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Cover Illustration: Nuclei and mitotic chromosomes of acetic acid/ethanol-fixed Drosophila melanogaster larval neuroblasts were spread by drying in acetic acid onto poly-L-lysine-coated slides. Multiple probes were used after light alkaline denaturation to simultaneously detect rDNA repeats (green) and the single-copy Su(f) and white genes (red). Samples were counterstained with DAPI (blue) and images were captured using a Leica DMRB microscope with a 100X oil objective. Diagrams illustrate the white-mottled chromosomal inversion that results in the stochastic down-regulation of white in its new rDNA-proximal location. The associated Position-Effect Variegation phenotype is reflected by the mottled eye color of adult flies. Su(f) lies within X-chromosome heterochromatin while white is located at the distal end of X-chromosome euchromatin. Their position is inverted in white-mottled flies. These methods permit resolutive mapping of the sequences under study on diploid mitotic chromosomes and allow for tentative localization of putative insulators that serve as heterochromatin/euchromatin boundaries. (Images and illustrations courtesy of Emmanuel Käs.) For more information on the methods used, see Fluorescent In Situ Hybridization (FISH) on Diploid Nuclei and Mitotic Chromosomes from Drosophila melanogaster Larval Tissues (doi:10.1101/pdb.prot5290).
The Starlet Sea Anemone Nematostella vectensis: An Anthozoan Model Organism for Studies in Comparative Genomics and Functional Evolutionary Developmental Biology
Grigory Genikhovich and Ulrich Technau
CSH Protocols; 2009; doi:10.1101/pdb.emo129
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Cephalochordates (Amphioxus or Lancelets): A Model for Understanding the Evolution of Chordate Characters
J.K. Sky Yu and Linda Z. Holland
CSH Protocols; 2009; doi:10.1101/pdb.emo130
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The Western Clawed Frog (Xenopus tropicalis): An Emerging Vertebrate Model for Developmental Genetics and Environmental Toxicology
Chris Showell and Frank L. Conlon
CSH Protocols; 2009; doi:10.1101/pdb.emo131
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In Vivo Imaging of Mammalian Cells: Cell Engineering and Viability
Jason R. Swedlow, Paul D. Andrews, and Melpomeni Platani
CSH Protocols; 2009; doi:10.1101/pdb.ip69
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In Vivo Imaging of Mammalian Cells: Image Acquisition and Analysis
Jason R. Swedlow, Paul D. Andrews, and Melpomeni Platani
CSH Protocols; 2009; doi:10.1101/pdb.ip70
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In Vivo DNase I, MNase, and Restriction Enzyme Footprinting via Ligation-Mediated Polymerase Chain Reaction (LM-PCR)
Michael F. Carey, Craig L. Peterson, and Stephen T. Smale
CSH Protocols; 2009; doi:10.1101/pdb.prot5277
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In Vivo Dimethyl Sulfate (DMS) Footprinting via Ligation-Mediated Polymerase Chain Reaction (LM-PCR)
Michael F. Carey, Craig L. Peterson, and Stephen T. Smale
CSH Protocols; 2009; doi:10.1101/pdb.prot5278
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Chromatin Immunoprecipitation (ChIP)
Michael F. Carey, Craig L. Peterson, and Stephen T. Smale
CSH Protocols; 2009; doi:10.1101/pdb.prot5279
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Position-Based Clustering of Microarray Expression Data
Christopher Faulk and Joomyeong Kim
CSH Protocols; 2009; doi:10.1101/pdb.prot5280
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Induction of Spawning in the Starlet Sea Anemone Nematostella vectensis, In Vitro Fertilization of Gametes, and Dejellying of Zygotes
Grigory Genikhovich and Ulrich Technau
CSH Protocols; 2009; doi:10.1101/pdb.prot5281
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In Situ Hybridization of Starlet Sea Anemone (Nematostella vectensis) Embryos, Larvae, and Polyps
Grigory Genikhovich and Ulrich Technau
CSH Protocols; 2009; doi:10.1101/pdb.prot5282
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Anti-acetylated Tubulin Antibody Staining and Phalloidin Staining in the Starlet Sea Anemone Nematostella vectensis
Grigory Genikhovich and Ulrich Technau
CSH Protocols; 2009; doi:10.1101/pdb.prot5283
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Bromodeoxyuridine Labeling of S-Phase Nuclei in the Starlet Sea Anemone Nematostella vectensis
Grigory Genikhovich and Ulrich Technau
CSH Protocols; 2009; doi:10.1101/pdb.prot5284
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Amphioxus (Branchiostoma floridae) Spawning and Embryo Collection
J.K. Sky Yu and Linda Z. Holland
CSH Protocols; 2009; doi:10.1101/pdb.prot5285
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Amphioxus Whole-Mount In Situ Hybridization
J.K. Sky Yu and Linda Z. Holland
CSH Protocols; 2009; doi:10.1101/pdb.prot5286
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Extraction of DNA from Adult Amphioxus Tissue
J.K. Sky Yu and Linda Z. Holland
CSH Protocols; 2009; doi:10.1101/pdb.prot5287
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Extraction of RNA from Amphioxus Embryos or Adult Amphioxus Tissue
J.K. Sky Yu and Linda Z. Holland
CSH Protocols; 2009; doi:10.1101/pdb.prot5288
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Extraction of RNA from Small Amounts of Amphioxus Embryos for cDNA Synthesis by RT-PCR
J.K. Sky Yu and Linda Z. Holland
CSH Protocols; 2009; doi:10.1101/pdb.prot5289
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Fluorescent In Situ Hybridization (FISH) on Diploid Nuclei and Mitotic Chromosomes from Drosophila melanogaster Larval Tissues
Roxane Blattes and Emmanuel Käs
CSH Protocols; 2009; doi:10.1101/pdb.prot5290
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Construction of Gene-Targeting Vectors by Recombineering
Song-Choon Lee and Pentao Liu
CSH Protocols; 2009; doi:10.1101/pdb.prot5291
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Natural Mating and Tadpole Husbandry in the Western Clawed Frog Xenopus tropicalis
Chris Showell and Frank L. Conlon
CSH Protocols; 2009; doi:10.1101/pdb.prot5292
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Egg Collection and In Vitro Fertilization of the Western Clawed Frog Xenopus tropicalis
Chris Showell and Frank L. Conlon
CSH Protocols; 2009; doi:10.1101/pdb.prot5293
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Tissue Sampling and Genomic DNA Purification from the Western Clawed Frog Xenopus tropicalis
Chris Showell and Frank L. Conlon
CSH Protocols; 2009; doi:10.1101/pdb.prot5294
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RNA Extraction from Arabidopsis for Northern Blots and Reverse Transcriptase-PCR
Ji H. Ahn
CSH Protocols; 2009; doi:10.1101/pdb.prot5295
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Semiquantitative Analysis of Arabidopsis RNA by Reverse Transcription Followed by Noncompetitive PCR
Ji H. Ahn
CSH Protocols; 2009; doi:10.1101/pdb.prot5296
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Semiquantitative Analysis of Arabidopsis RNA by Reverse Transcription Followed by PCR Using Mimics
Igor Kardailsky
CSH Protocols; 2009; doi:10.1101/pdb.prot5297
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