Gold Standard
Here is presented the first version of a fully annotated corpus of experimental protocols in life sciences. We are working in improving this annotated corpus to serve as a research resource for the biomedical natural language processing community.
Corpus Characteristics
- 58 fully annotated protocols,
- 1769 concepts related to Samples, Instruments and Reagents. These concepts were mapped to concepts represented in ontologies
Corpus Annotation
- Thirty four annotators. The skills of the annotators was diverse, from students to university professors their areas of expertise were related to the content of the protocols.
- Three-annotators per document (randomly chosen)
- Two annotation phases
Download
- Corpus of protocols
- Annotation guidelines
- Guidelines to use BioH tool (an extension of Hypothesis annotation tool)
Explore Annotation Results
| Journal | # | Title | DOI | URL |
|---|---|---|---|---|
| bio-protocols | 1 | Generation of Non-typeable Haemophilus influenzae Directed Gene Deletion Mutants | 10.21769/BioProtoc.1066 | https://bio-protocol.org/e1066 |
| bio-protocols | 2 | Mouse Retinal Whole Mounts and Quantification of Vasculature Protocol | 10.21769/BioProtoc.1546 | https://bio-protocol.org/e1546 |
| bio-protocols | 3 | Electroporation of Embryonic Chick Eyes | 10.21769/BioProtoc.1498 | https://bio-protocol.org/e1498 |
| bio-protocols | 4 | In vitro Migration Assays for Neural Stem Cells, Intermediate Neurogenic Progenitors and Immature Neurons | 10.21769/BioProtoc.1371 | https://bio-protocol.org/e1371 |
| bio-protocols | 5 | In utero Electroporation of the Embryonic Mouse Retina | 10.21769/BioProtoc.1255 | https://bio-protocol.org/e1255 |
| bio-protocols | 6 | In situ Chemotaxis Assay in Caenorhabditis elegans (for the Study of Circadian Rhythms) | 10.21769/BioProtoc.1040 | https://bio-protocol.org/e1040 |
| bio-protocols | 7 | Fluorescence Microscopy for Cilia in Cultured Cells and Zebrafish Embryos | 10.21769/BioProtoc.1188 | https://bio-protocol.org/e1188 |
| bio-protocols | 8 | Wnt Reporter Activity Assay | 10.21769/BioProtoc.1183 | https://bio-protocol.org/e1183 |
| bio-protocols | 9 | Hedgehog (Hh) Reporter Activity Assay | 10.21769/BioProtoc.1182 | https://bio-protocol.org/e1182 |
| bio-protocols | 10 | Open-book Preparations from Chick Embryos and DiI Labeling of Commissural Axons | 10.21769/BioProtoc.1176 | https://bio-protocol.org/e1176 |
| bio-protocols | 11 | Barrier Function Assay | 10.21769/BioProtoc.1133 | https://bio-protocol.org/e1133 |
| bio-protocols | 12 | DNA Fragmentation Analysis | 10.21769/BioProtoc.1203 | https://bio-protocol.org/e1203 |
| bio-protocols | 13 | Chloroform-ethanol Isolation of Genomic DNA from Mouse Tail | 10.21769/BioProtoc.131 | https://bio-protocol.org/bio101/e131 |
| bio-protocols | 14 | Extraction of Genomic DNA from Arabidopsis leaves (can be used for other tissues as well) | 10.21769/BioProtoc.90 | https://bio-protocol.org/bio101/e90 |
| bio-protocols | 15 | Yeast Genomic DNA Miniprep Using A FastPrep Cell Lyser | 10.21769/BioProtoc.64 | https://bio-protocol.org/bio101/e64 |
| bio-protocols | 16 | Zebrafish Embryo DNA Preparation | 10.21769/BioProtoc.184 | https://bio-protocol.org/bio101/e184 |
| bio-protocols | 17 | Determination of Mutation Frequency During Viral DNA Replication | 10.21769/BioProtoc.1076 | https://bio-protocol.org/e1076 |
| bio-protocols | 18 | Genotyping for Single Zebrafish (Fin Clip) or Zebrafish Embryo | 10.21769/BioProtoc.182 | https://bio-protocol.org/bio101/e182 |
| bio-protocols | 19 | Genotyping Transgenic Zebrafish Using Genomic DNA Extracted from Clutch of Embryos | 10.21769/BioProtoc.181 | https://bio-protocol.org/bio101/e181 |
| bio-protocols | 20 | PCR-RFLP Genotyping of Point Mutations in Caenorhabditis elegans | 10.21769/BioProtoc.128 | https://bio-protocol.org/e128 |
| bio-protocols | 21 | Detection of piggyBac-mediated Transposition by Splinkerette PCR in Transgenic Lines of Strongyloides ratti | 10.21769/BioProtoc.1015 | https://bio-protocol.org/e1015 |
| bio-protocols | 22 | DNA PCR Assays for Igh Rearrangement | 10.21769/BioProtoc.1046 | https://bio-protocol.org/e1046 |
| bio-protocols | 23 | Promoter Orientation of Prokaryotic Phase-variable Genes by PCR | 10.21769/BioProtoc.274 | https://bio-protocol.org/e274 |
| bio-protocols | 24 | Pulsed-field Gel Electrophoresis Typing of Gram-negative Bacteria (E. coli) | 10.21769/BioProtoc.103 | https://bio-protocol.org/bio101/e103 |
| bio-protocols | 25 | Purification and Sequencing of DNA Guides from Prokaryotic Argonaute | 10.21769/BioProtoc.1293 | https://bio-protocol.org/e1293 |
| bio-protocols | 26 | Yeast DNA Replication 2D Gel Protocol | 10.21769/BioProtoc.213 | https://bio-protocol.org/e213 |
| bio-protocols | 27 | A Quick, No Frills Approach to Mouse Genotyping | 10.21769/BioProtoc.244 | https://bio-protocol.org/e244 |
| bio-protocols | 28 | Total RNA Extraction from Formalin-Fixed, Paraffin-Embedded (FFPE) Blocks | 10.21769/BioProtoc.161 | https://bio-protocol.org/e161 |
| bio-protocols | 29 | RNA Isolation from Synechocystis | 10.21769/BioProtoc.1428 | https://bio-protocol.org/e1428 |
| bio-protocols | 30 | Polysome Preparation, RNA Isolation and Analysis | 10.21769/BioProtoc.286 | https://bio-protocol.org/e286 |
| bio-protocols | 31 | RNA Isolation from Arabidopsis Pollen Grains | 10.21769/BioProtoc.67 | https://bio-protocol.org/bio101/e67 |
| bio-protocols | 32 | RNA Isolation and Northern Blot Analysis | 10.21769/BioProtoc.1077 | https://bio-protocol.org/e1077 |
| bio-protocols | 33 | RNA Extraction from RNase-Rich Senescing Leaf Samples | 10.21769/BioProtoc.248 | https://bio-protocol.org/e248 |
| bio-protocols | 34 | Phenol-chloroform Based RNA Extraction from Yeast | 10.21769/BioProtoc.138 | https://bio-protocol.org/bio101/e138 |
| bio-protocols | 35 | Separation of Microspores from Anthers of Lilium longiflorum (Lily) and Subsequent RNA Extraction | 10.21769/BioProtoc.1400 | https://bio-protocol.org/e1400 |
| bio-protocols | 36 | Total RNA Isolation after Laser-capture Microdissection of Human Cervical Squamous Epithelial Cells from Fresh Frozen Tissue | 10.21769/BioProtoc.848 | https://bio-protocol.org/e848 |
| bio-protocols | 37 | Extraction of Small RNA and qPCR Validation of miRNAs in Vigna mungo | 10.21769/BioProtoc.1417 | https://bio-protocol.org/e1417 |
| bio-protocols | 38 | RNA Isolation From Meloidogyne Spp. Galls | 10.21769/BioProtoc.879 | https://bio-protocol.org/e879 |
| bio-protocols | 39 | Isolating RNA from the Soil | 10.21769/BioProtoc.903 | https://bio-protocol.org/e903 |
| bio-protocols | 40 | Site-Directed Mutagenesis Using Dpn1 | 10.21769/BioProtoc.29 | https://bio-protocol.org/bio101/e29 |
| Biotechniques | 1 | Easy and efficient protocol for oomycete DNA extraction suitable for population genetic analysis | 10.1007/s10529-010-0478-3 | https://link.springer.com/article/10.1007/s10529-010-0478-3 |
| Biotechniques | 2 | A single protocol for extraction of gDNA from bacteria and yeast | 10.2144/000114263 | https://www.ncbi.nlm.nih.gov/pubmed/25757544 |
| Biotechniques | 3 | Extraction of nucleic acids from yeast cells and plant tissues using ethanol as medium for sample preservation and cell disruption | 10.2144/000113476 | https://www.ncbi.nlm.nih.gov/pubmed/20854267 |
| Biotechniques | 4 | Comparison and optimization of ancient DNA extraction | 10.2144/000112383 | https://www.biotechniques.com/BiotechniquesJournal/2007/March/Comparison-and-optimization-of-ancient-DNA-extraction/biotechniques-41414.html |
| Biotechniques | 5 | Rapid method for the isolation of mammalian sperm DNA | 10.2144/000114280 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4486329/ |
| Biotechniques | 6 | Ultra High Purification of Oligonucleotides-DNA and siRNA | https://www.biotechniques.com/protocols/Electrophoresis/DNARNA_Analysis_and_Purificatio/Ultra-High-Purification-of-Oligonucleotides-DNA-and-siRNA/biotechniques-115451.html | |
| Biotechniques | 7 | Simplified DGS procedure for large-scale genome structural study | 10.2144/00013307 | https://www.biotechniques.com/multimedia/archive/00075/Practical_DGS_protoc_75203a.pdf |
| Biotechniques | 8 | Alkaline polyethylene glycol-based method for direct PCR from bacteria, eukaryotic tissue samples, and whole blood | 10.2144/000112149 | https://www.biotechniques.com/BiotechniquesJournal/2006/April/Alkaline-polyethylene-glycol-based-method-for-direct-PCR-from-bacteria-eukaryotic-tissue-samples-and-whole-blood/biotechniques-45688.html |
| Biotechniques | 9 | Rare allele enrichment and detection by allele-specific PCR, competitive probe blocking and melting analysis | 10.2144/000113783 | https://www.biotechniques.com/protocols/2012_Protocol_Guide/Rare-allele-enrichment-and-detection-by-allele-specific-PCR-competitive-probe----blocking-and-melting-analysis/biotechniques-324732.html?service=print |
| Biotechniques | 10 | Extraction of total RNA from fresh/frozen tissue (FT) | 10.2144/000113260 | https://www.biotechniques.com/protocols/Peer-Reviewed_Protocols/Extraction-of-total-RNA-from-freshfrozen-tissue-FT/biotechniques-181792.html?service=print |
| Biotechniques | 11 | Preparation of formalin-fixed paraffin-embedded (FFPE) tissues for RNA extraction | 10.2144/000113261 | https://www.biotechniques.com/protocols/Peer-Reviewed_Protocols/Preparation-of-formalin-fixed-paraffin-embedded-FFPE-tissues-for-RNA----extraction/biotechniques-181793.html |
| Biotechniques | 12 | Improving sequencing quality from PCR products containing long mononucleotide repeats. | 10.2144/000113369 | https://www.ncbi.nlm.nih.gov/pubmed/20569204 |
| Biotechniques | 13 | Practical SA-cloning protocol | 10.2144/000113781 | https://www.biotechniques.com/multimedia/archive/00170/BTN_A_000113781_O_170495a.pdf |
| Biotechniques | 14 | Quantitation of proteins expressed on the plasma membrane using cold-adapted proteases | 10.2144/000113784 | https://www.biotechniques.com/protocols/2012_Protocol_Guide/Quantitation-of-proteins-expressed-on-the-plasma-membrane-using-cold-adapted----proteases/biotechniques-324728.html |
| Biotechniques | 15 | Yeast genomic DNA extraction with LiOAc-SDS | 10.2144/000113785 | https://www.biotechniques.com/protocols/2012_Protocol_Guide/Yeast-genomic-DNA-extraction-with-LiOAc-SDS/biotechniques-324723.html |
| Biotechniques | 16 | Protocol for intelligent high-content screening of zebrafish embryos on a standard widefield screening microscope | 10.2144/000113782 | https://www.biotechniques.com/protocols/2012_Protocol_Guide/Protocol-for-intelligent-high-content-screening-of-zebrafish-embryos-on-a----standard-widefield-screening-microscope/biotechniques-324719.html |
| Cold Spring Harbor Protocols | 1 | Molecular Cloning: A Laboratory Manual (Fourth Edition) | https://cshlpress.com/default.tpl?action=full&src=pdf&--eqskudatarq=934 | |
| Cold Spring Harbor Protocols | 2 | Analysis of RNA-Protein Complexes by RNA Coimmunoprecipitation and RT-PCR Analysis from Caenorhabditis elegans | 10.1101/pdb.prot5300 | http://cshprotocols.cshlp.org/content/2009/10/pdb.prot5300.abstract |
| Cold Spring Harbor Protocols | 3 | RNAi in Cultured Mammalian Cells Using Synthetic siRNAs | 10.1101/pdb.prot071076 | http://cshprotocols.cshlp.org/content/2012/9/pdb.prot071076.abstract |
| Cold Spring Harbor Protocols | 4 | An Agar Mount for Observation of Caenorhabditis elegans Embryos | 10.1101/pdb.prot5540 | http://cshprotocols.cshlp.org/content/2010/12/pdb.prot5540.abstract |
| Cold Spring Harbor Protocols | 5 | Culturing Human Embryonic Stem Cells in Feeder-Free Conditions | 10.1101/pdb.prot5044 | http://cshprotocols.cshlp.org/content/2008/9/pdb.prot5044.abstract |
| Cold Spring Harbor Protocols | 6 | Design and Cloning of an shRNA into a Lentiviral Silencing Vector: Version A | 10.1101/pdb.prot5009 | http://cshprotocols.cshlp.org/content/2008/8/pdb.prot5009.short |
| Cold Spring Harbor Protocols | 7 | In Ovo Live Imaging of Avian Embryos | 10.1101/pdb.prot5446 | http://cshprotocols.cshlp.org/content/2010/6/pdb.prot5446.short |
| Cold Spring Harbor Protocols | 8 | Use of the Sleeping Beauty Transposon System for Stable Gene Expression in Mouse Embryonic Stem Cells | 10.1101/pdb.prot5270 | http://cshprotocols.cshlp.org/content/2009/8/pdb.prot5270.full |
| Cold Spring Harbor Protocols | 9 | Embedding Embryos for High-Resolution Episcopic Microscopy (HREM) | 10.1101/pdb.prot069583 | http://cshprotocols.cshlp.org/content/2012/6/pdb.prot069583.abstract |
| Cold Spring Harbor Protocols | 10 | FAST Technique for Agrobacterium-Mediated Transient Gene Expression in Seedlings of Arabidopsis and Other Plant Species | 10.1101/pdb.prot5428 | http://cshprotocols.cshlp.org/content/2010/5/pdb.prot5428.abstract |
| Cold Spring Harbor Protocols | 11 | Isolation and Whole-Cell Patch Clamping of Arabidopsis Guard Cell Protoplasts | 10.1101/pdb.prot5014 | http://cshprotocols.cshlp.org/content/2008/6/pdb.prot5014.full |
| Cold Spring Harbor Protocols | 12 | Polyacrylamide Gel Electrophoresis of RNA | 10.1101/pdb.prot5444 | http://cshprotocols.cshlp.org/content/2010/6/pdb.prot5444.full |
| Cold Spring Harbor Protocols | 13 | Preparation of Small RNA Libraries for High-Throughput Sequencing | 10.1101/pdb.prot071431 | http://cshprotocols.cshlp.org/content/2012/10/pdb.prot071431.short |
| Cold Spring Harbor Protocols | 14 | Mapping Protein–Protein Interactions Using Yeast Two-Hybrid Assays | 10.1101/pdb.prot086157 | http://cshprotocols.cshlp.org/content/2015/5/pdb.prot086157 |
| Cold Spring Harbor Protocols | 15 | Bimolecular Affinity Purification (BAP): Tandem Affinity Purification Using Two Protein Baits | 10.1101/pdb.prot5318 | http://cshprotocols.cshlp.org/content/2009/11/pdb.prot5318.abstract |
| Cold Spring Harbor Protocols | 16 | Chromatin Immunoprecipitation (ChIP) | 10.1101/pdb.prot5279 | http://cshprotocols.cshlp.org/content/2009/9/pdb.prot5279.abstract |
| Cold Spring Harbor Protocols | 17 | Combined 3C-ChIP-Cloning (6C) Assay: A Tool to Unravel Protein-Mediated Genome Architecture | 10.1101/pdb.prot5168 | http://cshprotocols.cshlp.org/content/2009/3/pdb.prot5168.short |
| Cold Spring Harbor Protocols | 18 | Creation of Baculovirus Display Libraries | 10.1101/pdb.prot5393 | http://cshprotocols.cshlp.org/content/2010/3/pdb.prot5393.full |
| Cold Spring Harbor Protocols | 19 | Development of Mammalian Cell Lines with lac Operator-Tagged Chromosomes | 10.1101/pdb.prot4903 | http://cshprotocols.cshlp.org/content/2008/1/pdb.prot4903.abstract |
| Cold Spring Harbor Protocols | 20 | Preparation of Peptides from Yeast Cells for iTRAQ Analysis | 10.1101/pdb.prot5616 | http://cshprotocols.cshlp.org/content/2011/6/pdb.prot5616.abstract |
| Cold Spring Harbor Protocols | 21 | Injection of dsRNA into DrosophilaEmbryos for RNA Interference (RNAi) | 10.1101/pdb.prot4918 | http://cshprotocols.cshlp.org/content/2008/2/pdb.prot4918.abstract |
| Cold Spring Harbor Protocols | 22 | SNP Mining from Maize 454 EST Sequences | 10.1101/pdb.prot4786 | http://cshprotocols.cshlp.org/content/2007/7/pdb.prot4786.full |
| Cold Spring Harbor Protocols | 23 | Virus-Induced Gene Silencing as a Tool for Delivery of dsRNA into Plants | 10.1101/pdb.prot5139 | http://cshprotocols.cshlp.org/content/2009/2/pdb.prot5139.full |
| Cold Spring Harbor Protocols | 24 | Whole-Mount In Situ Hybridization of RNA Probes to Plant Tissues | 10.1101/pdb.prot4944 | http://cshprotocols.cshlp.org/content/2008/2/pdb.prot4944.abstract |
| current protocols | 1 | CRISPR‐Cas9 Genome Editing in Drosophila | 10.1002/0471142727.mb3102s111 | https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/0471142727.mb3102s111 |
| current protocols | 2 | Interpretation of genomic copy number variants using DECIPHER | 10.1002/0471142905.hg0814s72 | https://www.ncbi.nlm.nih.gov/pubmed/22241657 |
| current protocols | 3 | Assessment of metabolic stability using the rainbow trout (Oncorhynchus mykiss) liver S9 fraction. | 10.1002/0471140856.tx1410s53 | https://www.ncbi.nlm.nih.gov/m/pubmed/22896006/ |
| current protocols | 4 | Bioremediation of Turbid Surface Water Using Seed Extract from Moringa oleifera Lam. (Drumstick) Tree | 10.1002/9780471729259.mc01g02s16 | https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/9780471729259.mc01g02s16 |
| current protocols | 5 | Biological Sand Filters: Low-Cost Bioremediation Technique for Production of Clean Drinking Water | 10.1002/9780471729259.mc01g01s9 | |
| current protocols | 6 | Characterization and Validation of Cre-Driver Mouse Lines | 10.1002/9780470942390.mo100103 | https://www.ncbi.nlm.nih.gov/m/pubmed/26068985/ |
| current protocols | 7 | Assaying Cell Cycle Status Using Flow Cytometry | 10.1002/0471142727.mb2806s111 | https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471142727.mb2806s111 |
| current protocols | 8 | Cytometry in malaria-A practical replacement for microscopy? | 10.1002/0471142956.cy1120s65 | https://cwru.pure.elsevier.com/en/publications/cytometry-in-malaria-a-practical-replacement-for-microscopy-4 |
| current protocols | 9 | Fluorescence Polarization (FP) Assays for Monitoring Peptide‐Protein or Nucleic Acid‐Protein Binding | 10.1002/9780470559277.ch090102 | https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/9780470559277.ch090102 |
| current protocols | 10 | Fluorescent speckle microscopy (FSM) of microtubules and actin in living cells | https://www.ncbi.nlm.nih.gov/m/pubmed/18228403/ | |
| current protocols | 11 | Genotyping of apolipoprotein E: comparative evaluation of different protocols | 10.1002/0471142905.hg0914s38 | https://www.ncbi.nlm.nih.gov/pubmed/18428347 |
| current protocols | 12 | Growing and Analyzing Static Biofilms | 10.1002/9780471729259.mc01b01s22 | |
| current protocols | 13 | In vivo measurement of blood-brain barrier permeability | 10.1002/0471142301.ns0719s15 | https://www.ncbi.nlm.nih.gov/pubmed/18428529 |
| current protocols | 14 | The Polymerase Chain Reaction | 10.1002/0471142727.mb1500s88 | https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/0471142727.mb1500s88 |
| current protocols | 15 | Measurement of bacterial ingestion and killing by macrophages | 10.1002/0471142735.im1406s12 | https://www.ncbi.nlm.nih.gov/pubmed/18432724 |
| current protocols | 16 | Measurement of glutathione transport | 10.1002/0471140856.tx0603s00 | https://www.ncbi.nlm.nih.gov/pubmed/23045055 |
| current protocols | 17 | Models of inflammation: measuring gastrointestinal ulceration in the rat | 10.1002/0471141755.ph1002s00 | https://www.ncbi.nlm.nih.gov/pubmed/21971793 |
| current protocols | 18 | Oligonucleotide Microarrays for Clinical Diagnosis of Copy Number Variation and Zygosity Status | 10.1002/0471142905.hg0812s74 | |
| current protocols | 19 | Preparing a Minimum Information about a Flow Cytometry Experiment (MIFlowCyt) Compliant Manuscript Using the International Society for Advancement of Cytometry (ISAC) FCS File Repository (FlowRepository.org) | 10.1002/0471142956.cy1018s61 | https://currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/0471142956.cy1018s61 |
| current protocols | 20 | Purification of sequence-specific DNA-binding proteins by affinity chromatography | 10.1002/0471140864.ps0906s11 | https://www.ncbi.nlm.nih.gov/pubmed/18429215 |
| current protocols | 21 | Searching NCBI Databases Using Entrez | 10.1002/0471142905.hg0610s71 | https://www.ncbi.nlm.nih.gov/pubmed/21975942 |
| current protocols | 22 | Some Phenotype Association Tools in Galaxy: Looking for Disease SNPs in a Full Genome | 10.1002/0471250953.bi1502s39 | https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/0471250953.bi1502s39 |
| current protocols | 23 | Uridine 2'-carbamates: facile tools for oligonucleotide 2'-functionalization | 10.1002/0471142700.nc0421s15 | https://www.ncbi.nlm.nih.gov/pubmed/18428928 |
| current protocols | 24 | Using Cloud Computing Infrastructure with CloudBioLinux, CloudMan, and Galaxy | 10.1002/0471250953.bi1109s38 | https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/0471250953.bi1109s38 |
| current protocols | 25 | Using Galaxy to perform large-scale interactive data analyses | 10.1002/0471250953.bi1005s38 | https://www.ncbi.nlm.nih.gov/pubmed/22700312 |
| current protocols | 26 | Using OrthoMCL to Assign Proteins to OrthoMCL‐DB Groups or to Cluster Proteomes Into New Ortholog Groups | 10.1002/0471250953.bi0612s35 | https://currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/0471250953.bi0612s35 |
| current protocols | 27 | CRISPR/Cas9-Directed Genome Editing of Cultured Cells | 10.1002/0471142727.mb3101s107 | https://currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/0471142727.mb3101s107 |
| current protocols | 28 | Cell‐Free Expression of G Protein–Coupled Receptors | 10.1002/0471140864.ps2914s81 | https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/0471140864.ps2914s81 |
| current protocols | 29 | Using Single Lectins to Enrich Glycoproteins in Conditioned Media | 10.1002/0471140864.ps2406s81 | https://www.ncbi.nlm.nih.gov/pubmed/26237673 |
| current protocols | 30 | Detergent Analysis in Protein Samples Using Mid‐Infrared (MIR) Spectroscopy | 10.1002/0471140864.ps2912s81 | https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471140864.ps2912s81 |
| current protocols | 31 | Applications of Lipid Nanodiscs for the Study of Membrane Proteins by Surface Plasmon Resonance | 10.1002/0471140864.ps2913s81 | https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471140864.ps2913s81 |
| Genentic and molecular research | 1 | A protocol for high-quality genomic DNA extraction from legumes | http://dx.doi.org/10.4238/2012.September.14.1 | http://www.funpecrp.com.br/gmr/year2012/vol11-4/pdf/gmr2263.pdf |
| Genentic and molecular research | 2 | A simplified universal genomic DNA extraction protocol suitable for PCR | 10.4238/vol10-1gmr1055 | https://www.ncbi.nlm.nih.gov/pubmed/21476197 |
| Genentic and molecular research | 3 | An inexpensive and rapid method for extracting papilionoid genomic DNA from herbarium specimens | 10.4238/vol9-3gmr839 | https://www.ncbi.nlm.nih.gov/m/pubmed/20645258/ |
| Genentic and molecular research | 4 | Isolation of retro-transcribed RNA from in vitro Mycosphaerella fijiensis-infected banana leaves | 10.4238/vol9-3gmr865 | https://www.ncbi.nlm.nih.gov/pubmed/20677135 |
| Genentic and molecular research | 5 | Optimization of DNA extraction from seeds and fresh leaf tissues of wild marigold (Tagetes minuta) for polymerase chain reaction analysis | 10.4238/vol9-1gmr747 | https://www.ncbi.nlm.nih.gov/pubmed/20309824 |
| Journal of visualized experiments | 1 | Isolation of Protoplasts from Tissues of 14-day-old Seedlings of Arabidopsis thaliana | 10.3791/1149 | http://www.jove.com/details.php?id=1149 |
| Journal of visualized experiments | 2 | Denaturing Urea Polyacrylamide Gel Electrophoresis (Urea PAGE) | 10.3791/1485 | http://www.jove.com/video/1485/ |
| Journal of visualized experiments | 3 | Choice and No-Choice Assays for Testing the Resistance of A. thaliana to Chewing Insects | 10.3791/683 | http://www.jove.com/video/683 |
| Journal of visualized experiments | 4 | Protocols for Oral Infection of Lepidopteran Larvae with Baculovirus | 10.3791/888 | http://www.jove.com/video/888 |
| Journal of visualized experiments | 5 | Non-radioactive in situ Hybridization Protocol Applicable for Norway Spruce and a Range of Plant Species | 10.3791/1205 | http://www.jove.com/video/1205 |
| Journal of visualized experiments | 6 | Assay for Pathogen-Associated Molecular Pattern (PAMP)-Triggered Immunity (PTI) in Plants | 10.3791/1442 | http://www.jove.com/video/1442 |
| Journal of visualized experiments | 7 | Robotics and Dynamic Image Analysis for Studies of Gene Expression in Plant Tissues | 10.3791/1733 | http://www.jove.com/video/1733 |
| Journal of visualized experiments | 8 | Comprehensive Compositional Analysis of Plant Cell Walls (Lignocellulosic biomass) Part I: Lignin | 10.3791/1745 | http://www.jove.com/video/1745 |
| Journal of visualized experiments | 9 | Comprehensive Compositional Analysis of Plant Cell Walls (Lignocellulosic biomass) Part II: Carbohydrates | 10.3791/1837 | http://www.jove.com/video/1837 |
| Journal of visualized experiments | 10 | Assessing Stomatal Response to Live Bacterial Cells using Whole Leaf Imaging Imaging | 10.3791/2185 | http://www.jove.com/video/2185 |
| Journal of visualized experiments | 11 | Environmentally Induced Heritable Changes in Flax | 10.3791/2332 | http://www.jove.com/video/2332 |
| Journal of visualized experiments | 12 | Generation of Composite Plants in Medicago truncatula used for Nodulation Assays | 10.3791/2633 | http://www.jove.com/video/2633 |
| Journal of visualized experiments | 13 | Microwave Assisted Rapid Diagnosis of Plant Virus Diseases by Transmission Electron Microscopy | 10.3791/2950 | http://www.jove.com/video/2950 |
| Journal of visualized experiments | 14 | Characterizing Herbivore Resistance Mechanisms: Spittlebugs on Brachiaria spp. as an Example | 10.3791/3047 | http://www.jove.com/video/3047 |
| Journal of visualized experiments | 15 | Single Cell Fate Mapping in Zebrafish | 10.3791/3172 | http://www.jove.com/video/3172 |
| Journal of visualized experiments | 16 | A PCR-based Genotyping Method to Distinguish Between Wild-type and Ornamental Varieties of Imperata cylindrica | 10.3791/3265 | http://www.jove.com/video/3265 |
| Journal of visualized experiments | 17 | Ice-Cap: A Method for Growing Arabidopsis and Tomato Plants in 96-well Plates for High-Throughput Genotyping | 10.3791/3280 | http://www.jove.com/video/3280 |
| Journal of visualized experiments | 18 | In Situ Hybridization for the Precise Localization of Transcripts in Plants | 10.3791/3328 | http://www.jove.com/video/3328 |
| Journal of visualized experiments | 19 | Isolation and Biophysical Study of Fruit Cuticles | 10.3791/3529 | http://www.jove.com/video/3529 |
| Journal of visualized experiments | 20 | High and Low Throughput Screens with Root-knot Nematodes Meloidogyne spp. | 10.3791/3629 | http://www.jove.com/video/3629 |
| Journal of visualized experiments | 21 | Profiling Thiol Redox Proteome Using Isotope Tagging Mass Spectrometry | 10.3791/3766 | http://www.jove.com/video/3766 |
| Nature Protocols Exchange | 1 | Reprogramming of mouse fibroblasts into iPSCs | 10.1038/protex.2015.086 | https://www.nature.com/protocolexchange/protocols/4283 |
| Nature Protocols Exchange | 2 | Generation of murine sympathoadrenergic progenitor-like cells from embryonic stem cells | 10.1038/protex.2015.083 | https://www.nature.com/protocolexchange/protocols/4191 |
| Nature Protocols Exchange | 3 | Collagen Gel Contraction Assay | 10.1038/protex.2015.082 | https://www.nature.com/protocolexchange/protocols/4169 |
| Nature Protocols Exchange | 4 | Isolation of mouse bone marrow-derived monocytes | 10.1038/protex.2015.081 | https://www.nature.com/protocolexchange/protocols/4167 |
| Nature Protocols Exchange | 5 | Northern Blot | 10.1038/protex.2015.080 | https://www.nature.com/protocolexchange/protocols/4165 |
| Nature Protocols Exchange | 6 | Human Treg cell suppressive assays | 10.1038/protex.2015.078 | https://www.nature.com/protocolexchange/protocols/4155 |
| Nature Protocols Exchange | 7 | Proteomic mapping of ER-PM junctions in living HEK293 cells | 10.1038/protex.2015.072 | https://www.nature.com/protocolexchange/protocols/4109 |
| Nature Protocols Exchange | 8 | Transposon mapping using flanking sequence exponential anchored (FLEA) PCR | 10.1038/protex.2015.071 | https://www.nature.com/protocolexchange/protocols/4153 |
| Nature Protocols Exchange | 9 | Isolation and expansion of the hepatic progenitor cell (HPC) population | 10.1038/protex.2015.051 | https://www.nature.com/protocolexchange/protocols/3933 |
| Nature Protocols Exchange | 10 | Directed differentiation of stomach tissue from mouse embryonic stem cells | 10.1038/protex.2015.046 | https://www.nature.com/protocolexchange/protocols/3949 |
| Nature Protocols Exchange | 11 | Microfluidic device design, fabrication, and testing protocols | 10.1038/protex.2015.069 | https://www.nature.com/protocolexchange/protocols/4049 |
| Nature Protocols Exchange | 12 | Reprogramming mouse embryo fibroblasts (MEF) | 10.1038/protex.2015.058 | https://www.nature.com/protocolexchange/protocols/4009 |
| Nature Protocols Exchange | 13 | Reprogramming mouse embryonic fibroblasts using different reprogramming factors | 10.1038/protex.2015.063 | https://www.nature.com/protocolexchange/protocols/3911 |
| Nature Protocols Exchange | 14 | Epiblast grafting and in vitro embryo culture | 10.1038/protex.2015.042 | https://www.nature.com/protocolexchange/protocols/3899 |
| Nature Protocols Exchange | 15 | Direct Conversion of Adult Human Fibroblasts into Induced Neural Precursor Cells by Non-Viral Transfection | 10.1038/protex.2015.034 | https://www.nature.com/protocolexchange/protocols/3885 |
| Nature Protocols Exchange | 16 | Preparation of cell-sized water-in-oil droplets for in vitroreconstitution of biological processes in cellular compartments | 10.1038/protex.2015.029 | https://www.nature.com/protocolexchange/protocols/3815 |
| Nature Protocols Exchange | 17 | Immunofluorescence of Cultured Cells | 10.1038/protex.2015.021 | https://www.nature.com/protocolexchange/protocols/3783 |
| Nature Protocols Exchange | 18 | Orthotopic lung epithelial cell transplantation | 10.1038/protex.2015.019 | https://www.nature.com/protocolexchange/protocols/3495 |
| Nature Protocols Exchange | 19 | Tamoxifen Administration for Lineage Tracing Using CreERT2 mice | 10.1038/protex.2015.018 | https://www.nature.com/protocolexchange/protocols/3497 |
| Nature Protocols Exchange | 20 | Lung Epithelial Cell Prep | 10.1038/protex.2015.017 | https://www.nature.com/protocolexchange/protocols/3493 |
| Nature Protocols Exchange | 21 | Reprogramming mouse embryonic fibroblasts using different systems | 10.1038/protex.2015.001 | https://www.nature.com/protocolexchange/protocols/3587 |
| Nature Protocols Exchange | 22 | Maize Single Tetrad-stage Microspore Sequencing | 10.1038/protex.2015.014 | https://www.nature.com/protocolexchange/protocols/3661 |
| Nature Protocols Exchange | 23 | Detecting changes in the mitochondrial membrane potential by quantitative fluorescence microscopy | 10.1038/protex.2015.009 | https://www.nature.com/protocolexchange/protocols/3673 |
| Nature Protocols Exchange | 24 | Isolation of extracellular vesicle RNA from cell culture supernatant | 10.1038/protex.2015.006 | https://www.nature.com/protocolexchange/protocols/3615 |
| Nature Protocols Exchange | 25 | Isolation of extracellular vesicle RNA from bile | 10.1038/protex.2015.003 | https://www.nature.com/protocolexchange/protocols/3613 |
| Nature Protocols Exchange | 26 | Chlorophyll and starch assays | 10.1038/nprot.2009.12 | https://www.nature.com/protocolexchange/protocols/521 |
| Nature Protocols Exchange | 27 | Chromatin immunoprecipitation (ChIP) assay | 10.1038/nprot.2009.11 | https://www.nature.com/protocolexchange/protocols/500 |
| Nature Protocols Exchange | 28 | Cloning circadian promoters | 10.1038/nprot.2009.14 | https://www.nature.com/protocolexchange/protocols/523 |
| Nature Protocols Exchange | 29 | Protocol for DNA extraction from any plant species (alkaline PVPP method) | 10.1038/protex.2017.004 | https://www.nature.com/protocolexchange/protocols/5359 |
| Nature Protocols Exchange | 30 | Multiplex amplification of ancient DNA | 10.1038/nprot.2006.84 | https://www.ncbi.nlm.nih.gov/pubmed/17406302 |
| Nature Protocols Exchange | 31 | Non-invasive measurement of real-time oxygen flux in plant systems with a self-referencing optrode | 10.1038/protex.2011.266 | https://www.nature.com/protocolexchange/protocols/2241 |
| Nature Protocols Exchange | 32 | DNA isolation protocol for Vigna radiata with free of phenolics | 10.1038/nprot.2009.167 | https://www.nature.com/protocolexchange/protocols/608 |
| Nature Protocols Exchange | 33 | Validation of artificial microRNA expression by poly(A) tailing-based RT-PCR | 10.1038/protex.2012.003 | https://www.nature.com/protocolexchange/protocols/2304 |
| Nature Protocols Exchange | 34 | A method for counting cotton mature fibers per seed | 10.1038/protex.2011.220 | https://www.nature.com/protocolexchange/protocols/2059 |
| Nature Protocols Exchange | 35 | Expression and accumulation of heterologous molecules in the protein storage vacuoles of soybean seeds | 10.1038/protex.2011.206 | https://www.nature.com/protocolexchange/protocols/2012 |
| Nature Protocols Exchange | 36 | Modeling evolution of insect resistance to genetically modified crops | 10.1038/nprot.2008.125 | https://www.nature.com/protocolexchange/protocols/462 |
| Nature Protocols Exchange | 37 | Assessment of cry1Ab transgene cassette in commercial Bt corn MON810: gene, event, construct and GMO specific concurrent characterization | 10.1038/nprot.2007.440 | https://www.nature.com/protocolexchange/protocols/362 |
| Nature Protocols Exchange | 38 | High throughput phenotype screening pipeline for functional genomics in Magnaporthe oryzae | 10.1038/nprot.2007.168 | https://www.nature.com/protocolexchange/protocols/187 |
| Nature Protocols Exchange | 39 | Electrophoretic mobility shift assay (EMSA) for detecting protein–nucleic acid interactions | 10.1038/nprot.2007.249 | https://www.nature.com/articles/nprot.2007.249 |
| Plant methods | 1 | A novel procedure for the quantitative analysis of metabolites, storage products and transcripts of laser microdissected seed tissues of Brassica napus | 10.1186/1746-4811-7-19 | https://www.ncbi.nlm.nih.gov/pubmed/21718489 |
| Plant methods | 2 | A simple and efficient method for the long-term preservation of plant cell suspension cultures | 10.1186/1746-4811-8-4 | https://www.ncbi.nlm.nih.gov/pubmed/22289515 |
| Plant methods | 3 | Agrobacterium-mediated transformation of safflower and the efficient recovery of transgenic plants via grafting | 10.1186/1746-4811-7-12 | https://plantmethods.biomedcentral.com/articles/10.1186/1746-4811-7-12 |
| Plant methods | 4 | An improved protocol for efficient transformation and regeneration of diverse indica rice cultivars | 10.1186/1746-4811-7-49 | https://plantmethods.biomedcentral.com/articles/10.1186/1746-4811-7-49 |
| Plant methods | 5 | A simple and efficient method for isolating small RNAs from different plant species | 10.1186/1746-4811-7-4 | https://plantmethods.biomedcentral.com/articles/10.1186/1746-4811-7-4 |
| Plant methods | 6 | Protocol: high throughput silica-based purification of RNA from Arabidopsis seedlings in a 96-well format | 10.1186/1746-4811-7-40 | https://plantmethods.biomedcentral.com/articles/10.1186/1746-4811-7-40 |
| Plant methods | 7 | Protocol: A high-throughput DNA extraction system suitable for conifers | 10.1186/1746-4811-4-20 | https://plantmethods.biomedcentral.com/articles/10.1186/1746-4811-4-20 |
| Plant methods | 8 | Protocol: using virus-induced gene silencing to study the arbuscular mycorrhizal symbiosis in Pisum sativum | 10.1186/1746-4811-6-28 | https://plantmethods.biomedcentral.com/articles/10.1186/1746-4811-6-28 |
| Plant methods | 9 | Protocol: a beginner’s guide to the analysis of RNA-directed DNA methylation in plants | 10.1186/1746-4811-10-18 | https://plantmethods.biomedcentral.com/articles/10.1186/1746-4811-10-18 |
| Plant methods | 10 | Protocol: a simple method for extracting next-generation sequencing quality genomic DNA from recalcitrant plant species | 10.1186/1746-4811-10-21 | https://plantmethods.biomedcentral.com/articles/10.1186/1746-4811-10-21 |
| Plant methods | 11 | Protocol: a highly sensitive RT-PCR method for detection and quantification of microRNAs | 10.1186/1746-4811-3-12 | https://plantmethods.biomedcentral.com/articles/10.1186/1746-4811-3-12 |
| Plant methods | 12 | Protocol: Streamlined sub-protocols for floral-dip transformation and selection of transformants in Arabidopsis thaliana | 10.1186/1746-4811-5-3 | https://plantmethods.biomedcentral.com/articles/10.1186/1746-4811-5-3 |
| Plos One | 1 | A Yeast Metabolite Extraction Protocol Optimised for Time-Series Analyses | 10.1371/journal.pone.0044283 | http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0044283 |
| Plos One | 2 | A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq | 10.1371/journal.pone.0026426 | http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0026426 |
| Plos One | 3 | Multiplexed Strand-specific RNA-Seq Library Preparation for Illumina Sequencing Platforms | http://journals.plos.org/plosone/article/file?type=supplementary&id=info:doi/10.1371/journal.pone.0026426.s015 | |
| Plos One | 4 | An Optimized Chloroplast DNA Extraction Protocol for Grasses (Poaceae) Proves Suitable for Whole Plastid Genome Sequencing and SNP Detection | 10.1371/journal.pone.0002813 | http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0002813 |
| Plos One | 5 | SNP Discovery and Development of a High-Density Genotyping Array for Sunflower | 10.1371/journal.pone.0029814 | http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0029814 |
| springer protocols | 1 | Competitive RT-PCR Strategy for Quantitative Evaluation of the Expression of Tilapia (Oreochromis niloticus) Growth Hormone Receptor Type I | 10.1007/s12575-009-9002-3 | https://www.ncbi.nlm.nih.gov/pubmed/19495916 |
| springer protocols | 2 | Easy and efficient protocol for oomycete DNA extraction suitable for population genetic analysis | 10.1007/s10529-010-0478-3 | https://link.springer.com/article/10.1007/s10529-010-0478-3 |
| springer protocols | 3 | Inter-laboratory reproducibility of fast gas chromatography–electron impact–time of flight mass spectrometry (GC–EI–TOF/MS) based plant metabolomics | 10.1007/s11306-009-0169-z | https://link.springer.com/article/10.1007/s11306-009-0169-z |
| springer protocols | 4 | A method for purification, identification and validation of DNMT1 mRNA binding proteins | 10.1251/bpo142 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2591025/ |
| springer protocols | 5 | A Modified Protocol for Bisulfite Genomic Sequencing of Difficult Samples | 10.1007/s12575-009-9010-3 | https://biologicalproceduresonline.biomedcentral.com/articles/10.1007/s12575-009-9010-3 |
| MethodsX | 1 | Improved internal control for molecular diagnosis assays | 10.1016/j.mex.2015.03.002 | https://www.sciencedirect.com/science/article/pii/S2215016115000163?via%3Dihub |
| MethodsX | 2 | Isolation of novel sequences targeting highly variable viral protein hemagglutinin | 10.1016/j.mex.2015.02.005 | https://www.sciencedirect.com/science/article/pii/S2215016115000084?via%3Dihub |
| MethodsX | 3 | Improved method for extraction and detection of Helicobacter pylori DNA in formalin-fixed paraffin embedded gastric biopsies using laser micro-dissection | 10.1016/j.mex.2014.11.003 | https://www.sciencedirect.com/science/article/pii/S2215016114000272?via%3Dihub |
| MethodsX | 4 | Modification of a commercial DNA extraction kit for safe and rapid recovery of DNA and RNA simultaneously from soil, without the use of harmful solvents | 10.1016/j.mex.2015.03.007 | https://www.sciencedirect.com/science/article/pii/S2215016115000217?via%3Dihub |
| MethodsX | 5 | Plant and metagenomic DNA extraction of mucilaginous seeds | 10.1016/j.mex.2014.09.005 | https://www.sciencedirect.com/science/article/pii/S2215016114200628?via%3Dihub |
| MethodsX | 6 | Efficient purification and concentration of viruses from a large body of high turbidity seawater | 10.1016/j.mex.2014.09.001 | https://www.sciencedirect.com/science/article/pii/S2215016114000119?via%3Dihub |
| MethodsX | 7 | Recombination-assisted megaprimer (RAM) cloning | 10.1016/j.mex.2014.05.001 | https://www.sciencedirect.com/science/article/pii/S2215016114200161?via%3Dihub |
| Journal of biological methods | 1 | A noninvasive assay for monitoring renal allograft status | http://dx.doi.org/10.14440/jbm.2014.19 | http://www.jbmethods.org/jbm/article/view/19 |
| Journal of biological methods | 2 | Inducing gene expression by targeting promoter sequences using small activating RNAs | http://dx.doi.org/10.14440/jbm.2015.39 | http://www.jbmethods.org/jbm/article/view/39 |
| Journal of biological methods | 3 | Assessing phytase activity–methods, definitions and pitfalls | http://dx.doi.org/10.14440/jbm.2015.58 | http://www.jbmethods.org/jbm/article/view/58 |
| Journal of biological methods | 4 | Automated high-throughput measurement of body movements and cardiac activity of Xenopus tropicalis tadpoles | http://dx.doi.org/10.14440/jbm.2014.29 | http://www.jbmethods.org/jbm/article/view/29 |
| Journal of biological methods | 5 | Generation of axolotl hematopoietic chimeras | http://dx.doi.org/10.14440/jbm.2015.43 | http://www.jbmethods.org/jbm/article/view/43 |
| Journal of biological methods | 6 | A stepwise procedure for isolation of murine bone marrow and generation of dendritic cells | http://dx.doi.org/10.14440/jbm.2014.12 | http://www.jbmethods.org/jbm/article/view/12/0 |
| Journal of biological methods | 7 | Use of retroviral-mediated gene transfer to deliver and test function of chimeric antigen receptors in human T-cells | http://dx.doi.org/10.14440/jbm.2014.30 | http://www.jbmethods.org/jbm/article/view/30 |