reconstruction. ..
Article Title: The actin networks of chytrid fungi reveal evolutionary loss of cytoskeletal complexity in the fungal kingdom.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Penicillin/streptomycin Thermo-Fisher Cat#P4333-20ML Concanavalin A Sigma Cat#C2010 LatrunculinB Millipore Cat#4280201MG CK666 Calbiochem/Sigma Cat#182515 CK689 Calbiochem/Sigma Cat#182517 SMIFH2 Tocris Bioscience Cat#440110 DAPI Life Technologies Cat#D1306 Alexa Fluor488 Phalloidin Life Technologies Cat#A12379 Polyethyleneimine Sigma Cat#P3143 Chitinase Sigma Cat#C6137-5UN Experimental models: organisms/strains Batrachochytrium dendrobatidis strain JEL423 Joyce Longcore JEL423 Batrachochytrium salamandrivorans isolate AMFP1 Frank Pasmans AMFP1 Spizellomyces punctatus Koch type isolate NG-3 ATCC 48900 Rhizoclosmatium globosum strain JEL800 Tim James (https://czeum.herb.lsa.umich.edu/) JEL800 Software and algorithms Basic Local Alignment Search Tool (BLAST) 67 https://blast.ncbi.nlm.nih.gov/Blast.cgi Position Specific Iteration-BLAST (PSI-BLAST) 68 https://blast.ncbi.nlm.nih.gov/Blast.cgi UniprotKB https://www.uniprot.org/ N/A HMMER suite v3.2.1 http://Hmmer.org http://Hmmer.org Pfam database v32 69 http://pfam.xfam.org European Bioinformatics Institute (EMBL-EBI) https://www.ebi.ac.uk/ https://www.ebi.ac.uk/ Coiled-Coil predictor 70 N/A Phobius program 71 N/A CD-hit program 72,73 N/A IQTree webserver 74 http://iqtree.cibiv.univie.ac.at/ iTOL v5.5.1 75 https://itol.embl.de/ FIJI 76 https://imagej.net/Fiji/Downloads CellCounter FIJI plugin Kurt De Vos https://imagej.nih.gov/ij/plugins/ cell-counter.html Autoquant X3 vX3.1.3 Media Cybernetics https://www.mediacy.com/79- products/autoquant-x3 NIS Elements w/ Advanced Research Package Nikon https://www.microscope.healthcare. nikon.com/products/software/niselements/nis-elements-advancedresearch Other Batrchochytirum dendrobatidis JAM81 reference assembly v1.0 US DOE Joint Genome Institute NCBI: GCA_000203795.1 Batrachochytirum dendrobatidis JEL423 assembly Broad Institute NCBI: GCA_000149865.1 Batrachochytrium salamandrivorans representative assembly (assembly Batr_sala_BS_V1) Broad Institute NCBI: GCA_002006685.1 Spizellomyces punctatus DAOM BR117 representative assembly (S_punctatus_V1) Broad Institute NCBI: GCA_000182565.2 (Continued on next page) e1 Current Biology 31, 1192–1205.e1–e6, March 22, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Rhizoclosmatium globosum JEL800 representative assembly (Rhihy1) DOE Joint Genome Institute NCBI: GCA_002104985.1 Allomyces macrogynus ATCC 38327 representative assembly (A_macrogynus_V3) Broad Institute NCBI: GCA_000151295.1 Saccharomyces cerevisiae S288C NCBI RefSeq build R64 assembly Saccharomyces Genome Database NCBI: GCF_000146045.2 Schizosaccharomyces pombe strain 972 NCBI RefSeq assembly S. pombe European Sequencing Consortium (EUPOM) NCBI: GCF_000002945.2 Schizosaccharomyces japonicus strain yFS275 NCBI RefSeq assembly Broad Institute NCBI: GCF_000149845.2 Candida albicans strain SC5314 NCBI RefSeq assembly (assembly ASM18296v3) Stanford University NCBI: GCA_000182965.3 Aspergillus nidulans strain FGSC A4 NCBI RefSeq assembly (assembly ASM14920v2) Broad Institute NCBI: GCA_000149205.2 Magnaporthe oryzae strain 70-15 NCBI RefSeq assembly (Pyricularia oryzae 70-15 assembly MG8)) International Rice Blast Genome Consortium NCBI: GCA_000002495.2 Neurospora crassa strain OR74A NCBI RefSeq assembly (assembly NC12) Broad Institute NCBI: GCA_000182925.2 Ustilago maydis strain 512 NCBI RefSeq assembly (assembly Umaydis521_2.0) Broad Institute NCBI: GCA_000328475.2 Dictyostelium discoideum AX4 NCBI Reference assembly (assembly dicty2.7) The Dictyostelium discoideum Sequencing Consortium NCBI: GCA_000004695.1 Human reference genome on NCBI (assembly GRCh38.p13) Genome Reference Consortium NCBI: GCA_000001405.28 Mus musculus reference genome on NCBI (assembly GRCm39) Genome Reference Consortium NCBI: GCF_000001635.27 Arabidopsis thaliana reference genome on NCBI (assembly TAIR10.1) The Arabidopsis Information Resource NCBI: GCA_000001735.2 Oryctolagus cuniculus reference genome on NCBI (assembly OryCun2.0) The Genome Sequencing Platform, The Assembly Computation and Development Core Team NCBI: GCA_000003625.1 Giardia intestinalis representative genome on NCBI (assembly UU_WB_2.1) Marine Biological Laboratory NCBI: GCA_000002435.2 Chlamydomonas reinhardtii representative genome on NCBI (assembly v3.0) DOE Joint Genome Institute NCBI: GCA_000002595.2 Neocallimastix californiae G1 genome 53 https://mycocosm.jgi.doe.gov/Neosp1/ Neosp1.home.html Orpinomyces sp. strain C1A v1.0 genome 53 https://mycocosm.jgi.doe.gov/Orpsp1_ 1/Orpsp1_1.home.html Chytriomyces hyalinus JEL632 v1.0 genome 54 https://mycocosm.jgi.doe.gov/Chyhya1/ Chyhya1.home.html ll OPEN ACCESSArticle
Control:Article Title: Turn-key mapping of cell receptor force orientation and magnitude using a commercial structured illumination microscope
Article Snippet: .. Accordingly, we have switched from the ImageJ plugin FairSIM to the Nikon Elements 12 software, which offers greater control over reconstruction. ..
Recombinant:Article Title: The actin networks of chytrid fungi reveal evolutionary loss of cytoskeletal complexity in the fungal kingdom.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Penicillin/streptomycin Thermo-Fisher Cat#P4333-20ML Concanavalin A Sigma Cat#C2010 LatrunculinB Millipore Cat#4280201MG CK666 Calbiochem/Sigma Cat#182515 CK689 Calbiochem/Sigma Cat#182517 SMIFH2 Tocris Bioscience Cat#440110 DAPI Life Technologies Cat#D1306 Alexa Fluor488 Phalloidin Life Technologies Cat#A12379 Polyethyleneimine Sigma Cat#P3143 Chitinase Sigma Cat#C6137-5UN Experimental models: organisms/strains Batrachochytrium dendrobatidis strain JEL423 Joyce Longcore JEL423 Batrachochytrium salamandrivorans isolate AMFP1 Frank Pasmans AMFP1 Spizellomyces punctatus Koch type isolate NG-3 ATCC 48900 Rhizoclosmatium globosum strain JEL800 Tim James (https://czeum.herb.lsa.umich.edu/) JEL800 Software and algorithms Basic Local Alignment Search Tool (BLAST) 67 https://blast.ncbi.nlm.nih.gov/Blast.cgi Position Specific Iteration-BLAST (PSI-BLAST) 68 https://blast.ncbi.nlm.nih.gov/Blast.cgi UniprotKB https://www.uniprot.org/ N/A HMMER suite v3.2.1 http://Hmmer.org http://Hmmer.org Pfam database v32 69 http://pfam.xfam.org European Bioinformatics Institute (EMBL-EBI) https://www.ebi.ac.uk/ https://www.ebi.ac.uk/ Coiled-Coil predictor 70 N/A Phobius program 71 N/A CD-hit program 72,73 N/A IQTree webserver 74 http://iqtree.cibiv.univie.ac.at/ iTOL v5.5.1 75 https://itol.embl.de/ FIJI 76 https://imagej.net/Fiji/Downloads CellCounter FIJI plugin Kurt De Vos https://imagej.nih.gov/ij/plugins/ cell-counter.html Autoquant X3 vX3.1.3 Media Cybernetics https://www.mediacy.com/79- products/autoquant-x3 NIS Elements w/ Advanced Research Package Nikon https://www.microscope.healthcare. nikon.com/products/software/niselements/nis-elements-advancedresearch Other Batrchochytirum dendrobatidis JAM81 reference assembly v1.0 US DOE Joint Genome Institute NCBI: GCA_000203795.1 Batrachochytirum dendrobatidis JEL423 assembly Broad Institute NCBI: GCA_000149865.1 Batrachochytrium salamandrivorans representative assembly (assembly Batr_sala_BS_V1) Broad Institute NCBI: GCA_002006685.1 Spizellomyces punctatus DAOM BR117 representative assembly (S_punctatus_V1) Broad Institute NCBI: GCA_000182565.2 (Continued on next page) e1 Current Biology 31, 1192–1205.e1–e6, March 22, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Rhizoclosmatium globosum JEL800 representative assembly (Rhihy1) DOE Joint Genome Institute NCBI: GCA_002104985.1 Allomyces macrogynus ATCC 38327 representative assembly (A_macrogynus_V3) Broad Institute NCBI: GCA_000151295.1 Saccharomyces cerevisiae S288C NCBI RefSeq build R64 assembly Saccharomyces Genome Database NCBI: GCF_000146045.2 Schizosaccharomyces pombe strain 972 NCBI RefSeq assembly S. pombe European Sequencing Consortium (EUPOM) NCBI: GCF_000002945.2 Schizosaccharomyces japonicus strain yFS275 NCBI RefSeq assembly Broad Institute NCBI: GCF_000149845.2 Candida albicans strain SC5314 NCBI RefSeq assembly (assembly ASM18296v3) Stanford University NCBI: GCA_000182965.3 Aspergillus nidulans strain FGSC A4 NCBI RefSeq assembly (assembly ASM14920v2) Broad Institute NCBI: GCA_000149205.2 Magnaporthe oryzae strain 70-15 NCBI RefSeq assembly (Pyricularia oryzae 70-15 assembly MG8)) International Rice Blast Genome Consortium NCBI: GCA_000002495.2 Neurospora crassa strain OR74A NCBI RefSeq assembly (assembly NC12) Broad Institute NCBI: GCA_000182925.2 Ustilago maydis strain 512 NCBI RefSeq assembly (assembly Umaydis521_2.0) Broad Institute NCBI: GCA_000328475.2 Dictyostelium discoideum AX4 NCBI Reference assembly (assembly dicty2.7) The Dictyostelium discoideum Sequencing Consortium NCBI: GCA_000004695.1 Human reference genome on NCBI (assembly GRCh38.p13) Genome Reference Consortium NCBI: GCA_000001405.28 Mus musculus reference genome on NCBI (assembly GRCm39) Genome Reference Consortium NCBI: GCF_000001635.27 Arabidopsis thaliana reference genome on NCBI (assembly TAIR10.1) The Arabidopsis Information Resource NCBI: GCA_000001735.2 Oryctolagus cuniculus reference genome on NCBI (assembly OryCun2.0) The Genome Sequencing Platform, The Assembly Computation and Development Core Team NCBI: GCA_000003625.1 Giardia intestinalis representative genome on NCBI (assembly UU_WB_2.1) Marine Biological Laboratory NCBI: GCA_000002435.2 Chlamydomonas reinhardtii representative genome on NCBI (assembly v3.0) DOE Joint Genome Institute NCBI: GCA_000002595.2 Neocallimastix californiae G1 genome 53 https://mycocosm.jgi.doe.gov/Neosp1/ Neosp1.home.html Orpinomyces sp. strain C1A v1.0 genome 53 https://mycocosm.jgi.doe.gov/Orpsp1_ 1/Orpsp1_1.home.html Chytriomyces hyalinus JEL632 v1.0 genome 54 https://mycocosm.jgi.doe.gov/Chyhya1/ Chyhya1.home.html ll OPEN ACCESSArticle
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