Table of Contents

Emerging Model Organisms

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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
Cold Spring Harb Protoc; 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
Cold Spring Harb Protoc; 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
Cold Spring Harb Protoc; 2009; doi:10.1101/pdb.emo131

Information Panels

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In Vivo Imaging of Mammalian Cells: Cell Engineering and Viability
- Jason R. Swedlow,
- Paul D. Andrews,
- and Melpomeni Platani
Cold Spring Harb Protoc; 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
Cold Spring Harb Protoc; 2009; doi:10.1101/pdb.ip70

Protocols

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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
Cold Spring Harb Protoc; 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
Cold Spring Harb Protoc; 2009; doi:10.1101/pdb.prot5278
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Chromatin Immunoprecipitation (ChIP)
- Michael F. Carey,
- Craig L. Peterson,
- and Stephen T. Smale
Cold Spring Harb Protoc; 2009; doi:10.1101/pdb.prot5279
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Position-Based Clustering of Microarray Expression Data
- Christopher Faulk and
- Joomyeong Kim
Cold Spring Harb Protoc; 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
Cold Spring Harb Protoc; 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
Cold Spring Harb Protoc; 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
Cold Spring Harb Protoc; 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
Cold Spring Harb Protoc; 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
Cold Spring Harb Protoc; 2009; doi:10.1101/pdb.prot5285
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Amphioxus Whole-Mount In Situ Hybridization
- J.K. Sky Yu and
- Linda Z. Holland
Cold Spring Harb Protoc; 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
Cold Spring Harb Protoc; 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
Cold Spring Harb Protoc; 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
Cold Spring Harb Protoc; 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
Cold Spring Harb Protoc; 2009; doi:10.1101/pdb.prot5290
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Construction of Gene-Targeting Vectors by Recombineering
- Song-Choon Lee and
- Pentao Liu
Cold Spring Harb Protoc; 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
Cold Spring Harb Protoc; 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
Cold Spring Harb Protoc; 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
Cold Spring Harb Protoc; 2009; doi:10.1101/pdb.prot5294
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RNA Extraction from Arabidopsis for Northern Blots and Reverse Transcriptase-PCR
- Ji H. Ahn
Cold Spring Harb Protoc; 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
Cold Spring Harb Protoc; 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
Cold Spring Harb Protoc; 2009; doi:10.1101/pdb.prot5297

Emerging Model Organisms

The Starlet Sea Anemone Nematostella vectensis: An Anthozoan Model Organism for Studies in Comparative Genomics and Functional Evolutionary Developmental Biology

Cephalochordates (Amphioxus or Lancelets): A Model for Understanding the Evolution of Chordate Characters

The Western Clawed Frog (Xenopus tropicalis): An Emerging Vertebrate Model for Developmental Genetics and Environmental Toxicology

Information Panels

In Vivo Imaging of Mammalian Cells: Cell Engineering and Viability

In Vivo Imaging of Mammalian Cells: Image Acquisition and Analysis

Protocols

In Vivo DNase I, MNase, and Restriction Enzyme Footprinting via Ligation-Mediated Polymerase Chain Reaction (LM-PCR)

In Vivo Dimethyl Sulfate (DMS) Footprinting via Ligation-Mediated Polymerase Chain Reaction (LM-PCR)

Chromatin Immunoprecipitation (ChIP)

Position-Based Clustering of Microarray Expression Data

Induction of Spawning in the Starlet Sea Anemone Nematostella vectensis, In Vitro Fertilization of Gametes, and Dejellying of Zygotes

In Situ Hybridization of Starlet Sea Anemone (Nematostella vectensis) Embryos, Larvae, and Polyps

Anti-acetylated Tubulin Antibody Staining and Phalloidin Staining in the Starlet Sea Anemone Nematostella vectensis

Bromodeoxyuridine Labeling of S-Phase Nuclei in the Starlet Sea Anemone Nematostella vectensis

Amphioxus (Branchiostoma floridae) Spawning and Embryo Collection

Amphioxus Whole-Mount In Situ Hybridization

Extraction of DNA from Adult Amphioxus Tissue

Extraction of RNA from Amphioxus Embryos or Adult Amphioxus Tissue

Extraction of RNA from Small Amounts of Amphioxus Embryos for cDNA Synthesis by RT-PCR

Fluorescent In Situ Hybridization (FISH) on Diploid Nuclei and Mitotic Chromosomes from Drosophila melanogaster Larval Tissues

Construction of Gene-Targeting Vectors by Recombineering

Natural Mating and Tadpole Husbandry in the Western Clawed Frog Xenopus tropicalis

Egg Collection and In Vitro Fertilization of the Western Clawed Frog Xenopus tropicalis

Tissue Sampling and Genomic DNA Purification from the Western Clawed Frog Xenopus tropicalis

RNA Extraction from Arabidopsis for Northern Blots and Reverse Transcriptase-PCR

Semiquantitative Analysis of Arabidopsis RNA by Reverse Transcription Followed by Noncompetitive PCR

Semiquantitative Analysis of Arabidopsis RNA by Reverse Transcription Followed by PCR Using Mimics

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