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About MODB
The MOrpholino DataBase was established as a web-based database for the purpose of our morpholino screen that currently contains over 700 morpholinos including control and multiple morpholinos against the same target. A publicly accessible sequence-based search opens this database for morpholinos against a particular target for the zebrafish community.
We are currently expanding public access to our database. In the future we
will provide:
- Mortality curves and dose range for each morpholino
- Preliminary data regarding the effectiveness of each morpholino
- Expanded annotation for each morpholino
- External linkage of our morpholino sequences to ZFIN and Ensembl.
Morpholino Screens
Besides examination the effects of specific gene knock-down we have in collaboration conducted several large-scale screens. Target name and sequence for each morpholino reflects the original sequence used to generate the morpholino. Since many of these morpholinos were designed against tentative consensus (TC) from TIGR and other non-assigned sequences it is important to maintain the context under which these morpholinos were designed. Subsequent gene target assignments have been made. General screen information can be found in several publications (Nasevicius and Ekker 2000; Chen et al., 2004; Chen et al., 2005; Eckfeldt et al., 2005; Leung et al, 2005; Pickart et al., 2006, Chen et al., 2006).
The screen types referred to in the search functions are the specific areas of development that we examined during the various screens, which include behavior, general morphology, pigmentation, toxicity, Pax2 expression, and development of the craniofacial structures, eyes, kidneys, pituitary, and skin. Only data pertaining to specific tests performed are presented. Due to the complexity of this international collaboration and time constraints, not all morpholinos were subjected to all screen types.
Behavior Screen- Embryos were examined at 24 and 48 hours for movement and response to stimuli including touch and light.
Blood Screen- Embryos were examined at 24, 48 and 72 hours either hemoglobin levels or for levels and localization of dsRED in dsRED:Gata1 transgenic embryos. Reduction in gata1 and disruptions in hematopoeisis was confirmed by quantitative RT-PCR.
Cranial Motor Neuron Screen- Embryos were examined for number and localization of the IV, VII and X axons.
Craniofacial Screen- Embryos were examined at 72 and 120 hours for general appearance under a dissecting microscope and by alcian blue staining for structure.
Eye Screen- Embryos were examined at 48 and 72 hours for general eye morphology, placement, pigmentation and pupil area versus total eye area.
Kidney Screen- Embryos were examined at 72 hours using Elf-staining to examine kidney development and structure including formation of the glomeruli and tubules. Kidney function was accessed by clearance of fluorescently labeled dextran.
Morphology Screen- Embryos were examined at 24 and 48 hours for defects in embryogenesis and general morphology including notochord, heart, head, fin development, somites, tail, otolith, and yolk extension,
Pax2 Screen- Embryos were examined at 48 hours by in situ hybridization for pax2 expression in the optic fissure, optic stalk, midbrain/hindbrain boundary, pronephros, otic vesicle, and spinal neurons.
Pigment Screen- Embryos were examined at 24 and 48 hours for body pigmentation including melanophores distribution, color and shape.
Pituitary Screen- Embryos were examined at 72 hours by in situ hybridization for pomc, ihx3, pitx3, gh, tsh, prl, and pit1 expression.
Skin Screen- Embryos were examined at 72 hours by in situ hybridization for p63 expression.
Toxicity Screen- Embryos were examined at 24 and 48 hours for high mortality rates and patterns of cell death in neural tissue considered as non-specific and are often rescued by co-injection with p53 morpholino.
Vasculature Screen- Embryos were examined at 24 and 48 hours for general vasculature structure and circulation using microangiography or examining GFP and dsRED expression in GFP:Fli1 and dsRED:Gata1 double transgenic embryos.
Search Features
The information stored within the morpholino database can be accessed by different search options.
- On the morpholino page the first search option available allows users to search by all terms, morpholino name, morpholino target and gene targeted. The results can further be sorted by morpholino name, morpholino target or gene targeted. An asterisk (*) can be used as a wild card character.
- Using the advanced search function morpholinos with specific defects can be searched by anatomical structure affected and PATO defect description or vice versa.
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A sequence-based search is also possible using our BLAST feature.
Search FAQ’s
- How do I find a morpholino for a specific gene target?
- BLAST MODB with a gene sequence
- Search by gene name in main menu search bar (See Search Features 1)
- Use * as a wild card at the beginning and/or end of gene name to increase search results
- How do I find all morpholinos against a gene target?
- BLAST MODB with a gene sequence
- Search by gene name in main menu search bar (See Search Features 1)
- Use * as a wild card at the beginning and/or end of gene name to increase search results
- In the morpholino summary for each morpholino there is an option to display all morpholinos for the same gene target
- How do I find morpholinos with a specific defect?
- The Advanced Search function can be used to generate morpholinos with a given defect in a specific anatomical structure (See Search Features 2)
- Use * as a wild card at the beginning and/or end of gene name to increase search results
- To view all anatomical or PATO defects search with only the wild card (*).
- A collapsible anatomy list used by MODB can be viewed at ZFIN.
Morpholino Summary
A summary page is available for each morpholino containing general information such as morpholino name, sequence, target name, target sequence, gene targeted etc. In additional, graphs describe the survival rate at each dose tested and normality curve describing the percent of embryos with normal phenotypes in each screen type. Co-injection with p53 morpholino was used to suppress non-specific morpholino toxicity (Robu et al., 2007). The number of tests performed per screen type is listed and as are the phenotypes observed with dose and penetrance.
Data Submission
To submit morpholino-knockdown results to MODB please contact the administrator for a user name and password.
Last Modified:
10/17/2007
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