Protocols: Difference between revisions

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/* Cold Spring Harbor Xenopus Protocols 2019 and 2020. [http://cshprotocols.cshlp.org/search?fulltext=Xenopus&submit=yes&x=18&y=12&tocsectionid=protocol&tocsectionid=recipe&tocsectionid=topic+introduction&tocsectionid=emerging+model+organisms&tocsecti...
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**Lymphocyte Deficiency Induced by Sublethal Irradiation in ''Xenopus''. Louise A. Rollins-Smith and Jacques Robert. 2019. [http://cshprotocols.cshlp.org/content/2019/1/pdb.prot097626.full?sid=8e4aa418-f7f4-4ebb-bf83-c6a0f37997de].
**Lymphocyte Deficiency Induced by Sublethal Irradiation in ''Xenopus''. Louise A. Rollins-Smith and Jacques Robert. 2019. [http://cshprotocols.cshlp.org/content/2019/1/pdb.prot097626.full?sid=8e4aa418-f7f4-4ebb-bf83-c6a0f37997de].
**Microinjection of DNA Constructs into Xenopus Embryos for Gene Misexpression and cis-Regulatory Module Analysis. Yuuri Yasuoka and Masanori Taira. 2019. [http://cshprotocols.cshlp.org/content/2019/1/pdb.prot097279.full?sid=2fc9436b-3641-44d3-b3c6-c967a7433e1a]
**Microinjection of DNA Constructs into Xenopus Embryos for Gene Misexpression and cis-Regulatory Module Analysis. Yuuri Yasuoka and Masanori Taira. 2019. [http://cshprotocols.cshlp.org/content/2019/1/pdb.prot097279.full?sid=2fc9436b-3641-44d3-b3c6-c967a7433e1a]
=neurobiology and regeneration=
=neurobiology and regeneration=
**Tracing Central Nervous System Axon Regeneration in ''Xenopus''. Kurt M. Gibbs and Ben G. Szaro. 2018. [http://cshprotocols.cshlp.org/content/2018/12/pdb.prot101030.full?sid=2fc9436b-3641-44d3-b3c6-c967a7433e1a]
**Tracing Central Nervous System Axon Regeneration in ''Xenopus''. Kurt M. Gibbs and Ben G. Szaro. 2018. [http://cshprotocols.cshlp.org/content/2018/12/pdb.prot101030.full?sid=2fc9436b-3641-44d3-b3c6-c967a7433e1a]

Revision as of 11:24, 22 January 2020


Books for Xenopus Research and Protocols

  • Xenopus Protocols: Post-Genomic Approaches. Hoppler and Vize, 2012 [1]
    • expanded second edition with novel approaches inspired by X. tropicalis genome sequencing.
  • The Laboratory Xenopus sp. Green, 2010 [2]
    • a highly detailed manual containing Xenopus husbandry, management, veterinary care, and frog and equipment vendor information
  • Xenopus Protocols: Cell Biology and Signal Transduction Liu (First edition), 2006 [3]
    • step-by-step laboratory instructions, an introduction outlining the principles behind the technique, lists of the necessary equipment and reagents.
  • Color Atlas of Xenopus laevis Histology, Wiechmann and Wirsig-Wiechmann, 2003 [4]
    • central source on the microscopic anatomy of cells, tissues, and major organs of Xenopus laevis.
  • Early Development of Xenopus laevis: A Laboratory Manual, Sive, Grainger, and Harland, 2000 [5]
    • comprehensive collection of protocols for the study of early development in Xenopus embryos
  • Transgenic Xenopus: Microinjection Methods and Developmental Neurobiology, Seidman and Soreq, 1997 [6]
    • referenced guide to the use of microinjected embryos studying the role and regulation of nervous system proteins during development.
  • Atlas of Xenopus Development, Bernardini, Prati, Bonetti, and Scari, 1999 [7]
    • scanning, transmission, and light microscopy images of Xenopus embryonic development.
  • Normal Table of Xenopus laevis (Daudin), Nieuwkoop and Faber (Third edition), 1994 [8]
    • a systematic and chronological description of Xenopus laevis development.
  • Xenopus laevis: Practical Uses in Cell and Molecular Biology, Volume 36, Kay and Peng, 1991 [9]
    • detailed description of a wide range of uses for Xenopus laevis oocytes and embryos in cell and molecular biology.
  • The early development of Xenopus laevis. An atlas of the histology, Hausen and Riebesell, 1991 [10]
    • detailed histological sections of Xenopus embryonic development

Online Xenopus Resources

External links to the Journal of Visualized Experiments (JOVE) - Xenopus embryo [11] - excellent video demonstrations

    • Functional Evaluation of Olfactory Pathways in Living Xenopus Tadpoles - Terni et al. -[12]
    • Obtaining Eggs from Xenopus laevis Females - Cross & Powers [13]
    • Microinjection of Xenopus Laevis Oocytes - Cohen et al. - [14]
    • Fertilization of Xenopus oocytes, Host Transfer Method - Schneider et al. [15]
    • Tissue Determination Using Animal Cap Transplant (ACT) Assay in X. laevis - Viczian & Zuber [16]
    • Blastomere Explants to Test for Cell Fate Commitment - Grant et al. [17]
    • Transgenic Xenopus laevis by Restriction Enzyme Mediated Integration and Nuclear Transplantation - Amaya & Kroll [18]
    • Organizer and Animal Pole Explants from X. laevis Embryos and Cell Adhesion Assay - Ogata & Cho [19]
    • Plastic Embedding and Sectioning of X. laevis Embryos - Ogata1 et al. [20]
    • Visualizing RNA Localization in Xenopus Oocytes - Gagnon & Mowry [21]
    • Neural Explant Cultures from Xenopus laevis - Lowery et al. [22]
    • Translocation of Fluorescent Proteins in Xenopus Ectoderm in Response to Wnt Signaling - Itoh & Sokol [23]
    • Dissection, Culture, and Analysis of X. laevis Embryonic Retinal Tissue - McDonough et al. [24]
    • X. tropicalis Egg Extracts to Identify Microtubule-associated RNAs - Sharp & Blower [25]
    • Electroporation of Craniofacial Mesenchyme - Tabler & Liu [26]
    • Electrophysiological Recording from Xenopus Nerve-muscle Co-cultures - Yazejian et al. [27]
    • Single Cell Electroporation in vivo within the Intact Developing Brain - Hewapathirane & Haas - [28]
    • Live-cell Imaging and Quantitative Analysis of Embryonic Epithelial Cells - Joshi & Davidson [29]
    • Preparation and Fractionation of Xenopus laevis Egg Extracts - Cross & Powers [30]
    • In Vitro Nuclear Assembly Using Fractionated Xenopus Egg Extracts - Cross & Powers [31]
    • Study of the DNA Damage Checkpoint using Xenopus Egg Extracts - Willis et al. [32]
    • Two Types of Assays for Detecting Frog Sperm Chemoattraction - Burnett et al. [33]
    • Comparative in vivo Study of gp96 Adjuvanticity in X. laevis - Nedelkovska et al. [34]
    • Patch Clamp and Perfusion Techniques - Yang et al. [35]
    • Patch Clamp Recording of Ion Channels - Brown et al. [36]
    • Cation Transport in Xenopus Oocytes - Dürr et al.[37]
    • Stem cell-like Xenopus Embryonic Explants to Study Early Neural Developmental Features In Vitro and In Vivo - BC.Durand [38]
    • Dissection of Xenopus laevis Neural Crest for in vitro Explant Culture or in vivo Transplantation - Millet & Monsoro-Burq [39]

Morpholino Studies in Xenopus Brain Development

Bestman and Cline 2019, Brain Development pp 377-395, Part of the Methods in Molecular Biology book series (MIMB, volume 2047) [[40]]

Cold Spring Harbor Xenopus Protocols 2018, 2019 and 2020. [41] - Nore: external links provided as a subscription is required for access to some protocols.

All articles are Copyright 2019  Cold Spring Harbor Laboratory Press, or Copyright 2020  Cold Spring Harbor Laboratory Press- please cite and request permission to re-use images/figures accordingly.
    • Raising Antibodies for Use in Xenopus. Maya Z. Piccinni and Matthew J. Guille. 2020. [42]
    • Purifying Antibodies Raised against Xenopus Peptides. Maya Z. Piccinni and Matthew J. Guille. 2020. [43]
    • Assessing the Immune Response When Raising Antibodies for Use in Xenopus. Maya Z. Piccinni and Matthew J. Guille. 2020. [44].
    • In Vitro Transcription Systems. Michael R. Green and Joseph Sambrook. [45]
    • Applying Tensile and Compressive Force to Xenopus Animal Cap Tissue. Georgina K. Goddard, Nawseen Tarannum, and Sarah Woolner. 2020. [46].
    • Microinjection of mRNAs and Oligonucleotides. Sally A. Moody. 2018. [47]
    • Whole-Mount Immunofluorescence for Visualizing Endogenous Protein and Injected RNA in Xenopus Oocytes. Samantha P. Jeschonek and Kimberly L. Mowry. 2018. [48]
    • Transcriptomics and Proteomics Methods for Xenopus Embryos and Tissues. Michael J. Gilchrist, Gert Jan C. Veenstra, and Ken W.Y. Cho. 2020. ''Topic Introduction'' [49]
    • In Vivo Assessment of Neural Precursor Cell Cycle Kinetics in the Amphibian Retina. Morgane Locker and Muriel Perron2019. [50], Supplemental Material [51]
    • Following Endocrine-Disrupting Effects on Gene Expression in Xenopus laevis. Petra Spirhanzlova, Michelle Leemans, Barbara A. Demeneix, and Jean-Baptiste Fini. 2019. Full-text link: [52].
    • Analysis of Chromatin Binding of Ectopically Expressed Proteins in Early Xenopus Embryos. Laura J.A. Hardwick and Anna Philpott. 2019. [53].
    • Analysis of Phosphorylation Status of Ectopically Expressed Proteins in Early Xenopus Embryos. Laura J.A. Hardwick and Anna Philpott. 2019. [54].
    • An RNA-Seq Protocol for Differential Expression Analysis. Nick D.L. Owens, Elena De Domenico, and Michael J. Gilchrist. 2019. [55]
    • Calculating the Degradation Rate of Individual Proteins Using Xenopus Extract Systems. Gary S. McDowell and Anna Philpott. 2019. [56].
    • The Use of Cell-Free Xenopus Extracts to Investigate Cytoplasmic Events. Romain Gibeaux and Rebecca Heald. 2019.''Topic Introduction'' [57]
    • Mass Spectrometry-Based Absolute Quantification of Single Xenopus Embryo Proteomes. Rik G.H. Lindeboom, Arne H. Smits, Matteo Perino, Gert Jan C. Veenstra, and Michiel Vermeulen. [58]
    • Assessing Ubiquitylation of Individual Proteins Using Xenopus Extract Systems. Gary S. McDowell and Anna Philpott. 2019. [59]
    • INTACT Proteomics in Xenopus. Lauren Wasson, Nirav M. Amin, and Frank L. Conlon. 2019. [60]
    • Special Considerations for Making Explants and Transplants with Xenopus tropicalis. 2019. Marilyn Fisher and Robert M. Grainger. [61]. Supplemental Material [62].
    • Skin Grafting in Xenopus laevis: A Technique for Assessing Development and Immunological Disparity. Yumi Izutsu. 2019. [63]
    • Adoptive Transfer of Fluorescently Labeled Immune Cells in Xenopus. Kun Hyoe Rhoo and Jacques Robert. [64]
    • Generating a Three-Dimensional Genome from Xenopus with Hi-C. Ian K. Quigley and Sven Heinz. 2019. [65]
    • Assessing Antibody Responses to Pathogens or Model Antigens in Xenopus by Enzyme-Linked Immunosorbent Assay (ELISA). Francisco De Jesús Andino and Jacques Robert. 2019 [66]
    • DNase-seq to Study Chromatin Accessibility in Early Xenopus tropicalis Embryos. Jin Sun Cho, Ira L. Blitz, and Ken W.Y. Cho. 2019 [67]
    • Ex Vivo Eye Tissue Culture Methods for Xenopus. Jonathan J. Henry, Kimberly J. Perry, and Paul W. Hamilton. 2019. [68].
    • Methods for Examining Lens Regeneration in Xenopus. Jonathan J. Henry, Kimberly J. Perry, and Paul W. Hamilton. 2019. [69]
    • Mapping Chromatin Features of Xenopus Embryos. George E. Gentsch and James C. Smith. 2019. [70]
    • Reconstituting Nuclear and Chromosome Dynamics Using Xenopus Extracts. Susannah Rankin. 2019 [71]
    • Extracts for Analysis of DNA Replication in a Nucleus-Free System. Justin Sparks and Johannes C. Walter. 2019. [72]
    • Endoplasmic Reticulum Network Formation with Xenopus Egg Extracts. Songyu Wang, Fabian B. Romano, and Tom A. Rapoport. 2019. [73].
    • Chromatin Characterization in Xenopus laevis Cell-Free Egg Extracts and Embryos. Wei-Lin Wang, Takashi Onikubo, and David Shechter. 2019. [74].
    • Filopodia-Like Structure Formation from Xenopus Egg Extracts. Helen M. Fox and Jennifer L. Gallop. 2019. [75].
    • Einsteck Transplants. Hélène Cousin. 2019 [76]
    • Chromosome Cohesion and Condensation in Xenopus Egg Extracts. Eulália M.L. da Silva and Susannah Rankin. 2019. [77]
    • Cleavage Blastomere Deletion and Transplantation to Test Cell Fate Commitment in Xenopus. Sally A. Moody. 2019. [78]
    • Cleavage Blastomere Explant Culture in Xenopus. Sally A. Moody. 2019. [79]
    • Lineage Tracing and Fate Mapping in Xenopus Embryos. Sally A. Moody. 2018. [http://cshprotocols.cshlp.org/content/2018/12/pdb.prot097253.full?sid=2fc9436b-3641-44d3-b3c6-c967a7433e1a}
    • ChIP-Sequencing in Xenopus Embryos. Saartje Hontelez, Ila van Kruijsbergen, and Gert Jan C. Veenstra. 2019. [80]
    • Lymphocyte Deficiency Induced by Sublethal Irradiation in Xenopus. Louise A. Rollins-Smith and Jacques Robert. 2019. [81].
    • Microinjection of DNA Constructs into Xenopus Embryos for Gene Misexpression and cis-Regulatory Module Analysis. Yuuri Yasuoka and Masanori Taira. 2019. [82]

neurobiology and regeneration

    • Tracing Central Nervous System Axon Regeneration in Xenopus. Kurt M. Gibbs and Ben G. Szaro. 2018. [83]
    • Cell Transplantation as a Method to Investigate Spinal Cord Regeneration in Regenerative and Nonregenerative Xenopus Stages. Emilio E. Méndez-Olivos and Juan Larraín. 2018. [84]
    • Infrared Laser-Mediated Gene Induction at the Single-Cell Level in the Regenerating Tail of Xenopus laevis Tadpoles. Riho Hasugata, Shinichi Hayashi, Aiko Kawasumi-Kita, Joe Sakamoto, Yasuhiro Kamei, and Hitoshi Yokoyama. 2018. [85]
    • Rod-Specific Ablation Using the Nitroreductase/Metronidazole System to Investigate Regeneration in Xenopus. Reyna I. Martinez-De Luna and Michael E. Zuber. 2018. [86]
    • Studies of Limb Regeneration in Larval Xenopus. Anthony L. Mescher and Anton W. Neff. 2019. [87].






.

2019/2020 CSHL Recipes

    • Embryo Lysis Buffer (Xenopus). (Recipe 1) CSHLP. 2019 [88]
    • Xenopus Embryo Lysis Buffer. (Recipe 2). CSHLP. 2019 [89]
    • Lysis Buffer for Xenopus (recipe3) CSHLP. 2019. [90]
    • DNA Isolation Buffer. CSHLP. 2019 [91]
    • Lysis Buffer for Xenopus Hi-C. CSHLP 2019. [92]
    • RIPA Buffer for Xenopus. CSHLP 2019. [93]
    • Amphibian Serum-Free (ASF) Medium Supplemented with Fetal Bovine Serum (FBS). CSHL 2019. [94]
    • Xenopus Eye Culture Medium. CSHLP 2019. [95]
    • Marc's Modified Ringer's (MMR) for Xenopus (20×). CSHLP. 2019. [96]
    • Injection Buffer for Xenopus. CSHLP 2019. [97]
    • TE Buffer for Xenopus. CSHLP 2019. [98]

Cold Spring Harbor Xenopus Protocols 2007. Edited by Hazel Sive

    • Housing and Feeding of Xenopus laevis - Sive et al. [99]
    • Inducing Ovulation in Xenopus laevis - Sive et al. [100]
    • Xenopus laevis In Vitro Fertilization and Natural Mating Methods - Sive et al. [101]
    • Egg Collection and In Vitro Fertilization of the Western Clawed Frog Xenopus tropicalis - Showell & Conlon [102]
    • Isolation of Xenopus Oocytes - Sive et al. [103]
    • Isolating Xenopus laevis Testes - Sive et al. [104]
    • Dejellying Xenopus laevis Embryos - Sive et al. [105]
    • Removing the Vitelline Membrane from Xenopus laevis Embryos - Sive et al. [106]
    • Microinjection of Xenopus Embryos - Sive et al. [107]
    • Defolliculation of Xenopus Oocytes - Sive et al. [108]
    • Microinjection of Xenopus Oocytes - Sive et al. [109]
    • Animal Cap Isolation from Xenopus laevis - Sive et al. [110]
    • Xenopus laevis Keller Explants - Sive et al. [111]
    • Microinjection of RNA and Preparation of Secreted Proteins from Xenopus Oocytes - Sive et al. [112]
    • Calibration of the Injection Volume for Microinjection of Xenopus Oocytes and Embryos - Sive et al. [113]
    • Isolation of DNA from Red Blood Cells in Xenopus - Sive et al. [114]
    • Investigating Morphogenesis in Xenopus Embryos: Imaging Strategies, Processing, and Analysis - Kim & Davidson [115]
    • Low-Magnification Live Imaging of Xenopus Embryos for Cell and Developmental Biology - Wallingford [116]
    • High-Magnification In Vivo Imaging of Xenopus Embryos for Cell and Developmental Biology - Keiserman et al. [117]
    • Preparation of Fixed Xenopus Embryos for Confocal Imaging - Wallingford [118]
    • Whole-Mount Fluorescence Immunocytochemistry on Xenopus Embryos - Lee et al. [119]
    • Generation of Transgenic Xenopus laevis - Kroll & Amaya - [120] [121] [122]
    • In Vivo Time-Lapse Imaging of Neuronal Development in Xenopus - Ruthazer et al. [123]
    • Photoconversion for Tracking the Dynamics of Cell Movement in Xenopus laevis Embryos - Chernet et al. [124]
    • Single-Cell Electroporation in Xenopus - Liu & Haas [125]
    • Imaging Axon Pathfinding in Xenopus In Vivo - Leung & Holt [126]
    • A Versatile Protocol for mRNA Electroporation of Xenopus laevis Embryos - Chernet & Levin [127]

General Research Protocols

Animal Husbandry


Lab Solutions and Reagents (click each to view expanded content)


Generating Embryos


Transgenesis


in situ Hybridization


Immunohistochemistry


ChIP protocols

  • Chromatin immunoprecipitation analysis of Xenopus embryos., Methods Mol Biol. 2012;917:279-92. [134] [135]
    • Akkers RC, Jacobi UG, Veenstra GJ.
  • Chromatin immunoprecipitation in early Xenopus laevis embryos., Dev Dyn. 2009 Jun;238(6):1422-32. [136] [137]
    • Blythe SA, Reid CD, Kessler DS, Klein PS.


Histology


Embryo Staining Protocols (non in situ)


Immuno and Protein Protocols


Nucleic Acid Protocols


Oocyte Transfer Technique (Heasman/Wylie labs)


Xenopus Oocyte and Egg Extracts


Xenopus Tissue Culture

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