Progress in science depends on new techniques, new discoveries and new ideas, probably in that order.
— Sydney Brenner

Caenorhabditis elegans(C. elegans)

Mus musculus

129S1 C57BL/6J BALB/cJ

Mouse genetics tools in brain vasculature system field

1. NG2DsRedBAC: NG2DsRedBAC transgenic mice is suitable for pericyte and Artery SMC labeling in central nervous system. NG2DsRedBAC transgenic mice express an optimized red fluorescent protein variant (DsRed.T1) under the control of the mouse NG2 (Cspg4) promoter/enhancer and may be useful for fluorescent labeling of NG2 cells (oligodendrocyte progenitor cells) in the central nervous system and NG2-expressing cells in other organs, as well as for isolating NG2 cell populations via FACS. [JAX Strain #:008241 | Genotyping Protocol] | DOI Link]

2. Tek-Cre: The Tie2-Cre (Tek-Cre) transgene has the mouse endothelial-specific receptor tyrosine kinase (Tek or Tie2) promoter directing expression of Cre recombinase. These Tek-Cre transgenic mice are a Cre-lox tool useful for deletion of floxed sequences in endothelial cells during embryogenesis and adulthood. Cre recombinase activity is also detected in microglia in central nervous system. [JAX Strain #:008863 | Genotyping Protocol | DOI Link]

3. Cdh5-PAC-CreERT2: [Genotyping Protocol | DOI Link]

4. Pdgfrb-cre: Pericyte labeling. DOI Link

5. Pdgfrb-CreERT2: Pdgfrb-CreERT2 transgenic mice is suitable for Pericyte labeling, the result of Pdgfrb-CreERT2::Ai14 is very clean and specific. [JAX Strain #:029684 | Genotyping Protocol | DOI Link]

6. BMX-CreERT2: Artery EC labeling. [Genotyping Protocol]

7. Slco1c1-KI-P2A-iCreERT2: Brain specific EC labeling(including spinal cord). [Woo-Ping Ge lab, Design by Jun-Liszt Li, Contact]

Astrocyte labeling

1. Aldh1l1-EGFP: In this transgenic strain, Aldh1l1 promoter-active cells in the brain and spinal cord (the majority being astrocytes) express EGFP. Cre-mediated excision of the floxed EGFP/Stop enables DTA-mediated ablation of these cells. [JAX Strain #:026033 | Genotyping Protocol | PDF | PMID: 22745251 | DOI Link]

2. Aldh1l1-CreERT2: Aldh1l1-Cre/ERT2 BAC transgenic mice have tamoxifen-inducible Cre recombinase expression directed at high levels to the vast majority of astrocytes, with no detectable expression in neurons. These mice allow pan-astrocytic, specific and inducible genetic manipulations in vivo for studying astrocyte biology at different developmental stages in neural circuitry/synapses, behavior, disease and injury/trauma. [JAX Strain #:029655 | Genotyping Protocol]

3. mGFAP-Cre

4. hGfap-CreERT2:

   • Park, Yongmin Mason, et al. “Astrocyte specificity and coverage of hGFAP-CreERT2 [Tg (GFAP-Cre/ERT2) 13Kdmc] mouse line in various brain regions.” Experimental Neurobiology 27.6 (2018): 508. [PMID: 30636902 | DOI Link]

5. Glast-CreERT2

6. Fgfr3-iCreERT2

Neuron labeling

1. Thy1-YFP-M: These Thy1-GFP-M transgenic mice may be useful in neurobiological studies for fluorescent labeling of neural tissues, especially for mossy fibers in the cerebellum and intense, yet sparse, labeling of a variety of neuronal subsets. [JAX Strain #:007788 | Genotyping Protocol]
2. Thy1-YFP-16J: These thy1-YFP-16 transgenic mice express yellow fluorescent protein at high levels in motor and sensory neurons, as well as in subsets of central neurons. This line provides a strong and specific vital marker for axons, and expression is strong from a mid-gestational stage into adulthood. [JAX Strain #:003709 | Genotyping Protocol]
3. Gad1-EGFP: Also called Gad67-EGFP, Inhibitory GABAnergic neuron labeling. [JAX Strain #:007677 | Genotyping Protocol | DOI Link]
4. Slc32a1-IRES2-FlpO: Slc32a1-IRES2-FlpO-D knock-in mice are designed to have optimized FLP recombinase expression directed to VGAT-expressing cells. FlpO expression/activity largely recapitulates the endogenous Slc32a1 gene in the brain - scattered Cre expression is observed throughout many brain regions, including the cortex, hippocampus, striatum and thalamus. These mice may be used to generate conditional mutations for studying gain-or-loss of function and/or fate mapping related to GABAergic neuronal function. [JAX Strain #:031331 | Genotyping Protocol | PMID: 30007418 | DOI Link]
5. Vip-Cre: Vip+ Interneuron labeling.
6. Sst-Cre: Sst+ Interneuron labeling.
7. Som-Cre: Som+ Interneuron labeling.
8. PV-Cre: PV+ Interneuron labeling.
9. CamKIIa-Cre: Random insertion, Expression pattern in brain(Throughout the cortex, hippocampus, striatum, and other structures) | [Susumu Tonegawa] |
10. Snap25-IRES2-Cre-D: Snap25-IRES2-Cre-D knockin mice have widespread Cre recombinase expression directed throughout the brain, without disrupting endogenous synaptosomal-associated protein 25 expression. These mice may be useful for studying t-SNARE proteins and synaptic vesicle/plasma membrane fusion. [Strain #:023525 | Genotyping Protocol | DOI Link]
    • Snap25-IRES2-cre is superior to Syn1-cre as a pan-neuronal Cre driver.
11. Slc17a7-IRES2-Cre: Slc17a7 (VGlut1), Excitatory neuron labeling [PMID: 25071457 | DOI Link]
12. Drd1-Cre: These mice express Cre recombinase under the control of the mouse Drd1a (dopamine receptor D1A) promoter. DRD1A is s a G-protein coupled receptor involved in the regulation of neuronal growth and development. The D1 subtype is the most abundant dopamine receptor in the central nervous system. Homozygotes are viable and fertile. [MMRRC Strain #037156-JAX | DOI Link]
13. Drd2-Cre

Microglia labeling

1. CX3CR1-EGFP: [JAX Strain #:005582 | Genotyping Protocol]
2. CX3CR1-iCreERT2:
3. Tmem119-P2A-iCreERT2: [JAX Strain #:031820 | Genotyping Protocol | DOI Link]

Oligodendrocytes

1. Oligo2-Cre: Oligo2-cre mice have a Cre recombinase inserted into the only exon of the oligodendrocyte transcription factor 2 Olig2 gene. The presence of cre abolishes expression of Olig2. OLIG2 is a basic helix-loop-helix transcription factor required for oligodendrocyte and motor neuron specification in the spinal cord, and for the development of somatic motor neurons in the hindbrain. Heterozygous mice are viable and fertile. [Strain #:025567 | Genotyping Protocol | DOI Link]

2. Plp1-CreERT2: These transgenic mice have a tamoxifen inducible Cre-mediated recombination system driven by the mouse Plp1, proteolipid protein (myelin) 1 promoter. When crossed with a strain containing a loxP site flanked sequence of interest, the offspring are useful for generating tamoxifen-induced, Cre-mediated targeted deletions. Tamoxifen administration allows for ablation of predetermined genes in oligodendrocytes and Schwann cells. [JAX Strain #:005975 | Genotyping Protocol | DOI Link]

Precusor cells

1. Nestin-Cre: This strain is commonly known as nestin-Cre. Nestin promoter driven Cre recombinase is expressed in the central and peripheral nervous system, including neuronal and glial cell precursors. There are reports of Cre recombinase activity in a few isolated kidney and heart cells. Hemizygous nestin-cre mice exhibit mild hypopituitarism, growth retardation, impaired fear response, and a metabolic phenotype. Mice also show a strong impairment in the acquisition of both contextual- and cued-fear conditioning. [Strain #:003771 | Genotyping Protocol | DOI Link]

Reporter Lines

1. Ai14(Rosa26-CAG-LSL-tdTomato-WPRE-pA)
2. Ai47(Rosa26-CAG-LSL-emerald-TagGFP-hrGFP-WPRE-pA): The Rosa-CAG targeting vector was designed with (from 5’ to 3’) a CMV-IE enhancer/chicken beta-actin/rabbit beta-globin hybrid promoter (CAG), an FRT site, a loxP-flanked STOP cassette (with stop codons in all 3 reading frames and a triple polyA signal), triple GFP reporter genes (emerald, TagGFP (Aequorea macrodactyla GFP), and hrGFP (Humanized Renilla reniformis GFP)), a woodchuck hepatitis virus post-transcriptional regulatory element (WPRE; to enhance the mRNA transcript stability), a polyA signal, and an attB/attP-flanked PGK-FRT-Neo-polyA cassette. This entire construct was inserted between exons 1 and 2 of the Gt(ROSA)26Sor locus. [MGI:5750793 | PMID: 30007418 | DOI Link]
3. Ai140(TIT2L-EGFP-ICL-tTA2): Ai140 (also called Ai140(TIT2L-EGFP-ICL-tTA2)) is a Cre-dependent, Tet-controllable fluorescent reporter line, created by targeted insertion at the Igs7 locus (TIGRE). Exposure to Cre recombinase removes both STOP cassettes - resulting in tTA2 expression and robust EGFP fluorescence. EGFP expression may be expected to be diminished/eliminated by doxycycline. [JAX Strain #:034100 | Genotyping Protocol | PMID: 30007418 | DOI Link]

Transgenic mouse line for disease modeling

1. 5xFAD mouse (Alzheimer disease model): These 5XFAD transgenic mice overexpress mutant human amyloid beta (A4) precursor protein 695 (APP) with the Swedish (K670N, M671L), Florida (I716V), and London (V717I) Familial Alzheimer’s Disease (FAD) mutations along with human presenilin 1 (PS1) harboring two FAD mutations, M146L and L286V. Both transgenes are regulated by the mouse Thy1 promoter to drive overexpression in the brain. 5XFAD mice recapitulate major features of Alzheimer’s Disease amyloid pathology and may be a useful model of intraneuronal Abeta-42 induced neurodegeneration and amyloid plaque formation. [JAX Strain #:006554 | Genotyping Protocol | PMID: 17021169 | DOI Link]

Transgenic line for Calcium imaging

1. Thy1-GCaMP6f: These transgenic mice, made by the Genetically-Encoded Neuronal Indicator and Effector (GENIE) Project, express the green fluorescent calcium indicator, GCaMP6f, in subsets of excitatory neurons in the brain and possibly other cell types and tissues. The GCaMP6f indicator is an ultrasensitive detector of single neuronal action potentials and has fast response kinetics. [JAX Strain #:024339 | Genotyping Protocol | PMID: 23868258 | DOI Link]
2. Thy1-JRGECO1a
3. Ai96(Rosa26-CAG-LSL-GCaMP6s)

Transgenic line for genome editing

1. Rosa26-CAG-LSL-SpCas9-P2A-EGFP(Rosa26-floxed STOP-Cas9 knockin): These CRISPR/Cas9 knockin mice have Cre recombinase-dependent expression of CRISPR associated protein 9 (cas9) endonuclease, a 3X-FLAG epitope tag and EGFP directed by a CAG promoter. Expression of Cas9 and EGFP is prevented by an upstream Lox-Stop-Lox (LSL) sequence. When used in combination with single guide RNAs and a Cre source, they allow editing of single or multiple mouse genes in vivo or ex vivo. [Strain #:024857 | Genotyping Protocol | PMID: 25263330 | DOI Link]
2. Rosa26-CAG-SpCas9-P2A-EGFP(Rosa26-Cas9 knockin): These CRISPR/Cas9 knockin mice constitutively express CRISPR associated protein 9 (cas9) endonuclease, a 3X-FLAG epitope tag and EGFP in a widespread fashion under the direction of a CAG promoter. Breeding to a germ-line expressed Cre strain during development removed a Lox-Stop-Lox (LSL) sequence to allow ubiquitous expression of the knockin construct. When used in combination with single guide RNAs, they allow editing of single or multiple mouse genes in vivo or ex vivo. [Strain #:024858 | Genotyping Protocol | PMID: 25263330 | DOI Link]

Ref. public websites

1. The Jackson Laborary: The laboratory is also the world’s source for more than 8,000 strains of genetically defined mice, and serves as a worldwide center for scientific courses, conferences, training, and education.
2. Mouse Genome Informatics: MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease.
3. Allen Institute for Brain Research

Ref. Labs

1. Susumu Tonegawa Lab, MIT
2. Joe Z. Tsien Lab, Princeton University

• Subregion- and Cell Type–Restricted Gene Knockout in Mouse Brain with phage P1–derived Cre/loxP recombination system
  • Tsien, Joe Z., et al. “Subregion-and cell type–restricted gene knockout in mouse brain.” Cell 87.7 (1996): 1317-1326. [PDF | PMID: 8980237 | DOI Link]

3. Masashi Yanagisawa Lab, The International Institute for Integrative Sleep(IIIS)
4. Z. Josh Huang Lab, Duke University

Ref. Protocols

1. Long ssDNA for Knockin

• Guide-it Long ssDNA Production System v2 [Takara Cat. #: 632666 | User Manual]
  • The kit employs a simple and fast method that involves conversion of a dsDNA PCR product into ssDNA via selective digestion of either the sense or the antisense strand. Following digestion, ssDNA products are purified using silica membrane spin columns included with the kit.
  • It has been demonstrated that ssDNA offers two key advantages over dsDNA templates for precise genome editing applications: greatly reduced toxicity and a much lower likelihood of random or off-target integration.
• Easi-CRISPR
  • Miura, Hiromi, et al. “Easi-CRISPR for creating knock-in and conditional knockout mouse models using long ssDNA donors.” Nature protocols 13.1 (2018): 195-215. [PDF | PMID: 29266098 | DOI Link]

2. Genetic screen

• ENU mutagenesis, forward genetic screen
  • Funato H, Miyoshi C, Fujiyama T, et al. Forward-genetics analysis of sleep in randomly mutagenized mice[J]. Nature, 2016, 539(7629): 378-383. [PDF | PMID: 27806374 | DOI Link]
• CRISPR based pool screen, in cell line.

Vendor company

1. The Jackson Laboratory
2. Charles River, China
3. Charles River, International
4. GenPharmatech, China

Rat

Drosophila melanogaster

Seymour Benzer with mega-Drosophila, 1974.

Pioneers

• Seymour Benzer(1921-2007), California Institute of Technology \

  • [Public Interview | Read the Interview]
  • Pioneer works: [phage genome structure mapping, 1959, PNAS | Clock Mutants of Drosophila melanogaster, 1971, PNAS]

• Norbert Perrimon, Harvard Medical School/HHMI [Lab Link]

  • Developed the Gal4/UAS system, with Andrea Brand
    Brand A H, Perrimon N. Targeted gene expression as a means ofaltering cell fates and generating dominant phenotypes. development, 1993,118(2): 401-415.[PMID:8223268 | DOI Link]
  • Developed the RNAi screen system in Drosophila cells
    Boutros M, Kiger A A, Armknecht S, et al. Genome-wide RNAi analysis of growth and viability in Drosophila cells. Science, 2004, 303(5659): 832-835. [PMID:14764878 | DOI Link]

Ref. Websites

1. FlyBase: A Database of Drosophila Genes & Genomes
2. DRSC/TRiP Functional Genomics Resources & DRSC-BTRR: Drosophila RNAi Screening Center (DRSC), Transgenic RNAi Project (TRiP) and Drosophila Research & Screening Center-Biomedical Technology Research Resource (DRSC-BTRR)

Zebrafish

Ref. Websites

1. ZFIN: The Zebrafish Information Network (ZFIN) is the database of genetic and genomic data for the zebrafish (Danio rerio) as a model organism. ZFIN provides a wide array of expertly curated, organized and cross-referenced zebrafish research data.

Ref protocol

2. Genetic screen

• ENU mutagenesis, forward genetic screen
  • Patton E E, Zon L I. The art and design of genetic screens: zebrafish[J]. Nature Reviews Genetics, 2001, 2(12): 956-966. [PDF | PMID: 11733748 | DOI Link]

Nobel laureates

• Michael W. Young, Rockefeller University, New York, NY, USA
  The Nobel Prize in Physiology or Medicine 2017
  Time Travels: A 40 Year Journey from Drosophila’s Clock Mutants to Human Circadian Disorders [Nobel Lecture video | Lecture Slides | Read the Lecture | Source]

• Robert G. Edwards(1925-2013), University of Cambridge, Cambridge, United Kingdom
  The Nobel Prize in Physiology or Medicine 2010
  Robert Edwards: Nobel Laureate in Physiology or Medicine [Nobel Lecture video | Lecture Slides | Read the Lecture | Source]

• Sydney Brenner(1927-2019), The Molecular Sciences Institute, Berkeley, CA
  The Nobel Prize in Physiology or Medicine 2002
  Nature’s Gift to Science [Nobel Lecture video | Read the Lecture | Source]

• Barbara McClintock(1902-1992), Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
  The Nobel Prize in Physiology or Medicine 1983
  The Significance of Responses of the Genome to Challenge [Nobel Lecture video | Read the Lecture | Source]

• Max Delbrück(1906-1981), California Institute of Technology (Caltech), Pasadena, CA, USA
  The Nobel Prize in Physiology or Medicine 1969
  A Physicist’s Renewed Look at Biology–Twenty Years Later [Read the Lecture | Source]

• Alfred D. Hershey(1908-1997), Carnegie Institution of Washington, Long Island, New York, NY, USA
  The Nobel Prize in Physiology or Medicine 1969
  Idiosyncrasies of DNA Structure [Read the Lecture | Source]

• Salvador E. Luria(1912-1991), Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
  The Nobel Prize in Physiology or Medicine 1969
  Phage, colicins and macroregulatory phenomena [Read the Lecture | Source]

• Thomas Hunt Morgan(1866-1945), California Institute of Technology (Caltech), Pasadena, CA, USA
  The Nobel Prize in Physiology or Medicine 1933
  The Relation of Genetics to Physiology and Medicine [Read the Lecture | Source]